Daily Papers

General-purpose agents can plan, reason, and act over long horizons, yet their production capabilities remain fragmented across text, images, audio, video, documents, 3D assets, and code. Extending a foundation model to additional modalities ties capability growth to costly model updates, while assembling specialist models and tools leaves unresolved how procedures, dependencies, intermediate assets, and cross-turn revisions should be coordinated. We present Omni-IO Skills, a plug-and-play Agent Harness that makes existing agents omni-native through hierarchical Skills, a standardized multimodal execution interface, dependency-aware orchestration, and a persistent Asset Registry. Multi-asset workflows are represented as Declare Execution Graphs, which schedule independent operations concurrently and register successful outputs for downstream and cross-turn reuse across replaceable execution backends. Its 27 Skills cover 38 representative tasks spanning seven artifact modalities and four capability families: understanding, generation, reasoning, and retrieval. On UniM-90, the harness raises the input-support rates of GPT-5.6 Sol and Claude Sonnet 5 from 40.00% and 38.89% to 100%, while increasing relative Semantic--Quality Coupled Score from 26.99 to 74.94 and from 27.82 to 77.78, respectively; Strict Structure Score reaches 100.00 and 99.78. These results establish harness-level capability composition as a practical route to broad, evolvable Omni systems without changing the host agent's reasoning core.

AI agents are emerging as a dominant workload in a wide range of applications, promising to be the vehicle that delivers the promised benefits of AI to enterprises and consumers. Unlike conventional software or static inference, agentic workloads are dynamic and structurally complex. Often these agents are directed graphs of compute and IO operations that span multi-modal data input and conversion), data processing and context gathering (e.g vector DB lookups), multiple LLM inferences, tool calls, etc. To scale AI agent usage, we need efficient and scalable deployment and agent-serving infrastructure. To tackle this challenge, in this paper, we present a system design for dynamic orchestration of AI agent workloads on heterogeneous compute infrastructure spanning CPUs and accelerators, both from different vendors and across different performance tiers within a single vendor. The system delivers several building blocks: a framework for planning and optimizing agentic AI execution graphs using cost models that account for compute, memory, and bandwidth constraints of different HW; a MLIR based representation and compilation system that can decompose AI agent execution graphs into granular operators and generate code for different HW options; and a dynamic orchestration system that can place the granular components across a heterogeneous compute infrastructure and stitch them together while meeting an end-to-end SLA. Our design performs a systems level TCO optimization and preliminary results show that leveraging a heterogeneous infrastructure can deliver significant TCO benefits. A preliminary surprising finding is that for some workloads a heterogeneous combination of older generation GPUs with newer accelerators can deliver similar TCO as the latest generation homogenous GPU infrastructure design, potentially extending the life of deployed infrastructure.

AI agents execute tens to hundreds of chained LLM calls per task, yet GPU schedulers treat each call as independent, discarding gigabytes of intermediate state between steps and inflating end-to-end latency by 3-8x. We argue that this request-level abstraction is fundamentally mismatched to compound AI workloads, and propose a shift to program-level scheduling: treating the entire agent workflow (not individual inference calls) as the first-class schedulable unit. We present SAGA, a distributed scheduler that implements this abstraction through three mechanisms: (1) Agent Execution Graphs that capture workflow structure to predict KV cache reuse across tool-call boundaries, achieving within 1.31x of Bélády's optimal offline policy; (2) session-affinity batching with work stealing that co-locates correlated requests while maintaining global load balance; and (3) Agent Fair Share, a task-completion-time fairness metric with provable bounded-deviation guarantees. On a 64-GPU cluster serving SWE-bench coding agents and WebArena browser tasks, SAGA reduces task completion time by 1.64x (geometric mean, p < 0.001) over vLLM v0.15.1 with prefix caching and affinity routing, while improving GPU memory utilization by 1.22x and achieving 99.2% SLO attainment under multi-tenant interference. These latency gains come at a quantified cost: approximately 30% lower peak throughput than throughput-optimal batch scheduling, a tradeoff appropriate for the latency-sensitive interactive deployments that dominate compound AI usage. Our results demonstrate that workflow-aware scheduling is essential for efficient compound AI serving.

Large Language Models (LLMs) increasingly act as agents whose procedural knowledge is stored in reusable skill packages and loaded at inference time. As skill libraries grow, a central challenge is to expose the smallest sufficient executable context under a limited context budget. Existing systems struggle to reuse routines below the whole-skill level, preserve procedural contracts during compression, keep compressed routines executable and expandable, and update the compressed library as skills evolve. These challenges reveal a unit mismatch: skills are retrieved as packages, compressed as text, and converted into execution graphs only after retrieval, whereas reliable reuse requires a contract-bearing procedural unit. We propose SkillZip, an execution-aware procedural abstraction framework that performs contract-preserving compression over section-level graphs. SkillZip rewrites recurring contract-valid motifs into reversible ported macros while preserving boundary signatures, dependency closure, verifier reachability, and source-level expansion. At inference time, it hydrates a compact, dependency-closed context and expands macros only when required. ReZip further integrates new skills and revises risky macros using execution evidence. Comprehensive experiments1 on technical and embodied agent benchmarks show SkillZip consistently outperforms the strongest baseline by up to 12.2 points, while achieving a 3.46x compression ratio with 99.2% dependency preservation and 98.7% verifier reachability. Scaling analyses further confirm robust retrieval across skill libraries ranging from 200 to 100K skills.

Simulation offers unique values for both enumeration and extrapolation purposes, and is becoming increasingly important for managing the massive machine learning (ML) clusters and large-scale distributed training jobs. In this paper, we build Echo to tackle three key challenges in large-scale training simulation: (1) tracing the runtime training workloads at each device in an ex-situ fashion so we can use a single device to obtain the actual execution graphs of 1K-GPU training, (2) accurately estimating the collective communication without high overheads of discrete-event based network simulation, and (3) accounting for the interference-induced computation slowdown from overlapping communication and computation kernels on the same device. Echo delivers on average 8% error in training step -- roughly 3x lower than state-of-the-art simulators -- for GPT-175B on a 96-GPU H800 cluster with 3D parallelism on Megatron-LM under 2 minutes.

As telecommunication networks evolve toward autonomous 5G-Advanced and 6G operations, agentic artificial intelligence (AI) workflows, where large language models (LLMs) execute multi-step reasoning, invoke diagnostic tools, retrieve domain knowledge, and coordinate across agent teams, are increasingly embedded across the edge-cloud continuum. While the biological brain accomplishes complex cognition on an exceptionally modest metabolic power budget of approximately 20W contemporary LLMs are profoundly energy- and memory-intensive, making sustainable lifecycle orchestration a critical operational priority. However, existing AI lifecycle metrics evaluate only isolated, single-model inferences or overlook multi-agent execution graphs entirely. Consequently, network operators lack foundational models to determine whether distributed agent communication incurs meaningful energy costs and where across edge-cloud tiers agent teams should physically reside. To address this gap, we introduce agentic-eCAL, generalizing the Energy Cost of AI Lifecycle (eCAL) metric to directed multi-agent workflows by coupling a closed-form two-rate single-call energy model (compute-bound prefill and memory-bound decode) with 7-layer OSI data transport. Grounded in hundreds of GPU benchmark configurations on NVIDIA A100 and H100, 16 open-weight models and 8 orchestration topologies, we validate components of the metric and study workflow placement implications. Our findings demonstrate that inter-agent text transport incurs 0.25% of workflow energy across 5G RAN, metro, and optical links. Therefore in edge-cloud agent placement the dominant energy cost of distribution is often not the transmission of inter-agent text itself, but the additional inference and context processing induced by that communication.

While Large Language Models (LLMs) have demonstrated strong zero-shot reasoning capabilities, their deployment as embodied agents still faces fundamental challenges in long-horizon planning. Unlike open-ended text generation, embodied agents must decompose high-level intents into actionable sub-goals while adhering to the constraints of a dynamic environment. Standard LLM planners frequently fail to maintain strategy coherence over extended horizons due to context window limitations or hallucinate state transitions that violate environment constraints. We propose GiG, a planning framework that structures embodied agents' memory using a Graph-in-Graph architecture. Our approach employs a Graph Neural Network (GNN) to encode environmental states into embeddings, organizing these embeddings into action-connected execution trace graphs within an experience memory bank. GiG enables retrieval of structurally-similar priors, allowing agents to ground current decisions in relevant past structural patterns. Furthermore, we introduce a bounded lookahead module that leverages symbolic transition logic to enhance the agent's planning capabilities through grounded action projections. We evaluate our framework on three embodied planning benchmarks-Robotouille Synchronous, Robotouille Asynchronous, and ALFWorld. Our method outperforms state-of-the-art baselines, achieving Pass@1 performance gains of up to 22% on Robotouille Synchronous, 37% on Asynchronous, and 15% on ALFWorld while maintaining comparable or lower computational cost.

Multi-agent systems (MAS) enable complex reasoning by coordinating multiple agents, but often incur high inference latency due to multi-step execution and repeated model invocations, severely limiting their scalability and usability in time-sensitive scenarios. Most existing approaches primarily optimize task performance and inference cost, and explicitly or implicitly assume sequential execution, making them less optimal for controlling latency under parallel execution. In this work, we investigate learning-based orchestration of multi-agent systems with explicit latency supervision under parallel execution. We propose Latency-Aware Multi-agent System (LAMaS), a latency-aware multi-agent orchestration framework that enables parallel execution and explicitly optimizes the critical execution path, allowing the controller to construct execution topology graphs with lower latency under parallel execution. Our experiments show that our approach reduces critical path length by 38-46% compared to the state-of-the-art baseline for multi-agent architecture search across multiple benchmarks, while maintaining or even improving task performance. These results highlight the importance of explicitly optimizing latency under parallel execution when designing efficient multi-agent systems. The code is available at https://github.com/xishi404/LAMaS

Predicting program behavior without execution is an essential and challenging task in software engineering. Traditional models often struggle to capture dynamic dependencies and interactions within code. This paper introduces a novel machine learning-based framework called CodeFlowrepresents, which predicts code coverage and detects runtime errors through Dynamic Dependencies Learning. Utilizing control flow graphs (CFGs), CodeFlowrepresents all possible execution paths and the relationships between different statements, offering a comprehensive understanding of program behavior. It constructs CFGs to depict execution paths and learns vector representations for CFG nodes, capturing static control-flow dependencies. Additionally, it learns dynamic dependencies through execution traces, which reflect the impacts among statements during execution. This approach enables accurate prediction of code coverage and identification of runtime errors. Empirical evaluations show significant improvements in code coverage prediction accuracy and effective localization of runtime errors, surpassing current models.

As multi-agent AI systems are increasingly deployed in real-world settings - from automated customer support to DevOps remediation - failures become harder to diagnose due to cascading effects, hidden dependencies, and long execution traces. We present AgentTrace, a lightweight causal tracing framework for post-hoc failure diagnosis in deployed multi-agent workflows. AgentTrace reconstructs causal graphs from execution logs, traces backward from error manifestations, and ranks candidate root causes using interpretable structural and positional signals - without requiring LLM inference at debugging time. Across a diverse benchmark of multi-agent failure scenarios designed to reflect common deployment patterns, AgentTrace localizes root causes with high accuracy and sub-second latency, significantly outperforming both heuristic and LLM-based baselines. Our results suggest that causal tracing provides a practical foundation for improving the reliability and trustworthiness of agentic systems in the wild.

LLM-based agents have demonstrated strong capabilities in data-intensive analytical tasks, yet their outputs are rarely verifiable: a reliance on linear text trajectories makes their reasoning difficult to audit. In particular, deterministic computations over raw data and semantic deductions over natural-language claims are often entangled in an unstructured stream, leaving numerical conclusions hard to reproduce and qualitative judgments hard to inspect. To address this, we propose VeriGraph, a traceable neuro-symbolic reasoning framework that enables agents to construct an explicit heterogeneous evidence directed acyclic graph (DAG) during execution. VeriGraph introduces three evidence-expansion primitives, namely computational, grounding, and derivational expansion, to connect raw data, interpreter variables, computed results, and natural-language claims in a unified graph. Under this formulation, structural traceability is reduced to graph reachability from raw data sources to terminal claims, while semantic support is measured by claim-level evidence evaluation. To improve graph construction, we further design a graph-based policy optimization strategy with a composite reward that jointly supervises answer correctness, computational integrity, and derivational coherence. Experiments on four benchmarks show that VeriGraph-8B achieves the highest overall score among all baselines. More importantly, VeriGraph produces auditable evidence graphs with substantially stronger claim grounding, achieving a 87.61\% Grounding Rate under our claim-level evidence support evaluation. These results suggest that explicit evidence-graph construction is a promising path toward verifiable data-analytic agents. Our code is available at https://github.com/ignorejjj/VeriGraph.

Computer-Using Agents (CUAs) aim to autonomously operate computer systems to complete real-world tasks. However, existing agentic systems remain difficult to scale and lag behind human performance. A key limitation is the absence of reusable and structured skill abstractions that capture how humans interact with graphical user interfaces and how to leverage these skills. We introduce CUA-Skill, a computer-using agentic skill base that encodes human computer-use knowledge as skills coupled with parameterized execution and composition graphs. CUA-Skill is a large-scale library of carefully engineered skills spanning common Windows applications, serving as a practical infrastructure and tool substrate for scalable, reliable agent development. Built upon this skill base, we construct CUA-Skill Agent, an end-to-end computer-using agent that supports dynamic skill retrieval, argument instantiation, and memory-aware failure recovery. Our results demonstrate that CUA-Skill substantially improves execution success rates and robustness on challenging end-to-end agent benchmarks, establishing a strong foundation for future computer-using agent development. On WindowsAgentArena, CUA-Skill Agent achieves state-of-the-art 57.5% (best of three) successful rate while being significantly more efficient than prior and concurrent approaches. The project page is available at https://microsoft.github.io/cua_skill/.

Large language models are increasingly deployed as agents that plan over long horizons and act through external tools. Most agents select actions through unconstrained generation over an accumulating history, leaving implicit the procedural knowledge of what to do, in what order, and under which conditions. As trajectories lengthen, agents can lose track of their objectives, invoke tools out of order, and repeat unproductive actions. We introduce the Procedural Graph: just as a knowledge graph organizes factual knowledge into (entity, relation, entity) triplets for what-is questions, a Procedural Graph organizes procedural knowledge into (procedure, relation, procedure) triplets for what-to-do questions. At each decision step, the framework localizes the agent's active node, and a guidance model translates the surrounding subgraph into step-level situational guidance that biases the solver's next action without dictating it. The graph is self-evolving: an LLM refiner contrasts failed trajectories with successful ones and edits the graph's topology and attributes, committing edits that preserve or improve held-out validation performance while retaining rejected ones to discourage repetition. Starting from a minimal skeleton, the loop builds graphs that match or surpass hand-designed ones. It can also repair a flawed expert prior. Across multiple datasets, task types, and LLMs, the Procedural Graph delivers consistent gains over memory-based baselines, and self-evolution further improves performance without manual engineering.

The dominant paradigm for building LLM based agents is the Agent Loop, an iterative cycle where a single language model decides what to do next by reading an ever growing context window. This paradigm has three structural weaknesses: implicit dependencies between steps, unbounded recovery loops, and mutable execution history that complicates debugging. We characterize the Agent Loop as a single ready unit scheduler: at any moment, at most one executable unit is active, and the choice of which unit to activate comes from opaque LLM inference rather than an inspectable policy. This perspective places Agent Loops and graph based execution engines on a single semantic continuum. We propose SGH, Structured Graph Harness, which lifts control flow from implicit context into an explicit static DAG. SGH makes three commitments: execution plans are immutable within a plan version, planning execution and recovery are separated into three layers, and recovery follows a strict escalation protocol. These choices trade some expressiveness for controllability, verifiability, and implementability. Our contributions are fourfold: a scheduler unified framework that applies classical scheduling theory to LLM agent execution and identifies challenges introduced by non deterministic LLM nodes; a trade off analysis of controllability, expressiveness, and implementability across 70 surveyed systems; a formal specification including a node state machine with termination and soundness guarantees; and an attributable experimental framework with a seven group design for future validation. This is a position paper and design proposal. We provide a theoretical framework, design analysis, and experimental protocol, not a production implementation or empirical results.

Pitching strategy in baseball is expressed through both physical execution and the ordered context in which pitches are used, yet common representations collapse pitches into discrete types or aggregate statistics. We present Unified Pitch Graphs (UPG), a hierarchical graph representation for retrospective analysis of sequential spatiotemporal events. UPG preserves each pitch as an exact event with reconstructed three-dimensional trajectory and context, connects consecutive pitches through directed sequence edges, and organizes the same events across semantic and temporal resolutions. A support-adaptive mechanism backs off from fine, long sequences when repeated evidence is insufficient, while retaining exact event lineage. We evaluate UPG on 3.94 million MLB Statcast pitches from 2021 to 2026. Nominally identical pitch sequences exhibit distinct physical executions, and ordered structure becomes increasingly evident in longer context-conditioned paths. Support-adaptive backoff increases held-out path coverage from 18.9\% to 94.9\% while improving execution reconstruction from R^2=0.495 to 0.685. UPG also reliably localizes controlled execution changes that discrete pitch-mix and sequence representations cannot detect. These results demonstrate that UPG provides a traceable, multi-scale representation for identifying recurring strategy patterns without conflating retrospective associations with causal or future-performance claims.

We present the GEST-Engine, a complete system that goes from natural-language text to fully-annotated multi-actor video. At its core is an explicit world model: rather than encoding state as a learned latent, the engine maintains a complete, inspectable representation of the world (which actors exist, where they are, what they are doing, which objects they hold, and how events relate in time and space), expressed as a formal Graph of Events in Space and Time (GEST) and realized deterministically inside the open world of a commercial game engine driven through an open-source multiplayer scripting framework. GESTs are produced either procedurally or by an agentic text-to-GEST system in which an LLM Director plans a story through tool calls validated by a programmatic state backend, so every generated specification is executable by construction. A GEST then enters a four-stage execution pipeline: graph parsing and validation, entity and action grounding, temporal orchestration (Allen-style constraints resolved by Floyd-Warshall transitive closure), and execution and capture. In a single simulation pass the engine emits frame-aligned RGB video, dense per-pixel depth, instance segmentation, per-actor skeletal pose, per-frame pairwise spatial-relation graphs, 2D bounding boxes, event-to-frame temporal mappings, and natural-language descriptions, all at zero marginal annotation cost. We further describe an in-game world editor, runtime capability extraction, a text-generation pipeline, and a production system that renders corpora at scale across parallel virtual machines. Because every frame traces back to a semantic specification, the engine guarantees object permanence, multi-actor coordination, and temporal consistency by construction, making its output valuable as training data, evaluation benchmarks, and diagnostic tools for video understanding.

Skills can improve the performance of Large Language Model (LLM) agents by providing task-specific procedural guidance, while skill optimization further improves their effectiveness through iterative refinement. However, existing skill optimization methods typically represent skills as unstructured natural-language instructions, creating two key challenges: 1) Unstructured skills often lack explicit workflow-level guidance and contain substantial redundancy, making them difficult for LLMs to execute; 2) the vast search space of unconstrained natural-language skills makes skill optimization ineffective. To address these challenges, we propose representing skills as graph-structured natural-language artifacts. In graph-structured skills, each node represents an execution step together with its operational guidance, while directed edges encode context-dependent transitions between steps. Compared to unstructured skills, graph-structured skills can provide clear workflow-level guidance. Moreover, the proposed graph-structured skill can also facilitate skill optimization. Building on this structured representation, we introduce GraphSkillEvo, a population-based evolutionary optimization framework with mutation and crossover operators for graph-structured skills. By maintaining multiple candidate skills and combining effective components, GraphSkillEvo enables broader and more comprehensive exploration of the structured skill space than purely LLM-based iterative self-refinement. Extensive experiments across five agent benchmarks demonstrate that GraphSkillEvo consistently outperforms the strong skill optimization baseline SkillOpt, improving average accuracy by 4.01% on GPT-5.4-nano and 1.76% on GPT-5.4. Our code is available at https://github.com/ruisun7/GraphSkillEvo.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Terminal agents have demonstrated strong potential for autonomous command-line execution, yet their training remains constrained by the scarcity of high-quality and diverse execution trajectories. Existing approaches mitigate this bottleneck by synthesizing large-scale terminal task instances for trajectory sampling. However, they primarily focus on scaling the number of tasks while providing limited control over the diversity of execution trajectories that agents actually experience during training. In this paper, we present SkillSynth, an automated framework for terminal task synthesis built on a scenario-mediated skill graph. SkillSynth first constructs a large-scale skill graph, where scenarios serve as intermediate transition nodes that connect diverse command-line skills. It then samples paths from this graph as abstractions of real-world workflows, and uses a multi-agent harness to instantiate them into executable task instances. By grounding task synthesis in graph-sampled workflow paths, SkillSynth explicitly controls the diversity of minimal execution trajectories required to solve the synthesized tasks. Experiments on Terminal-Bench demonstrate the effectiveness of SkillSynth. Moreover, task instances synthesized by SkillSynth have been adopted to train Hy3 Preview, contributing to its enhanced agentic capabilities in terminal-based settings.

Most existing pre-trained language models for source code focus on learning the static code text, typically augmented with static code structures (abstract syntax tree, dependency graphs, etc.). However, program semantics will not be fully exposed before the real execution. Without an understanding of the program execution, statically pre-trained models fail to comprehensively capture the dynamic code properties, such as the branch coverage and the runtime variable values, and they are consequently less effective at code understanding tasks, such as retrieving semantic clones and detecting software vulnerabilities. To close the gap between the static nature of language models and the dynamic characteristics of programs, we introduce TRACED, an execution-aware pre-training strategy for source code. Specifically, we pre-train code language models with a combination of source code, executable inputs, and corresponding execution traces. Our goal is to teach code models the complicated execution logic during the pre-training, enabling the model to statically estimate the dynamic code properties without repeatedly executing code during task-specific fine-tuning. To illustrate the effectiveness of our proposed approach, we fine-tune and evaluate TRACED on three downstream tasks: static execution estimation, clone retrieval, and vulnerability detection. The empirical results show that TRACED relatively improves the statically pre-trained code models by 12.4% for complete execution path prediction and by 25.2% for runtime variable value predictions. TRACED also significantly outperforms statically pre-trained models in clone retrieval and vulnerability detection across four public benchmarks.

Retrieval-Augmented Generation (RAG) has become a robust framework for enhancing Large Language Models (LLMs) with external knowledge. Recent advances in RAG have investigated graph based retrieval for intricate reasoning; however, the influence of prompt design on enhancing the retrieval and reasoning process is still considerably under-examined. In this paper, we present a prompt-driven GraphRAG framework that underscores the significance of prompt formulation in facilitating entity extraction, fact selection, and passage reranking for multi-hop question answering. Our approach creates a symbolic knowledge graph from text data by encoding entities and factual relationships as structured facts triples. We use LLMs selectively during online retrieval to perform semantic filtering and answer generation. We also use entity-guided graph traversal through Personalized PageRank (PPR) to support efficient, scalable retrieval based on the knowledge graph we built. Our system gets state-of-the-art performance on HotpotQA and 2WikiMultiHopQA, with F1 scores of 80.7% and 78.9%, and Recall@5 scores of 97.1% and 98.1%, respectively. These results show that prompt design is an important part of improving retrieval accuracy and response quality. This research lays the groundwork for more efficient and comprehensible multi-hop question-answering systems, highlighting the importance of prompt-aware graph reasoning.

Current paradigms for code verification rely heavily on external mechanisms-such as execution-based unit tests or auxiliary LLM judges-which are often labor-intensive or limited by the judging model's own capabilities. This raises a fundamental, yet unexplored question: Can an LLM's functional correctness be assessed purely from its internal computational structure? Our primary objective is to investigate whether the model's neural dynamics encode internally decodable signals that are predictive of logical validity during code generation. Inspired by mechanistic interpretability, we propose to treat code verification as a mechanistic diagnostic task, mapping the model's explicit algorithmic trajectory into line-level attribution graphs. By decomposing complex residual flows, we aim to identify the structural signatures that distinguish sound reasoning from logical failure within the model's internal circuits. Analysis across Python, C++, and Java confirms that intrinsic correctness signals are robust across diverse syntaxes. Topological features from these internal graphs predict correctness more reliably than surface heuristics and enable targeted causal interventions to fix erroneous logic. These findings establish internal introspection as a decodable property for verifying generated code. Our code is at https:// github.com/bruno686/CodeCircuit.

Enterprise back office workflows require agentic systems that are auditable, policy-aligned, and operationally predictable, capabilities that generic multi-agent setups often fail to deliver. We present POLARIS (Policy-Aware LLM Agentic Reasoning for Integrated Systems), a governed orchestration framework that treats automation as typed plan synthesis and validated execution over LLM agents. A planner proposes structurally diverse, type checked directed acyclic graphs (DAGs), a rubric guided reasoning module selects a single compliant plan, and execution is guarded by validator gated checks, a bounded repair loop, and compiled policy guardrails that block or route side effects before they occur. Applied to document centric finance tasks, POLARIS produces decision grade artifacts and full execution traces while reducing human intervention. Empirically, POLARIS achieves a micro F1 of 0.81 on the SROIE dataset and, on a controlled synthetic suite, achieves 0.95 to 1.00 precision for anomaly routing with preserved audit trails. These evaluations constitute an initial benchmark for governed Agentic AI. POLARIS provides a methodological and benchmark reference for policy-aligned Agentic AI. Keywords Agentic AI, Enterprise Automation, Back-Office Tasks, Benchmarks, Governance, Typed Planning, Evaluation

Laboratory workflows in pharmaceutical and biomedical research encode substantial tacit knowledge -- expert judgment about failure conditions, decision branching logic, and contextual dependencies -- that remains inaccessible to protocol documents, sensor streams, and existing biomedical ontologies. We present a repeatable structured expert elicitation methodology and federated Semantic Knowledge Graph (SKG) architecture for capturing and querying this knowledge, demonstrated through deployment at the Biochemical and Cellular Pharmacology Department of Genentech. Knowledge is elicited via the Protocol Intelligence Co-pilot, a purpose-built AI interview agent that applies structured elicitation lenses to surface tacit procedural knowledge with expert-assigned confidence scores, producing graph representations across three tiers: program-level decision milestones, assay protocol knowledge, and physical execution infrastructure. Separately constructed subgraphs, exemplified by immunoassay (ELISA), quantitative mass spectrometry (LC-MS/PRM), and laboratory automation, are aligned through a shared upper ontology and queried as a single federated graph. Evaluation demonstrates seven query types structurally unavailable from any individual data source, including a cross-subgraph traversal that identifies automation-masked silent failures -- conditions where execution logs report success while scientific validity is compromised. Critically, the MASKED_BY graph relationship encodes a class of laboratory risk invisible to current informatics platforms -- the structural gap that prevents existing systems from reasoning about scientific validity. This architecture provides the semantic world model that AI laboratory agents currently lack: a queryable representation of where workflows fail silently, where human judgment is irreplaceable, and which execution assets mask rather than detect failure.

Late payments and limited working capital propagate liquidity stress across supply chains, especially among small and medium sized enterprises. This paper develops a path enabled clearing framework for invoice backed trade networks and evaluates Byppay, a local compensation procedure based on repeated three party reductions. Unlike cycle restricted netting, which can clear only obligations embedded in directed cycles, Byppay can also reduce obligations along open chains while preserving node net positions on a combined post settlement state composed of the residual invoice graph and a generated settlement instruction layer. The paper contributes by formalizing this framework for invoice networks, defining a comparable post settlement metric system, specifying deterministic benchmark procedures, and assessing them on the same real invoice graphs. The empirical analysis uses the 2021 IMI invoice corpus of 133,191 invoices totaling EUR 19.67 billion. On the annual aggregate, the cycle restricted Netting benchmark achieves EUR 4.13 billion of debt relief, or 20.99%, whereas Byppay achieves EUR 10.60 billion, or 53.87%. In the metric system adopted here, gross obligation reduction and liquidity relief are both measured on post settlement payable mass and are therefore identical for both procedures. The results show that path enabled local compensation reaches a substantially larger reduction fixed point than a cycle restricted benchmark on the same invoice graphs, while also supporting a deployable execution logic compatible with selective disclosure and distributed coordination.

As LLM agents adopt large skill libraries, selecting the right subset becomes a structural problem rather than a similarity-matching one: skills depend on, conflict with, specialize, or duplicate one another, a structure invisible to both full enumeration and embedding similarity. We present SkillDAG, which models inter-skill relationships as a typed directed graph and exposes it to an LLM agent as an inference-time, agent-callable structural retrieval interface, queried and evolved during execution rather than baked into a fixed retrieval pipeline: each search returns vector matches, typed-edge neighbors, and conflict signals, and a propose-then-commit protocol lets the agent register execution-backed edges so the graph accumulates structure across episodes. On ALFWorld and SkillsBench with MiniMax-M2.7, SkillDAG reaches 67.1% success and 27.3% reward, exceeding the strongest reported Graph-of-Skills baseline by +12.8 and +8.6 points; the advantage ports to gpt-5.2-codex, and intrinsic SkillsBench Ret@K rises from 65.5 to 78.2 under matched queries. These gains trace to isolable mechanisms: candidate ranking that stays robust as the pool grows 10x where a fixed seeding-diffusion pipeline degrades, and set-monotone online edits that enlarge ground-truth recall without evicting prior hits.

Skills have become an important abstraction for enabling large language model (LLM) agents to reuse past experience in long-horizon interactive tasks. However, existing trajectory-to-skill methods often produce flat collections of high-level textual skills that are stored and retrieved independently, leaving skill relations underutilized and maintaining a gap between high-level skills and executable actions. In this paper, we propose HiSkill, a hierarchical skill graph framework that organizes interaction trajectories into a directed graph with skill nodes, AtomicOp nodes, and typed edges. Specifically, the graph connects reusable high-level skills with executable action templates, while also capturing decomposition, temporal transition, compatibility, support, and recovery relations among them. At inference time, HiSkill retrieves a compact task-relevant subgraph and performs subgraph-guided task execution, where a symbolic task state, an active skill, and the retrieved subgraph guide the LLM agent to switch skills, select AtomicOps, and ground executable actions iteratively. Experiments on three interactive environments show that HiSkill outperforms state-of-the-art baselines while reducing inference token consumption, demonstrating the effectiveness of bridging high-level skills and executable action grounding through a hierarchical skill graph. Our data and code is available at https://github.com/BUPT-GAMMA/HiSkill.

Most AI-for-science systems focus on scaling a single reasoning process by using better models, larger context windows, long-horizon agentic execution, or digital co-scientists working with one principal user. However, challenging scientific problems are rarely solved by one reasoner alone. They are solved by teams whose members carry different priors, experimental background, tacit knowledge, and domain-trained intuitions. The open problem is therefore not only how to scale models, but how to develop "networked intelligence", scaling the connections between humans and AI systems so that a result or hypothesis produced in one context reaches another person, agent, instrument or robot that can act on it. We introduce Mycelium, an active shared workspace that automatically connects researchers and AI agents. As human users and agents work, the system captures important observations and hypotheses, tracks how they relate to the team's evolving knowledge model, and routes them to the person or agent whose next decision they can inform. We evaluate Mycelium through a real-world scientific discovery use case: a biological multi-omics campaign where shared context turned a local analytical finding into a cross-expert mechanistic constraint and ultimately into an experimental design. Finally, we describe networked intelligence as sparse conditional computation over distributed scientific contexts. This framework establishes when a scaled standalone agent is sufficient, and when isolated data and specialized expertise make a networked approach essential.

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and others parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

Wide deployment of machine learning models on edge devices has rendered the model intellectual property (IP) and data privacy vulnerable. We propose GNNVault, the first secure Graph Neural Network (GNN) deployment strategy based on Trusted Execution Environment (TEE). GNNVault follows the design of 'partition-before-training' and includes a private GNN rectifier to complement with a public backbone model. This way, both critical GNN model parameters and the private graph used during inference are protected within secure TEE compartments. Real-world implementations with Intel SGX demonstrate that GNNVault safeguards GNN inference against state-of-the-art link stealing attacks with negligible accuracy degradation (<2%).

Large Language Models (LLMs) have demonstrated promising reasoning capabilities in robotics; however, their application in multi-robot systems remains limited, particularly in handling task dependencies. This paper introduces DART-LLM, a novel framework that employs Directed Acyclic Graphs (DAGs) to model task dependencies, enabling the decomposition of natural language instructions into well-coordinated subtasks for multi-robot execution. DART-LLM comprises four key components: a Question-Answering (QA) LLM module for dependency-aware task decomposition, a Breakdown Function module for robot assignment, an Actuation module for execution, and a Vision-Language Model (VLM)-based object detector for environmental perception, achieving end-to-end task execution. Experimental results across three task complexity levels demonstrate that DART-LLM achieves state-of-the-art performance, significantly outperforming the baseline across all evaluation metrics. Among the tested models, DeepSeek-r1-671B achieves the highest success rate, whereas Llama-3.1-8B exhibits superior response time reliability. Ablation studies further confirm that explicit dependency modeling notably enhances the performance of smaller models, facilitating efficient deployment on resource-constrained platforms. Please refer to the project website https://wyd0817.github.io/project-dart-llm/ for videos and code.

Large language models (LLMs) have demonstrated remarkable capabilities in complex reasoning tasks when equipped with external tools. However, current frameworks predominantly rely on sequential processing, leading to inefficient execution particularly for tasks requiring extensive tool interaction. This paper introduces Flash-Searcher, a novel parallel agent reasoning framework that fundamentally reimagines the execution paradigm from sequential chains to directed acyclic graphs (DAGs). Flash-Searcher decomposes complex tasks into subtasks with explicit dependencies, enabling concurrent execution of independent reasoning paths while maintaining logical constraints. Through dynamic workflow optimization, our framework continuously refines the execution graph based on intermediate results, effectively integrating summary module. Comprehensive evaluations across multiple benchmarks demonstrate that Flash-Searcher consistently outperforms existing approaches. Specifically, it achieves 67.7% accuracy on BrowseComp and 83% on xbench-DeepSearch, while reducing agent execution steps by up to 35% compared to current frameworks. Furthermore, when distilling this parallel reasoning pipeline into single models, we observe substantial performance gains across diverse backbone architectures, underscoring the generalizability of our methodology. Our work thus represents a significant advance in agent architecture design, offering a more scalable and efficient paradigm for complex reasoning tasks.

Large language model (LLM)-based systems are becoming increasingly popular for solving tasks by constructing executable workflows that interleave LLM calls, information retrieval, tool use, code execution, memory updates, and verification. This survey reviews recent methods for designing and optimizing such workflows, which we treat as agentic computation graphs (ACGs). We organize the literature based on when workflow structure is determined, where structure refers to which components or agents are present, how they depend on each other, and how information flows between them. This lens distinguishes static methods, which fix a reusable workflow scaffold before deployment, from dynamic methods, which select, generate, or revise the workflow for a particular run before or during execution. We further organize prior work along three dimensions: when structure is determined, what part of the workflow is optimized, and which evaluation signals guide optimization (e.g., task metrics, verifier signals, preferences, or trace-derived feedback). We also distinguish reusable workflow templates, run-specific realized graphs, and execution traces, separating reusable design choices from the structures actually deployed in a given run and from realized runtime behavior. Finally, we outline a structure-aware evaluation perspective that complements downstream task metrics with graph-level properties, execution cost, robustness, and structural variation across inputs. Our goal is to provide a clear vocabulary, a unified framework for positioning new methods, a more comparable view of existing body of literature, and a more reproducible evaluation standard for future work in workflow optimizations for LLM agents.

Large language model (LLM)-based agents have demonstrated strong capabilities in complex reasoning and problem solving through multi-step interactions, yet most deployed agents remain behaviorally static, with knowledge acquired during execution rarely translating into systematic improvement over time. In response, a growing line of work on self-evolving agents explores how agents can improve through experience during deployment, but most existing approaches either rely on ad hoc reflection limited to single-task correction or adopt unstructured memory that accumulates fragmented experience with delayed usability. To address this limitation, we introduce EXG, an experience graph framework for self-evolving agents that explicitly organizes accumulated successes and failures into a structured, relational representation. EXG is the first experience graph designed for self-evolving agents, supporting both online, real-time graph growth during execution for immediate cross-task experience reuse, and offline reuse of a consolidated experience graph as an external memory module. This design also enables EXG to serve as a plug-and-play component for existing self-evolving agents, organizing prior experience into a unified experience graph and improving both solution quality and resource efficiency as deployment progresses. Extensive experiments across code generation and reasoning benchmarks show that EXG attains more favorable performance-efficiency trade-offs than reflection- and memory-based baselines in both online and offline evaluations. Our results suggest that structuring experience as a graph provides a principled foundation for scalable and transferable self-evolving agent behavior.

Graph and multi-agent orchestration frameworks make production large language model (LLM) workflows practical, but they do not by themselves solve conversational continuity when users maintain several interdependent objectives. This conceptual systems paper focuses on the high-complexity end of that design space, where goals can be suspended, resumed, revised, and invalidated by actions in other goals. We introduce the Goal-Oriented Dialogue Runtime (GODR), a framework-neutral design pattern that treats goals, task frames, lifecycle state, invalidation rules, and resumption contracts as first-class runtime objects while delegating bounded execution to graph runtimes, agents, tools, or application programming interfaces (APIs). GODR is not proposed as a replacement for workflow graphs in simple guided processes; it is intended for complex, multi-domain, interruptible conversations where objective continuity cannot be recovered reliably from agent identity, chat history, or execution-graph position alone. The paper formalizes the problem, proposes runtime objects and architecture-selection criteria, and frames evaluation as an agenda for future empirical validation rather than as a measured performance claim.

We present ControlLLM, a novel framework that enables large language models (LLMs) to utilize multi-modal tools for solving complex real-world tasks. Despite the remarkable performance of LLMs, they still struggle with tool invocation due to ambiguous user prompts, inaccurate tool selection and parameterization, and inefficient tool scheduling. To overcome these challenges, our framework comprises three key components: (1) a task decomposer that breaks down a complex task into clear subtasks with well-defined inputs and outputs; (2) a Thoughts-on-Graph (ToG) paradigm that searches the optimal solution path on a pre-built tool graph, which specifies the parameter and dependency relations among different tools; and (3) an execution engine with a rich toolbox that interprets the solution path and runs the tools efficiently on different computational devices. We evaluate our framework on diverse tasks involving image, audio, and video processing, demonstrating its superior accuracy, efficiency, and versatility compared to existing methods.

An elusive goal in navigation research is to build an intelligent agent that can understand multimodal instructions including natural language and image, and perform useful navigation. To achieve this, we study a widely useful category of navigation tasks we call Multimodal Instruction Navigation with demonstration Tours (MINT), in which the environment prior is provided through a previously recorded demonstration video. Recent advances in Vision Language Models (VLMs) have shown a promising path in achieving this goal as it demonstrates capabilities in perceiving and reasoning about multimodal inputs. However, VLMs are typically trained to predict textual output and it is an open research question about how to best utilize them in navigation. To solve MINT, we present Mobility VLA, a hierarchical Vision-Language-Action (VLA) navigation policy that combines the environment understanding and common sense reasoning power of long-context VLMs and a robust low-level navigation policy based on topological graphs. The high-level policy consists of a long-context VLM that takes the demonstration tour video and the multimodal user instruction as input to find the goal frame in the tour video. Next, a low-level policy uses the goal frame and an offline constructed topological graph to generate robot actions at every timestep. We evaluated Mobility VLA in a 836m^2 real world environment and show that Mobility VLA has a high end-to-end success rates on previously unsolved multimodal instructions such as "Where should I return this?" while holding a plastic bin.

LLM-based agents have shown strong potential for solving complex multi-step tasks, yet existing performance improvements often rely on either scaling to larger backbone models or task-specific fine-tuning. The former incurs substantial computational costs, while the latter typically generalizes poorly across different tasks. Although prompt-based control is training-free and broadly applicable, existing methods still leave input-output dependencies between subtasks implicit in textual trajectories, making verified intermediate results difficult to reuse. To address these limitations, we propose Atomic Task Graph (ATG), a unified control framework for planning and execution. Specifically, ATG maintains an explicit graph to expose dependencies and support reuse. During planning, it recursively decomposes a high-level task into subtasks, forming a sequence of directed acyclic graphs (DAGs) whose evolution can be traced. During execution, the dependencies exposed by ATG allow independent branches to be executed in parallel, thereby improving execution efficiency. When failures are detected, ATG leverages the graph evolution history to localize the error source and repair only the affected region, preserving validated regions unchanged. Experiments show that ATG consistently outperforms strong baselines in success rate and execution efficiency across three interactive benchmarks using only 7B-8B backbones.

Modern tools for class-agnostic image segmentation (e.g., SegmentAnything) and open-set semantic understanding (e.g., CLIP) provide unprecedented opportunities for robot perception and mapping. While traditional closed-set metric-semantic maps were restricted to tens or hundreds of semantic classes, we can now build maps with a plethora of objects and countless semantic variations. This leaves us with a fundamental question: what is the right granularity for the objects (and, more generally, for the semantic concepts) the robot has to include in its map representation? While related work implicitly chooses a level of granularity by tuning thresholds for object detection, we argue that such a choice is intrinsically task-dependent. The first contribution of this paper is to propose a task-driven 3D scene understanding problem, where the robot is given a list of tasks in natural language and has to select the granularity and the subset of objects and scene structure to retain in its map that is sufficient to complete the tasks. We show that this problem can be naturally formulated using the Information Bottleneck (IB), an established information-theoretic framework. The second contribution is an algorithm for task-driven 3D scene understanding based on an Agglomerative IB approach, that is able to cluster 3D primitives in the environment into task-relevant objects and regions and executes incrementally. The third contribution is to integrate our task-driven clustering algorithm into a real-time pipeline, named Clio, that constructs a hierarchical 3D scene graph of the environment online using only onboard compute, as the robot explores it. Our final contribution is an extensive experimental campaign showing that Clio not only allows real-time construction of compact open-set 3D scene graphs, but also improves the accuracy of task execution by limiting the map to relevant semantic concepts.

Large language models (LLMs) augmented with tools are emerging as autonomous agents capable of using Web engine, APIs, and code to solve complex, long-horizon tasks. Current tool-using benchmarks for information seeking on academic graphs rely on synthetic templates, simplified solution spaces, or narrow tasks such as paper-centric tasks, leaving key challenges underexplored - realistic user intent, complex multi-step API planning, rich parameter filling for APIs, grounded answers with references, and comprehensive evaluation of both the process and the outcome. We introduce AISE-Bench, a real-world, full-cycle annotated benchmark for information seeking on academic knowledge graphs. AISE-Bench release contains 1,133 QA pairs, including query taxonomies, full API execution trajectories, validated parameters, and source-grounded answers with reference links. To support high-quality annotation, we design a customized agent workflow to enable annotators to plan, execute, and revise complex API workflows efficiently. We develop a comprehensive evaluation protocol measuring answer quality, reference grounding, API-planning correctness, and execution success. Among the 14 evaluated methods, even the strongest model (PLAY2PROMPT with Gemini-3-Pro) achieves only moderate performance and often struggles with API planning and execution. AISE-Bench establishes a challenging new testbed for quantitatively evaluating and improving the stepwise correctness, grounded summarization, and traceable reasoning of multi-step API-using LLM agents. Our code and data are available at https://aise-bench.github.io/.

AI agents have become increasingly adept at complex tasks such as coding, reasoning, and multimodal understanding. However, building generalist systems requires moving beyond individual agents to collective inference -- a paradigm where multi-agent systems with diverse, task-specialized agents complement one another through structured communication and collaboration. Today, coordination is usually handled with imprecise, ad-hoc natural language, which limits complex interaction and hinders interoperability with domain-specific agents. We introduce Agent context protocols (ACPs): a domain- and agent-agnostic family of structured protocols for agent-agent communication, coordination, and error handling. ACPs combine (i) persistent execution blueprints -- explicit dependency graphs that store intermediate agent outputs -- with (ii) standardized message schemas, enabling robust and fault-tolerant multi-agent collective inference. ACP-powered generalist systems reach state-of-the-art performance: 28.3 % accuracy on AssistantBench for long-horizon web assistance and best-in-class multimodal technical reports, outperforming commercial AI systems in human evaluation. ACPs are highly modular and extensible, allowing practitioners to build top-tier generalist agents quickly.

Control Flow Graphs (CFGs) are critical for analyzing program execution and characterizing malware behavior. With the growing adoption of Graph Neural Networks (GNNs), CFG-based representations have proven highly effective for malware detection. This study proposes a novel framework that dynamically constructs CFGs and embeds node features using a hybrid approach combining rule-based encoding and autoencoder-based embedding. A GNN-based classifier is then constructed to detect malicious behavior from the resulting graph representations. To improve model interpretability, we apply state-of-the-art explainability techniques, including GNNExplainer, PGExplainer, and CaptumExplainer, the latter is utilized three attribution methods: Integrated Gradients, Guided Backpropagation, and Saliency. In addition, we introduce a novel aggregation method, called RankFusion, that integrates the outputs of the top-performing explainers to enhance the explanation quality. We also evaluate explanations using two subgraph extraction strategies, including the proposed Greedy Edge-wise Composition (GEC) method for improved structural coherence. A comprehensive evaluation using accuracy, fidelity, and consistency metrics demonstrates the effectiveness of the proposed framework in terms of accurate identification of malware samples and generating reliable and interpretable explanations.

Modern LLM agents increasingly rely on reusable skills, yet as skill libraries scale to thousands of entries, effective retrieval becomes a bottleneck. Graph-of-Skills (GoS) addresses this challenge by exploiting dependency-aware graph structure for scalable skill retrieval, while SkillDAG further demonstrates that skill graphs can accumulate execution-backed structure online. However, these approaches leave open whether historical execution traces can be systematically distilled into a better retrieval graph that generalizes to unseen tasks. We present Self-Evolving Graph-of-Skills (SE-GoS), a training-free framework that evolves an existing GoS graph from execution traces while preserving the original retrieval pipeline. SE-GoS performs three complementary updates: topology evolution that discovers and prunes skill relationships from execution evidence, edge-weight evolution that reinforces retrieval-relevant relationships based on historical effectiveness, and description evolution that optimizes retrieval-facing skill descriptions using execution feedback. Across three LLMs on SkillsBench, SE-GoS consistently improves task reward while reducing input tokens relative to full skill loading, with gains varying across model families. In a representative setting, one evolution round improves reward from 52.4\% to 59.4\% while reducing input tokens by approximately one-third relative to full skill loading, and the resulting graph transfers to a disjoint held-out split with a 5.4-point improvement over the static GoS baseline. These results show that skill graphs can be improved from execution experience without model training, changes to the retrieval algorithm, or modifications to skill content, turning a static retrieval graph into an evolving retrieval infrastructure.

Compact language models (LMs) reduce cost, latency, and deployment risk for tool agents. Yet MCP-style tool use requires more than isolated function calling: an agent must discover tools from live catalogs, satisfy schemas, preserve dependencies across intermediate outputs, and ground final responses in executed evidence. Small planners often generate plausible workflow graphs that fail under tool resolution, parameter validation, dependency tracking, or execution. We argue that this failure mode is poorly handled by small-corpus distillation. A few hundred teacher traces can teach workflow format, but rarely cover the recovery behavior needed to repair failed plans over changing tool catalogs. We introduce Evoflux, an inference-time evolutionary search method that treats compact tool use as the repair of executable tool workflows. It evolves typed workflow graphs through structured edits, execution feedback, adaptive intensity, meta-guided redesign, and diversity pruning. On held-out MCP-Bench tasks spanning live MCP servers and 250 tools, Evoflux raises execution feasibility from roughly 3% to 17-24% across small planners. In contrast, SFT and SFT+DPO on the same search-mined data match, underperform, or collapse below zero-shot performance; ReAct reaches higher peaks, but with higher variance and token cost. These results show that execution-grounded search is more reliable under scarce teacher-trace budgets.

Large Language Models (LLMs) have demonstrated exceptional abilities in reasoning for task planning. However, challenges remain under-explored for parallel schedules. This paper introduces a novel paradigm, plan-over-graph, in which the model first decomposes a real-life textual task into executable subtasks and constructs an abstract task graph. The model then understands this task graph as input and generates a plan for parallel execution. To enhance the planning capability of complex, scalable graphs, we design an automated and controllable pipeline to generate synthetic graphs and propose a two-stage training scheme. Experimental results show that our plan-over-graph method significantly improves task performance on both API-based LLMs and trainable open-sourced LLMs. By normalizing complex tasks as graphs, our method naturally supports parallel execution, demonstrating global efficiency. The code and data are available at https://github.com/zsq259/Plan-over-Graph.

Current Chain-of-Thought (CoT) verification methods predict reasoning correctness based on outputs (black-box) or activations (gray-box), but offer limited insight into why a computation fails. We introduce a white-box method: Circuit-based Reasoning Verification (CRV). We hypothesize that attribution graphs of correct CoT steps, viewed as execution traces of the model's latent reasoning circuits, possess distinct structural fingerprints from those of incorrect steps. By training a classifier on structural features of these graphs, we show that these traces contain a powerful signal of reasoning errors. Our white-box approach yields novel scientific insights unattainable by other methods. (1) We demonstrate that structural signatures of error are highly predictive, establishing the viability of verifying reasoning directly via its computational graph. (2) We find these signatures to be highly domain-specific, revealing that failures in different reasoning tasks manifest as distinct computational patterns. (3) We provide evidence that these signatures are not merely correlational; by using our analysis to guide targeted interventions on individual transcoder features, we successfully correct the model's faulty reasoning. Our work shows that, by scrutinizing a model's computational process, we can move from simple error detection to a deeper, causal understanding of LLM reasoning.

Tool agents--LLM-based systems that interact with external APIs--offer a way to execute real-world tasks. However, as tasks become increasingly complex, these agents struggle to identify and call the correct APIs in the proper order. To tackle this problem, we investigate converting API documentation into a structured API graph that captures API dependencies and leveraging it for multi-tool queries that require compositional API calls. To support this, we introduce In-N-Out, the first expert-annotated dataset of API graphs built from two real-world API benchmarks and their documentation. Using In-N-Out significantly improves performance on both tool retrieval and multi-tool query generation, nearly doubling that of LLMs using documentation alone. Moreover, graphs generated by models fine-tuned on In-N-Out close 90% of this gap, showing that our dataset helps models learn to comprehend API documentation and parameter relationships. Our findings highlight the promise of using explicit API graphs for tool agents and the utility of In-N-Out as a valuable resource. We release our dataset and code at https://github.com/holi-lab/In-N-Out-API-Graph.

The deployment and training of neural networks on edge computing devices pose many challenges. The low memory nature of edge devices is often one of the biggest limiting factors encountered in the deployment of large neural network models. Tensor rematerialization or recompute is a way to address high memory requirements for neural network training and inference. In this paper we consider the problem of execution time minimization of compute graphs subject to a memory budget. In particular, we develop a new constraint programming formulation called Moccasin with only O(n) integer variables, where n is the number of nodes in the compute graph. This is a significant improvement over the works in the recent literature that propose formulations with O(n^2) Boolean variables. We present numerical studies that show that our approach is up to an order of magnitude faster than recent work especially for large-scale graphs.

Methods that use Large Language Models (LLM) as planners for embodied instruction following tasks have become widespread. To successfully complete tasks, the LLM must be grounded in the environment in which the robot operates. One solution is to use a scene graph that contains all the necessary information. Modern methods rely on prebuilt scene graphs and assume that all task-relevant information is available at the start of planning. However, these approaches do not account for changes in the environment that may occur between the graph construction and the task execution. We propose LookPlanGraph - a method that leverages a scene graph composed of static assets and object priors. During plan execution, LookPlanGraph continuously updates the graph with relevant objects, either by verifying existing priors or discovering new entities. This is achieved by processing the agents egocentric camera view using a Vision Language Model. We conducted experiments with changed object positions VirtualHome and OmniGibson simulated environments, demonstrating that LookPlanGraph outperforms methods based on predefined static scene graphs. To demonstrate the practical applicability of our approach, we also conducted experiments in a real-world setting. Additionally, we introduce the GraSIF (Graph Scenes for Instruction Following) dataset with automated validation framework, comprising 514 tasks drawn from SayPlan Office, BEHAVIOR-1K, and VirtualHome RobotHow. Project page available at https://lookplangraph.github.io .

The rapid growth of large language models (LLMs) has outpaced the evolution of single-GPU hardware, making model scale increasingly constrained by memory capacity rather than computation. While modern training systems extend GPU memory through distributed parallelism and offloading across CPU and storage tiers, they fundamentally retain a GPU-centric execution paradigm in which GPUs host persistent model replicas and full autograd graphs. As a result, scaling large models remains tightly coupled to multi-GPU clusters, complex distributed runtimes, and unpredictable host memory consumption, creating substantial barriers for node-scale post-training workloads such as instruction tuning, alignment, and domain adaptation. We present Horizon-LM, a memory-centric training system that redefines the roles of CPU and GPU for large-model optimization. Horizon-LM treats host memory as the authoritative parameter store and uses GPUs solely as transient compute engines through a CPU-master, GPU-template execution model. By eliminating persistent GPU-resident modules and autograd graphs, employing explicit recomputation with manual gradient propagation, and introducing a pipelined double-buffered execution engine, Horizon-LM decouples model scale from GPU count and bounds memory usage to the theoretical parameter footprint. On a single H200 GPU with 1.5\,TB host RAM, Horizon-LM reliably trains models up to 120B parameters. On a standard single A100 machine, Horizon-LM achieves up to 12.2times higher training throughput than DeepSpeed ZeRO-3 with CPU offloading while preserving numerical correctness. Across platforms and scales, Horizon-LM sustains high device utilization and predictable memory growth, demonstrating that host memory, not GPU memory, defines the true feasibility boundary for node-scale large-model training.

Skill ecosystems for LLM agents have matured rapidly, yet recent benchmarks show that providing agents with more skills does not monotonically improve performance -- focused sets of 2-3 skills outperform comprehensive documentation, and excessive skills actually hurt. The bottleneck has shifted from skill availability to skill orchestration: agents need not more skills, but a structural mechanism to select, compose, and execute them with explicit causal dependencies. We propose GraSP, the first executable skill graph architecture that introduces a compilation layer between skill retrieval and execution. GraSP transforms flat skill sets into typed directed acyclic graphs (DAGs) with precondition-effect edges, executes them with node-level verification, and performs locality-bounded repair through five typed operators -- reducing replanning from O(N) to O(d^h). Across ALFWorld, ScienceWorld, WebShop, and InterCode with eight LLM backbones, GraSP outperforms ReAct, Reflexion, ExpeL, and flat skill baselines in every configuration, improving reward by up to +19 points over the strongest baseline while cutting environment steps by up to 41%. GraSP's advantage grows with task complexity and is robust to both skill over-retrieval and quality degradation, confirming that structured orchestration -- not larger skill libraries -- is the key to reliable agent execution.

There is growing interest in leveraging large language models (LLMs) for text-to-model translation and optimization tasks. This paper aims to advance this line of research by introducing Text2Model and Text2Zinc. Text2Model is a suite of copilots based on several LLM strategies with varying complexity, along with an online leaderboard. Text2Zinc is a cross-domain dataset for capturing optimization and satisfaction problems specified in natural language, along with an interactive editor with built-in AI assistant. While there is an emerging literature on using LLMs for translating combinatorial problems into formal models, our work is the first attempt to integrate both satisfaction and optimization problems within a unified architecture and dataset. Moreover, our approach is solver-agnostic unlike existing work that focuses on translation to a solver-specific model. To achieve this, we leverage MiniZinc's solver-and-paradigm-agnostic modeling capabilities to formulate combinatorial problems. We conduct comprehensive experiments to compare execution and solution accuracy across several single- and multi-call strategies, including; zero-shot prompting, chain-of-thought reasoning, intermediate representations via knowledge-graphs, grammar-based syntax encoding, and agentic approaches that decompose the model into sequential sub-tasks. Our copilot strategies are competitive, and in parts improve, recent research in this domain. Our findings indicate that while LLMs are promising they are not yet a push-button technology for combinatorial modeling. We contribute Text2Model copilots and leaderboard, and Text2Zinc and interactive editor to open-source to support closing this performance gap.

Progress in LLMs is increasingly measured through standardized benchmarks, where state-of-the-art improvements are often separated by fractions of a percentage point. At the same time, the computational cost of evaluating modern LLMs has driven widespread adoption of specialized inference backends, software systems that execute trained models efficiently at inference time. While critical for scalability, system-level optimizations, such as custom CUDA kernels and reduced-precision arithmetic, can alter token probabilities and introduce non-determinism, possibly cascading into divergent generation. In this work, we first survey the inference landscape, identifying 200 distinct engines, and analyze 35,000 ML publications, finding that the specific inference stack is rarely reported despite this widespread diversity. We then present a systematic empirical study of how inference backends affect LLM benchmark results. Holding model weights, decoding parameters, and hardware constant, we evaluate five widely used inference engines, including vLLM, SGLang, and llama.cpp, across multiple open-weight models and established benchmarks. We show that the choice of backend alone can shift benchmark scores by up to 16.6 percentage points and induce high rates of output disagreement. By isolating backend optimizations and tracing the execution pipeline, we find this divergence is driven by system-level optimizations like prefix caching and CUDA graphs, custom kernels, and engine-specific defaults in logit processing. Our findings identify the inference backend as a previously unreported but consequential hyperparameter in the evaluation of LLM and advocate standardized reporting of inference stacks to improve the reproducibility and interpretability of benchmark comparisons.

Enterprise property graphs vary widely in schema structure, internal terminology, domain assumptions, governance constraints, and user interaction patterns. A deployment-relevant Text2Cypher benchmark therefore reflects the questions users and agents actually ask of that graph. Creating such a benchmark is difficult because schemas and values are unique, and graph structure changes over time. Each NL-query pair must also be executable, use real graph entities, preserve diversity, and remain balanced across query types and difficulty levels. We present PIPE-Cypher, a local benchmark-generation pipeline that turns a live property graph and optional seed queries from customer questions, analyst logs, or agent tool calls into balanced NL-to-Cypher benchmarks. PIPE-Cypher combines schema profiling, reverse-query grounding, constrained generation, deterministic Cypher governance, execution validation, redaction, diversity controls, and a calibrated local LLM judge. Using local Qwen3.5-9B generation and judging, PIPE-Cypher exports 3,000 accepted FinBench/SNB examples, completes three audited ablation suites, calibrates judge behavior with human labels, and evaluates 11 local downstream models. The resulting benchmark is deliberately discriminative: zero-shot transfer is weak, while a few-shot control shows that schema-specific example banks can help compatible model families. Together, PIPE-Cypher makes Text2Cypher benchmarking a repeatable process that evolves with the graph, its users, and its target workloads.

LLM agents follow a practical execution loop in digital environments: they reason over structured states, invoke tools, inspect feedback, and revise actions. Extending this loop to physical robots is difficult because physical execution is continuous, embodiment-dependent, uncertain, and constrained by safety. Existing embodied-AI systems have advanced manipulation, spatial understanding, navigation, and humanoid control, but these capabilities often remain specialized modules or loosely coupled decision loops. In this work, we introduce HoloAgent-0, a unified embodied agent framework for real-world robot deployment. Embodied AgentOS converts language instructions into executable skill graphs, schedules robot resources, monitors execution, and triggers clarification or re-planning from runtime feedback. HoloAgent-0 organizes heterogeneous robot models and controllers through three coupled layers: Embodied AgentOS for closed-loop execution, 3D spatial memory for physical world grounding, and embodied skills for robot action. We deploy HoloAgent-0 on real hardware and evaluate its spatial memory, long-horizon navigation, and closed-loop execution across motion generation, object search, cross-robot coordination, and mobile manipulation.

In recent years, research in the area of human-robot interaction has focused on developing robots capable of understanding complex human instructions and performing tasks in dynamic and diverse environments. These systems have a wide range of applications, from personal assistance to industrial robotics, emphasizing the importance of robots interacting flexibly, naturally and safely with humans. This paper presents an advanced architecture for robotic action planning that integrates communication, perception, and planning with Large Language Models (LLMs). Our system is designed to translate commands expressed in natural language into executable robot actions, incorporating environmental information and dynamically updating plans based on real-time feedback. The Planner Module is the core of the system where LLMs embedded in a modified ReAct framework are employed to interpret and carry out user commands. By leveraging their extensive pre-trained knowledge, LLMs can effectively process user requests without the need to introduce new knowledge on the changing environment. The modified ReAct framework further enhances the execution space by providing real-time environmental perception and the outcomes of physical actions. By combining robust and dynamic semantic map representations as graphs with control components and failure explanations, this architecture enhances a robot adaptability, task execution, and seamless collaboration with human users in shared and dynamic environments. Through the integration of continuous feedback loops with the environment the system can dynamically adjusts the plan to accommodate unexpected changes, optimizing the robot ability to perform tasks. Using a dataset of previous experience is possible to provide detailed feedback about the failure. Updating the LLMs context of the next iteration with suggestion on how to overcame the issue.

Computer use agents (CUAs) today are primarily deployed as single serial agents. This setup is suboptimal for complex long-horizon tasks that benefit from task decomposition, parallel execution, and consistent re-planning based on new information. In this paper, we argue that we should instead move towards evaluating and building multi-agent computer use (MACU) systems. These systems, which emphasize planning and parallel execution, alleviate many of the shortcomings of single-agent CUAs. We propose a general multi-agent setup in which a manager model decomposes computer use tasks as a directed acyclic graph (DAG), encoding relevant dependencies and goals for subagents. At each iteration, the manager dispatches parallel CUA subagents to carry out nodes on the ready frontier of the DAG, and continuously revises the DAG (adding, canceling, or rewriting nodes) as new findings arrive from subagents. This design treats the partially observable environment of computer use as a first class challenge: information that downstream agents may not be able to re-observe are retained and passed forward through the manager and DAG structure. We demonstrate that MACU consistently improves over strong single-agent baselines by 3.4-25.5% on desktop (OSWorld) and web navigation (Online-Mind2Web, WebTailBench, Odysseys) benchmarks, exhibits more favorable test-time scaling, and solves complex long-horizon tasks where single-agent CUAs get stuck. On Odysseys, a long-horizon web navigation benchmark, MACU improves average task completion wall-clock time by {sim} 1.5 times, demonstrating its efficacy in speeding up traditionally slow CUA pipelines. Our findings highlight that multi-agent coordination is a promising axis for scaling computer use agents to work productively for longer and more effectively. We release all code and interactive visualizations at https://jykoh.com/multi-agent-computer-use.

With the rapid advancement of generative models, general-purpose generation has gained increasing attention as a promising approach to unify diverse tasks across modalities within a single system. Despite this progress, existing open-source frameworks often remain fragile and struggle to support complex real-world applications due to the lack of structured workflow planning and execution-level feedback. To address these limitations, we present ComfyMind, a collaborative AI system designed to enable robust and scalable general-purpose generation, built on the ComfyUI platform. ComfyMind introduces two core innovations: Semantic Workflow Interface (SWI) that abstracts low-level node graphs into callable functional modules described in natural language, enabling high-level composition and reducing structural errors; Search Tree Planning mechanism with localized feedback execution, which models generation as a hierarchical decision process and allows adaptive correction at each stage. Together, these components improve the stability and flexibility of complex generative workflows. We evaluate ComfyMind on three public benchmarks: ComfyBench, GenEval, and Reason-Edit, which span generation, editing, and reasoning tasks. Results show that ComfyMind consistently outperforms existing open-source baselines and achieves performance comparable to GPT-Image-1. ComfyMind paves a promising path for the development of open-source general-purpose generative AI systems. Project page: https://github.com/LitaoGuo/ComfyMind

Agentic tool use has gained traction with the rise of agentic tool calling, yet most existing work overlooks the complexity of multi-turn tool interactions. We introduce OrchDAG, a synthetic data generation pipeline that models tool execution as directed acyclic graphs (DAGs) with controllable complexity. Using this dataset, we benchmark model performance and propose a graph-based reward to enhance RLVR training. Experiments show that the dataset presents a challenging but solvable benchmark, and the proposed reward is effective when combined with GRPO-style algorithms, highlighting the importance of leveraging topological structure and data complexity in multi-turn tool use.

Layer-wise Relevance Propagation (LRP) provides principled attribution for neural networks through conservation properties and foundations in Deep Taylor Decomposition. However, existing implementations operate at the module level, requiring architecture-specific propagation rules and modifications. These limit the generality of target model and sustainability of implementations as architectures evolve. We introduce DynamicLRP, a model-agnostic LRP framework operating at the tensor operation level. By decomposing attribution to individual operations within computation graphs and introducing a novel mechanism for deferred activation resolution, named the Promise System, our approach achieves true architecture agnosticity while maintaining LRP's theoretical guarantees. This design operates independently of backpropagation machinery, enabling operation on arbitrary computation graphs without model modification and side-by-side execution with gradient backpropagation. Being based on computation graphs, this method is theoretically extensible to other deep learning libraries that support auto-differentiation. We demonstrate faithfulness matching or exceeding specialized implementations (1.77 vs 1.69 ABPC on VGG, equivalent performance on ViT, 93.70\% and 95.06\% top-1 attribution accuracy for explaining RoBERTa-large and Flan-T5-large answers on SQuADv2, respectively) while maintaining practical efficiency on models with hundreds of millions of parameters. We achieved 99.92\% node coverage across 31,465 computation graph nodes from 15 diverse architectures, including state-space models (Mamba), audio transformers (Whisper), and multimodal systems (DePlot) without any model-specific code with rules for 47 fundamental operations implemented. Our operation-level decomposition and Promise System establish a sustainable, extensible foundation for LRP across evolving architectures.

Achieving general-purpose robotic manipulation requires robots to seamlessly bridge high-level semantic intent with low-level physical interaction in unstructured environments. However, existing approaches falter in zero-shot generalization: end-to-end Vision-Language-Action (VLA) models often lack the precision required for long-horizon tasks, while traditional hierarchical planners suffer from semantic rigidity when facing open-world variations. To address this, we present UniManip, a framework grounded in a Bi-level Agentic Operational Graph (AOG) that unifies semantic reasoning and physical grounding. By coupling a high-level Agentic Layer for task orchestration with a low-level Scene Layer for dynamic state representation, the system continuously aligns abstract planning with geometric constraints, enabling robust zero-shot execution. Unlike static pipelines, UniManip operates as a dynamic agentic loop: it actively instantiates object-centric scene graphs from unstructured perception, parameterizes these representations into collision-free trajectories via a safety-aware local planner, and exploits structured memory to autonomously diagnose and recover from execution failures. Extensive experiments validate the system's robust zero-shot capability on unseen objects and tasks, demonstrating a 22.5% and 25.0% higher success rate compared to state-of-the-art VLA and hierarchical baselines, respectively. Notably, the system enables direct zero-shot transfer from fixed-base setups to mobile manipulation without fine-tuning or reconfiguration. Our open-source project page can be found at https://henryhcliu.github.io/unimanip.

Recent advances in large language models for test case generation have improved branch coverage via prompt-engineered mutations. However, they still lack principled mechanisms for steering models toward specific high-risk execution branches, limiting their effectiveness for discovering subtle bugs and security vulnerabilities. We propose GLMTest, the first program structure-aware LLM framework for targeted test case generation that seamlessly integrates code property graphs and code semantics using a graph neural network and a language model to condition test case generation on execution branches. This structured conditioning enables controllable and branch-targeted test case generation, thereby potentially enhancing bug and security risk discovery. Experiments on real-world projects show that GLMTest built on a Qwen2.5-Coder-7B-Instruct model improves branch accuracy from 27.4% to 50.2% on TestGenEval benchmark compared with state-of-the-art LLMs, i.e., Claude-Sonnet-4.5 and GPT-4o-mini.

As Large Language Model (LLM) agents become increasingly capable of automating complex, multi-step tasks, the need for robust, secure, and predictable architectural patterns is paramount. This paper provides a comprehensive guide to the ``Plan-then-Execute'' (P-t-E) pattern, an agentic design that separates strategic planning from tactical execution. We explore the foundational principles of P-t-E, detailing its core components - the Planner and the Executor - and its architectural advantages in predictability, cost-efficiency, and reasoning quality over reactive patterns like ReAct (Reason + Act). A central focus is placed on the security implications of this design, particularly its inherent resilience to indirect prompt injection attacks by establishing control-flow integrity. We argue that while P-t-E provides a strong foundation, a defense-in-depth strategy is necessary, and we detail essential complementary controls such as the Principle of Least Privilege, task-scoped tool access, and sandboxed code execution. To make these principles actionable, this guide provides detailed implementation blueprints and working code references for three leading agentic frameworks: LangChain (via LangGraph), CrewAI, and AutoGen. Each framework's approach to implementing the P-t-E pattern is analyzed, highlighting unique features like LangGraph's stateful graphs for re-planning, CrewAI's declarative tool scoping for security, and AutoGen's built-in Docker sandboxing. Finally, we discuss advanced patterns, including dynamic re-planning loops, parallel execution with Directed Acyclic Graphs (DAGs), and the critical role of Human-in-the-Loop (HITL) verification, to offer a complete strategic blueprint for architects, developers, and security engineers aiming to build production-grade, resilient, and trustworthy LLM agents.

Single-token autoregressive decode on CPUs is bound by memory bandwidth, not arithmetic: a modern CPU sustains roughly 1 TFLOP/s of compute but only about 50 GB/s from main memory, and each generated token must stream every active weight once. This report argues that the most effective response is to co-design the model architecture and the inference runtime together. It presents cflow, a CPU-first streaming engine, alongside a family of pipeline-native transformer architectures whose inter-layer dependency graphs are constructed to permit a vertical, stage-major execution schedule. cflow stores weights as L2-sized tiles in compute-consumption order, reads only the top-k experts of each mixture-of-experts layer, fuses projections, and executes a delay-aware schedule from per-model dependency parameters. Across five architectures trained on TinyStories, one (arch2_4_combined) achieves a 2.00x reduction in critical-path weight bandwidth (9.00 to 4.50 MB/token) within 0.24 perplexity of the best candidate, and the tile layout incurs 7.29x fewer L1-data read misses than a row-major baseline. On a 30.9-billion-parameter pipeline-native MoE, cflow decodes at 5.94 tokens/s (tok/s) on a 32-vCPU Ice Lake server, ahead of llama.cpp (4.75) and the vLLM CPU backend (1.65) on comparably sized dense models. Realizing the expert-delay window as asynchronous I/O overlap on a disk-resident expert tier yields a further net win of up to 1.68x, matching the overlap model within 1%. Measurement refutes one of the eight design claims and leaves a second inconclusive; both are reported in full, with the conditions under which they would hold.

Machine learning applications are increasingly deployed not only to serve predictions using static models, but also as tightly-integrated components of feedback loops involving dynamic, real-time decision making. These applications pose a new set of requirements, none of which are difficult to achieve in isolation, but the combination of which creates a challenge for existing distributed execution frameworks: computation with millisecond latency at high throughput, adaptive construction of arbitrary task graphs, and execution of heterogeneous kernels over diverse sets of resources. We assert that a new distributed execution framework is needed for such ML applications and propose a candidate approach with a proof-of-concept architecture that achieves a 63x performance improvement over a state-of-the-art execution framework for a representative application.

Document extraction is an important step before retrieval-augmented generation (RAG), knowledge bases, and downstream generative AI can work. It turns unstructured documents like PDFs and scans into structured text and layout-aware representations. We introduce NovaLAD, a comprehensive document parsing system that integrates two concurrent YOLO object detection models - element detection and layout detection - with rule-based grouping and optional vision-language enhancement. When a page image is sent in, the first thing that happens is that it goes through both models at the same time. The element model finds semantic content like the title, header, text, table, image, and so on, and the layout model finds structural regions like layout_box, column_group, multi_column, row_group, and so on. A key design decision is to first send an image or figure through an image classifier (ViT) that decides whether it is relevant or not. Only useful images are then submitted to the Vision LLM for title, summary, and structured information, which cuts down on noise and costs. NovaLAD is built for speed: it works on CPU, employs parallel execution for detection, classification, OCR, and conversion, and generates several forms, including structured JSON, Markdown, RAG-ready texts, and knowledge graphs. We test on the DP-Bench benchmark (upstage/dp-bench) and get 96.49% TEDS and 98.51% NID, which is better than both commercial and open-source parsers. This paper explains how to extract data, how the architecture works, how data flows, and how to make NovaLAD both accurate and usable without needing a GPU.

Recent advances in Large Language Models (LLMs) have enabled the development of increasingly complex agentic and multi-agent systems capable of planning, tool use and task decomposition. However, empirical evidence shows that many of these systems suffer from fundamental reliability issues, including hallucinated actions, unexecutable plans and brittle coordination. Crucially, these failures do not stem from limitations of the underlying models themselves, but from the absence of explicit architectural structure linking goals, capabilities and execution. This paper presents a declarative, model-independent architectural layer for grounded agentic workflows that addresses this gap. The proposed layer, referred to as DALIA (Declarative Agentic Layer for Intelligent Agents), formalises executable capabilities, exposes tasks through a declarative discovery protocol, maintains a federated directory of agents and their execution resources, and constructs deterministic task graphs grounded exclusively in declared operations. By enforcing a clear separation between discovery, planning and execution, the architecture constrains agent behaviour to a verifiable operational space, reducing reliance on speculative reasoning and free-form coordination. We present the architecture and design principles of the proposed layer and illustrate its operation through a representative task-oriented scenario, demonstrating how declarative grounding enables reproducible and verifiable agentic workflows across heterogeneous environments.

Recent advances in generative AI have enabled natural language-driven image editing, yet existing systems often fail in complex scenes with multiple interacting objects because they rely heavily on users crafting precise text prompts. To address the absence of structured control, we propose SceneCraft, a novel interactive framework that bridges user intent and model execution by representing images as editable scene graphs. Instead of guessing text prompts through trial and error, users interact directly with a visual graph to perform complex spatial and relational operations. These graph modifications are automatically translated into precise, context-aware editing prompts, effectively eliminating linguistic ambiguity. To ensure robust and diverse results, structured prompts are dispatched to multiple state-of-the-art generative models. Evaluations across diverse editing scenarios show that SceneCraft provides a more intuitive control mechanism, significantly reducing the cognitive burden of manual prompt engineering while generating outputs that users consistently rate as higher in quality and fidelity.

Geospatial reasoning, i.e., computing distances, containment, and other spatial relations over real-world entities, is central to navigation and logistics, yet large language models (LLMs) struggle with the required geometric and topological computation despite storing considerable geographic knowledge. Existing benchmarks localize these failures only partially: they are synthetic or smallscale, largely monolingual, and offer limited control over geographic coverage. We introduce MultiGlobeQA, a multilingual benchmark of 46,060 question-answer pairs spanning 14 spatial-function families and 15 answer formats, with execution-based ground truth over three knowledge graphs. It covers 201 countries and territories via income- and density-stratified sampling, with parallel questions in English and 16 additional high- and low-resource languages. Across parametric, reasoning, and agentic settings, LLMs collapse on tasks requiring grid indexing and shape computation, while topological relations and directions fare best. Retrieval and tool use yield considerable gains, yet performance plateaus below two thirds even when gold facts are supplied, indicating that computation, not access to knowledge, is the bottleneck. Models also underperform on low-income regions, a gap that gold facts widen rather than close.

While chain-of-thought (CoT) reasoning improves the performance of large language models (LLMs) in complex tasks, it still has two main challenges: the low reliability of relying solely on LLMs to generate reasoning chains and the interference of natural language reasoning chains on the inference logic of LLMs. To address these issues, we propose CoT-RAG, a novel reasoning framework with three key designs: (i) Knowledge Graph-driven CoT Generation, featuring knowledge graphs to modulate reasoning chain generation of LLMs, thereby enhancing reasoning credibility; (ii) Learnable Knowledge Case-aware RAG, which incorporates retrieval-augmented generation (RAG) into knowledge graphs to retrieve relevant sub-cases and sub-descriptions, providing LLMs with learnable information; (iii) Pseudo-Program Prompting Execution, which encourages LLMs to execute reasoning tasks in pseudo-programs with greater logical rigor. We conduct a comprehensive evaluation on nine public datasets, covering three reasoning problems. Compared with the-state-of-the-art methods, CoT-RAG exhibits a significant accuracy improvement, ranging from 4.0% to 23.0%. Furthermore, testing on four domain-specific datasets, CoT-RAG shows remarkable accuracy and efficient execution, highlighting its strong practical applicability and scalability.

Large language models (LLMs) enable autonomous agents for reasoning, planning, and tool use. Recent systems increasingly organize these agents as graphs of specialized, interconnected nodes. Although graph-based orchestration supports flexible decomposition and coordination, it creates a key challenge: attention allocation. As workflows grow, existing approaches often execute graph components uniformly, wasting resources on irrelevant or low-impact tasks. We introduce Attention Orchestration, a paradigm that extends Transformer-style attention from token representations to workflow-level agent coordination. Our framework, Adaptive Goal-aware Attention Orchestration (AGAO), dynamically estimates agent importance based on user objectives, graph dependencies, and computational constraints. AGAO combines three components: (1) goal-aware attention, measuring semantic relevance between user goals and agent capabilities; (2) topology-aware attention, modeling structural dependencies in agent graphs; and (3) resource-aware attention, allocating budgets and execution priorities across heterogeneous agents. Together, these mechanisms transform static agent graphs into adaptive systems that focus computation on goal-critical reasoning paths. Experiments across diverse multi-agent workloads show that AGAO improves task effectiveness while reducing unnecessary computation, latency, and token consumption compared with existing graph-based execution strategies. Our work establishes Attention Engineering as a direction for scalable, intelligent multi-agent systems. Code: https://github.com/MingzhouFan97/AGAO.

Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python programs suitable for training machine learning models. Our library admits the construction of control-flow graphs, data-flow graphs, and composite ``program graphs'' that combine control-flow, data-flow, syntactic, and lexical information about a program. We present the capabilities and limitations of the library, perform a case study applying the library to millions of competitive programming submissions, and showcase the library's utility for machine learning research.

Developers today use significant amounts of open source code, surfacing the need for ways to automatically audit and upgrade library dependencies, and giving rise to the subfield of Software Composition Analysis (SCA). SCA products are concerned with three tasks: discovering dependencies, checking the reachability of vulnerable code for false positive elimination, and automated remediation. The latter two tasks rely on call graphs of application and library code to check whether vulnerability-specific sinks identified in libraries are used by applications. However, statically-constructed call graphs introduce both false positives and false negatives on real-world projects. In this paper, we develop a novel, modular means of combining call graphs derived from both static and dynamic analysis to improve the performance of false positive elimination. Our experiments indicate significant performance improvements.

In the past years, predictive process monitoring (PPM) techniques based on artificial neural networks have evolved as a method to monitor the future behavior of business processes. Existing approaches mostly focus on interpreting the processes as sequences, so-called traces, and feeding them to neural architectures designed to operate on sequential data such as recurrent neural networks (RNNs) or transformers. In this study, we investigate an alternative way to perform PPM: by transforming each process in its directly-follows-graph (DFG) representation we are able to apply graph neural networks (GNNs) for the prediction tasks. By this, we aim to develop models that are more suitable for complex processes that are long and contain an abundance of loops. In particular, we present different ways to create DFG representations depending on the particular GNN we use. The tested GNNs range from classical node-based to novel edge-based architectures. Further, we investigate the possibility of using multi-graphs. By these steps, we aim to design graph representations that minimize the information loss when transforming traces into graphs.

AI agents are vulnerable to prompt injection attacks, where malicious content hijacks agent behavior to steal credentials or cause financial loss. The only known robust defense is architectural isolation that strictly separates trusted task planning from untrusted environment observations. However, applying this design to Computer Use Agents (CUAs) -- systems that automate tasks by viewing screens and executing actions -- presents a fundamental challenge: current agents require continuous observation of UI state to determine each action, conflicting with the isolation required for security. We resolve this tension by demonstrating that UI workflows, while dynamic, are structurally predictable. We introduce Single-Shot Planning for CUAs, where a trusted planner generates a complete execution graph with conditional branches before any observation of potentially malicious content, providing provable control flow integrity guarantees against arbitrary instruction injections. Although this architectural isolation successfully prevents instruction injections, we show that additional measures are needed to prevent Branch Steering attacks, which manipulate UI elements to trigger unintended valid paths within the plan. We evaluate our design on OSWorld, and retain up to 57% of the performance of frontier models while improving performance for smaller open-source models by up to 19%, demonstrating that rigorous security and utility can coexist in CUAs.

We introduce Native Parallel Reasoner (NPR), a teacher-free framework that enables Large Language Models (LLMs) to self-evolve genuine parallel reasoning capabilities. NPR transforms the model from sequential emulation to native parallel cognition through three key innovations: 1) a self-distilled progressive training paradigm that transitions from ``cold-start'' format discovery to strict topological constraints without external supervision; 2) a novel Parallel-Aware Policy Optimization (PAPO) algorithm that optimizes branching policies directly within the execution graph, allowing the model to learn adaptive decomposition via trial and error; and 3) a robust NPR Engine that refactors memory management and flow control of SGLang to enable stable, large-scale parallel RL training. Across eight reasoning benchmarks, NPR trained on Qwen3-4B achieves performance gains of up to 24.5% and inference speedups up to 4.6x. Unlike prior baselines that often fall back to autoregressive decoding, NPR demonstrates 100% genuine parallel execution, establishing a new standard for self-evolving, efficient, and scalable agentic reasoning.

Large language models are increasingly deployed as multi-agent systems, where specialized roles communicate and collaborate through structured interactions to solve complex tasks that often exceed the capacity of a single agent. However, most existing systems still rely on a fixed role library and an execution-frozen interaction topology, a rigid design choice that frequently leads to task mismatch, prevents timely adaptation when new evidence emerges during reasoning, and further inflates inference cost. We introduce MetaGen, a training-free framework that adapts both the role space and the collaboration topology at inference time, without updating base model weights. MetaGen generates and rewrites query-conditioned role specifications to maintain a controllable dynamic role pool, then instantiates a constrained execution graph around a minimal backbone. During execution, it iteratively updates role prompts and adjusts structural decisions using lightweight feedback signals. Experiments on code generation and multi-step reasoning benchmarks show that MetaGen improves the accuracy and cost tradeoff over strong multi-agent baselines.

Knowledge graphs have been proven extremely useful in powering diverse applications in semantic search and natural language understanding. In this paper, we present GraphGen4Code, a toolkit to build code knowledge graphs that can similarly power various applications such as program search, code understanding, bug detection, and code automation. GraphGen4Code uses generic techniques to capture code semantics with the key nodes in the graph representing classes, functions, and methods. Edges indicate function usage (e.g., how data flows through function calls, as derived from program analysis of real code), and documentation about functions (e.g., code documentation, usage documentation, or forum discussions such as StackOverflow). Our toolkit uses named graphs in RDF to model graphs per program, or can output graphs as JSON. We show the scalability of the toolkit by applying it to 1.3 million Python files drawn from GitHub, 2,300 Python modules, and 47 million forum posts. This results in an integrated code graph with over 2 billion triples. We make the toolkit to build such graphs as well as the sample extraction of the 2 billion triples graph publicly available to the community for use.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Graph databases are gaining momentum thanks to the flexibility and expressiveness of their data models and query languages. A standardization activity driven by the ISO/IEC standardization body is also ongoing and has already conducted to the specification of the first versions of two standard graph query languages, namely SQL/PGQ and GQL, respectively in 2023 and 2024. Apart from the standards, there exists a panoply of concrete graph query languages provided by current graph database systems, each offering different query features. A common limitation of current graph query engines is the absence of an algebraic approach for evaluating path queries. To address this, we introduce an abstract algebra for evaluating path queries, allowing paths to be treated as first-class entities within the query processing pipeline. We demonstrate that our algebra can express a core fragment of path queries defined in GQL and SQL/PGQ, thereby serving as a formal framework for studying both standards and supporting their implementation in current graph database systems. We also show that evaluation trees for path algebra expressions can function as logical plans for evaluating path queries and enable the application of query optimization techniques. Our algebraic framework has the potential to act as a lingua franca for path query evaluation, enabling different implementations to be expressed and compared.

Software engineering, whether performed by humans or by AI agents, requires reasoning about how software behaves. We call the internal model that supports such reasoning the software world model, and view current code-execution benchmarks as covering one well-studied slice of it -- control flow. In this paper, we take a step toward a broader evaluation by shifting the observable axis to execution resources: alongside test outcome and exception class, we predict peak memory, wall-clock time, and ranked profiler outputs at method and line granularity. We use SWE-bench Verified as the source of data to hold the test close to real-world software engineering tasks. All tested models, frontier ones included, show modest performance and brittle behaviour, suggesting a notable lack of understanding of how software is executed, as opposed to how its source code is written.

This work explores the problem of generating task graphs of real-world activities. Different from prior formulations, we consider a setting where text transcripts of instructional videos performing a real-world activity (e.g., making coffee) are provided and the goal is to identify the key steps relevant to the task as well as the dependency relationship between these key steps. We propose a novel task graph generation approach that combines the reasoning capabilities of instruction-tuned language models along with clustering and ranking components to generate accurate task graphs in a completely unsupervised manner. We show that the proposed approach generates more accurate task graphs compared to a supervised learning approach on tasks from the ProceL and CrossTask datasets.

This paper introduces Opus, a novel framework for generating and optimizing Workflows tailored to complex Business Process Outsourcing (BPO) use cases, focusing on cost reduction and quality enhancement while adhering to established industry processes and operational constraints. Our approach generates executable Workflows from Intention, defined as the alignment of Client Input, Client Output, and Process Context. These Workflows are represented as Directed Acyclic Graphs (DAGs), with nodes as Tasks consisting of sequences of executable Instructions, including tools and human expert reviews. We adopt a two-phase methodology: Workflow Generation and Workflow Optimization. In the Generation phase, Workflows are generated using a Large Work Model (LWM) informed by a Work Knowledge Graph (WKG) that encodes domain-specific procedural and operational knowledge. In the Optimization phase, Workflows are transformed into Workflow Graphs (WFGs), where optimal Workflows are determined through path optimization. Our experiments demonstrate that state-of-the-art Large Language Models (LLMs) face challenges in reliably retrieving detailed process data as well as generating industry-compliant workflows. The key contributions of this paper include: - The integration of a Work Knowledge Graph (WKG) into a Large Work Model (LWM), enabling the generation of context-aware, semantically aligned, structured and auditable Workflows. - A two-phase approach that combines Workflow Generation from Intention with graph-based Workflow Optimization. - Opus Alpha 1 Large and Opus Alpha 1 Small, models that outperform state-of-the-art LLMs by 38\% and 29\% respectively in Workflow Generation for a Medical Coding use case.

The advancement of graph-based malware analysis is critically limited by the absence of large-scale datasets that capture the inherent hierarchical structure of software. Existing methods often oversimplify programs into single level graphs, failing to model the crucial semantic relationship between high-level functional interactions and low-level instruction logic. To bridge this gap, we introduce \dataset, the largest public hierarchical graph dataset for malware analysis, comprising over 200M Control Flow Graphs (CFGs) nested within 595K Function Call Graphs (FCGs). This two-level representation preserves structural semantics essential for building robust detectors resilient to code obfuscation and malware evolution. We demonstrate HiGraph's utility through a large-scale analysis that reveals distinct structural properties of benign and malicious software, establishing it as a foundational benchmark for the community. The dataset and tools are publicly available at https://higraph.org.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional 'Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

Large language model agents can often make reasonable local decisions on short tasks, yet their performance degrades when success requires long sequences of dependent actions and tool calls. During execution, task requirements, historical evidence, and the current execution state may gradually become disconnected, so later decisions can drift from the original objective. We study this problem by introducing the Adaptive Consistency Graph (ACG) for long-horizon execution. ACG incrementally organizes execution evidence and its provenance in a persistent graph, then constructs a temporary requirement-centered view for each decision under a bounded context budget. Rather than replacing the base agent's planner or tool executor, ACG provides a structured and traceable context view for each decision. In the matched evaluation, ACG improves GPT-5.6-luna's average success from 44.5\% with ReAct to 50.2\%, with the largest gain on BrowseComp-Plus (73.5\% versus 62.4\%). We further analyze trajectory structure and inference cost to characterize this improvement.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

Knowledge graph engineering often distributes accepted state, observations, constraints, processes, and hypothetical scenarios across artifacts whose combined execution contract remains external. We present PULSE, an Object-Process-Methodology-inspired language that localizes four operational roles and their write effects in one typed runtime. Here, modes denote operational roles rather than modal or deontic logic. The implemented contract fixes evidence non-overwrite, branch isolation, grounded multi-subject timers, guarded state change, and declaration-ranked event ordering over time and space; an external runner still decides whether evidence becomes an authoritative move. GeoSPARQL, SOSA, and SHACL remain generated views. A core calculus gives an effect-confinement lemma and six safety properties. Lean 4 checks kernel analogues for positions, evidence, clocks, monitors, atomicity, and branch source retention; 88 tests, 3,534 bounded checks, and 32 Lean/Python runtime-kernel cases bound the implementation claim to the checked cases. First-author implementations of a standards composition and a separate Sismic statechart reproduce the tested cold-chain trace. Across 37,440 generated temporal traces, PULSE matches a separate workflow and distinguishes ten single-field mutants. On the complete NOAA IBTrACS since1980 subset it agrees with GEOS and an event sweep on 1,476,290 transition-zone pairs, including 4,800 sampled and 12,831 duration-qualified events. Project-specific GeoSPARQL probes measure interface coverage. Overall, the results support contract localization, safety arguments, and trace parity for the tested fragment; language superiority and usability remain outside the evaluation.

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

Legal documents including judgments and court orders require highly sophisticated legal knowledge for understanding. To disclose expert knowledge for non-experts, we explore the problem of visualizing legal texts with easy-to-understand diagrams and propose a novel dataset of LegalViz with 23 languages and 7,010 cases of legal document and visualization pairs, using the DOT graph description language of Graphviz. LegalViz provides a simple diagram from a complicated legal corpus identifying legal entities, transactions, legal sources, and statements at a glance, that are essential in each judgment. In addition, we provide new evaluation metrics for the legal diagram visualization by considering graph structures, textual similarities, and legal contents. We conducted empirical studies on few-shot and finetuning large language models for generating legal diagrams and evaluated them with these metrics, including legal content-based evaluation within 23 languages. Models trained with LegalViz outperform existing models including GPTs, confirming the effectiveness of our dataset.

We introduce the AutoGRAMS framework for programming multi-step interactions with language models. AutoGRAMS represents AI agents as a graph, where each node can execute either a language modeling instruction or traditional code. Likewise, transitions in the graph can be governed by either language modeling decisions or traditional branch logic. AutoGRAMS supports using variables as memory and allows nodes to call other AutoGRAMS graphs as functions. We show how AutoGRAMS can be used to design highly sophisticated agents, including self-referential agents that can modify their own graph. AutoGRAMS's graph-centric approach aids interpretability, controllability, and safety during the design, development, and deployment of AI agents. We provide our framework as open source at https://github.com/autograms/autograms .

We study the hop-constrained s-t path enumeration (HcPE) problem, which takes a graph G, two distinct vertices s,t and a hop constraint k as input, and outputs all paths from s to t whose length is at most k. The state-of-the-art algorithms suffer from severe performance issues caused by the costly pruning operations during enumeration for the workloads with the large search space. Consequently, these algorithms hardly meet the real-time constraints of many online applications. In this paper, we propose PathEnum, an efficient index-based algorithm towards real-time HcPE. For an input query, PathEnum first builds a light-weight index aiming to reduce the number of edges involved in the enumeration, and develops efficient index-based approaches for enumeration, one based on depth-first search and the other based on joins. We further develop a query optimizer based on a join-based cost model to optimize the search order. We conduct experiments with 15 real-world graphs. Our experiment results show that PathEnum outperforms the state-of-the-art approaches by orders of magnitude in terms of the query time, throughput and response time.

With the rapid increase in the amount of public code repositories, developers maintain a great desire to retrieve precise code snippets by using natural language. Despite existing deep learning based approaches(e.g., DeepCS and MMAN) have provided the end-to-end solutions (i.e., accepts natural language as queries and shows related code fragments retrieved directly from code corpus), the accuracy of code search in the large-scale repositories is still limited by the code representation (e.g., AST) and modeling (e.g., directly fusing the features in the attention stage). In this paper, we propose a novel learnable deep Graph for Code Search (calleddeGraphCS), to transfer source code into variable-based flow graphs based on the intermediate representation technique, which can model code semantics more precisely compared to process the code as text directly or use the syntactic tree representation. Furthermore, we propose a well-designed graph optimization mechanism to refine the code representation, and apply an improved gated graph neural network to model variable-based flow graphs. To evaluate the effectiveness of deGraphCS, we collect a large-scale dataset from GitHub containing 41,152 code snippets written in C language, and reproduce several typical deep code search methods for comparison. Besides, we design a qualitative user study to verify the practical value of our approach. The experimental results have shown that deGraphCS can achieve state-of-the-art performances, and accurately retrieve code snippets satisfying the needs of the users.

Large language models (LLMs) are increasingly explored for graph understanding and decision-making, while System One models such as Jev select directly from supplied options. However, the capabilities of System One models on graph-related tasks remain unclear. We introduce GraphDecide, a model-independent benchmark that combines structural task profiles, matched graph-text input contrasts and heuristic-proposal controls to diagnose graph decision performance. We evaluate Jev and related choice-based models alongside language-model baselines, covering fourteen model-interface configurations. Jev's results illustrate the benchmark's central distinctions: accurate adjacency recognition does not guarantee broader structural correctness, joint graph-text input does not consistently improve prediction, and feasible construction does not establish high solution quality. Its task contracts, candidate interfaces and scoring rules support comparison across native selectors and language-model adapters. Code and aggregate results are available at https://github.com/VictorYXL/JevGraphBench.

Distributed computation is always a tricky topic to deal with, especially in context of various requirements in various scenarios. A popular solution is to use Apache Spark with a setup of multiple systems forming a cluster. However, the prerequisite setup for a Spark cluster often induces an additional overhead, often limiting usage in constrained scenarios, especially in scenarios requiring context propagation. In this paper, we explore a relatively lightweight computational graph execution framework requiring little setup and fast speeds, coupled with context awareness.

The growing demand for automated graph algorithm reasoning has attracted increasing attention in the large language model (LLM) community. Recent LLM-based graph reasoning methods typically decouple task descriptions from graph data, generate executable code augmented by retrieval from technical documentation, and refine the code through debugging. However, we identify two key limitations in existing approaches: (i) they treat technical documentation as flat text collections and ignore its hierarchical structure, leading to noisy retrieval that degrades code generation quality; and (ii) their debugging mechanisms focus primarily on runtime errors, yet ignore more critical logical errors. To address them, we propose {\method}, an agentic hierarchical retrieval-augmented coding framework that exploits the document hierarchy through top-down traversal and early pruning, together with a self-debugging coding agent that iteratively refines code using automatically generated small-scale test cases. To enable comprehensive evaluation of complex graph reasoning, we introduce a new dataset, {\dataset}, covering small-scale, large-scale, and composite graph reasoning tasks. Extensive experiments demonstrate that our method achieves higher task accuracy and lower inference cost compared to baselinesThe code is available at \href{https://github.com/FairyFali/GraphSkill{blue{https://github.com/FairyFali/GraphSkill}}.}.

This paper presents a novel approach for source code similarity detection that integrates an additional output feature into the classification process with the goal of improving model performance. Our approach is based on the GraphCodeBERT model, extended with a custom output feature layer and a concatenation mechanism for improved feature representation. The model was trained and evaluated, achieving promising results in terms of precision, recall, and f-measure. The implementation details, including model architecture and training strategies are discussed. The source code that illustrates our approach can be downloaded from https://www.github.com/jorge-martinez-gil/graphcodebert-feature-integration.

In recent years, graph prompting has emerged as a promising research direction, enabling the learning of additional tokens or subgraphs appended to the original graphs without requiring retraining of pre-trained graph models across various applications. This novel paradigm, shifting from the traditional pretraining and finetuning to pretraining and prompting has shown significant empirical success in simulating graph data operations, with applications ranging from recommendation systems to biological networks and graph transferring. However, despite its potential, the theoretical underpinnings of graph prompting remain underexplored, raising critical questions about its fundamental effectiveness. The lack of rigorous theoretical proof of why and how much it works is more like a dark cloud over the graph prompt area to go further. To fill this gap, this paper introduces a theoretical framework that rigorously analyzes graph prompting from a data operation perspective. Our contributions are threefold: First, we provide a formal guarantee theorem, demonstrating graph prompts capacity to approximate graph transformation operators, effectively linking upstream and downstream tasks. Second, we derive upper bounds on the error of these data operations by graph prompts for a single graph and extend this discussion to batches of graphs, which are common in graph model training. Third, we analyze the distribution of data operation errors, extending our theoretical findings from linear graph models (e.g., GCN) to non-linear graph models (e.g., GAT). Extensive experiments support our theoretical results and confirm the practical implications of these guarantees.

Assessing the degree of similarity of code fragments is crucial for ensuring software quality, but it remains challenging due to the need to capture the deeper semantic aspects of code. Traditional syntactic methods often fail to identify these connections. Recent advancements have addressed this challenge, though they frequently sacrifice interpretability. To improve this, we present an approach aiming to improve the transparency of the similarity assessment by using GraphCodeBERT, which enables the identification of semantic relationships between code fragments. This approach identifies similar code fragments and clarifies the reasons behind that identification, helping developers better understand and trust the results. The source code for our implementation is available at https://www.github.com/jorge-martinez-gil/graphcodebert-interpretability.

Can one graph represent every kind of LLM agent's run? A trace records what each step did, never what it relied on, the state it read, and the results it reused. GRADE recovers that missing layer: it models any run as one graph over its step nodes with two edge layers, execution edges (what ran in what order) read from the trace for free, and dependency edges (what each step relied on) rarely logged, so each is graded by how it is known, observed, declared, or inferred. One representation, and each layer earns its place. Across six corpora of LLM agents spanning tool use, coding, and the web, the dependency layer can predict failure where run size is weak and, under leave-one-corpus-out transfer, stays above chance on every held-out class while run size fails. Meanwhile, the execution layer localizes the faulting step in a failed multi-agent run. This work also provides a more in-depth analysis of why generic graph neural networks may misread the dependency layer, unlike our feature-based alternative. The same graph representation opens further uses, carrying from failure diagnosis in a single run to efficiency and robustness optimization at scale.

Working agents need to read diverse files, coordinate tools, and produce deliverables. Training such agents requires tasks built on many real files with verifiable results, but few pipelines exist to synthesize this kind of data. Existing pipelines either generate files with models, which lack realism and diversity, or build tasks on real files without task-specific verifiers, leaving result quality unchecked. We introduce GraphForge, an evidence-graph based framework that grounds both the task and its verification in real files. Starting from occupation-grounded seeds for controlled diversity, GraphForge assembles a workspace of real files for each seed and builds an evidence graph over their relations. Since the task statement and rubrics are both derived from this graph, task requirements are backed by the workspace files and each criterion is anchored to the files needed to verify it. An initial rollout further tests executability, and a revision agent repairs the task and rubrics against the original files before trajectories are collected. Fine-tuning Qwen3.6-27B on 2,169 GraphForge trajectories brings GDPVal to 1445.7 (+65.7) under OpenHands, and Workspace-Bench-Lite and SpreadsheetBench II to 63.7 (+7.7) and 24.0 (+13.7) under Claude Code. Rejection fine-tuning on the SFT model's own rollouts, with candidates selected by the evidence-anchored rubrics, yields further improvements on all three benchmarks, suggesting that the rubrics provide a useful selection signal. The data and models are available.

Evaluating and enhancing the general capabilities of large language models (LLMs) has been an important research topic. Graph is a common data structure in the real world, and understanding graph data is a crucial part for advancing general intelligence. To evaluate and enhance the graph understanding abilities of LLMs, in this paper, we propose a benchmark named GraphInstruct, which comprehensively includes 21 classical graph reasoning tasks, providing diverse graph generation pipelines and detailed reasoning steps. Based on GraphInstruct, we further construct GraphLM through efficient instruction-tuning, which shows prominent graph understanding capability. In order to enhance the LLM with graph reasoning capability as well, we propose a step mask training strategy, and construct a model named GraphLM+. As one of the pioneering efforts to enhance the graph understanding and reasoning abilities of LLMs, extensive experiments have demonstrated the superiority of GraphLM and GraphLM+ over other LLMs. We look forward to more researchers exploring the potential of LLMs in the graph data mining domain through GraphInstruct. Our code for generating GraphInstruct is released publicly at: https://github.com/CGCL-codes/GraphInstruct.

Agents often repeatedly solve similar task instances from scratch, leading to unnecessary reasoning cost and long execution traces. Prior work has explored workflow reuse and executable skill induction, but it remains unclear which task scenarios admit procedural skills and how the shared procedural structure should be represented across successful traces. We study this problem in FSM-defined scenarios, where successful traces can be viewed as paths in an unknown transition graph, and formulate procedural skills as reusable parameterized control-flow subgraphs. Based on this view, we introduce SkillDisCo, a distillation-and-compilation framework that distills reusable PFSM subgraphs from successful traces and compiles them into callable, executable, and verifiable procedural skills. Experiments on ALFWorld and WebArena show that SkillDisCo improves success rates and reduces agent turns across benchmarks and model scales, demonstrating the benefits of representing shared experience as reusable execution structures.

Verifying the reliability of complex, multi-step reasoning in Large Language Models (LLMs) remains a fundamental challenge, as existing methods often lack both faithfulness and precision. To address this issue, we propose the Graph of Verification (GoV) framework. GoV offers three key contributions: First, it explicitly models the underlying deductive process as a directed acyclic graph (DAG), whether this structure is implicit or explicitly constructed. Second, it enforces a topological order over the DAG to guide stepwise verification. Third, GoV introduces the notion of customizable node blocks, which flexibly define the verification granularity, from atomic propositions to full paragraphs, while ensuring that all requisite premises derived from the graph are provided as contextual input for each verification unit. We evaluate GoV on the Number Triangle Summation task and the ProcessBench benchmark with varying levels of reasoning complexity. Experimental results show that GoV substantially improves verification accuracy, faithfulness, and error localization when compared to conventional end-to-end verification approaches. Our code and data are available at https://github.com/Frevor/Graph-of-Verification.

The opioid epidemic continues to ravage communities worldwide, straining healthcare systems, disrupting families, and demanding urgent computational solutions. To combat this lethal opioid crisis, graph learning methods have emerged as a promising paradigm for modeling complex drug-related phenomena. However, a significant gap remains: there is no comprehensive benchmark for systematically evaluating these methods across real-world opioid crisis scenarios. To bridge this gap, we introduce OPBench, the first comprehensive opioid benchmark comprising five datasets across three critical application domains: opioid overdose detection from healthcare claims, illicit drug trafficking detection from digital platforms, and drug misuse prediction from dietary patterns. Specifically, OPBench incorporates diverse graph structures, including heterogeneous graphs and hypergraphs, to preserve the rich and complex relational information among drug-related data. To address data scarcity, we collaborate with domain experts and authoritative institutions to curate and annotate datasets while adhering to privacy and ethical guidelines. Furthermore, we establish a unified evaluation framework with standardized protocols, predefined data splits, and reproducible baselines to facilitate fair and systematic comparison among graph learning methods. Through extensive experiments, we analyze the strengths and limitations of existing graph learning methods, thereby providing actionable insights for future research in combating the opioid crisis. Our source code and datasets are available at https://github.com/Tianyi-Billy-Ma/OPBench.

Various human-designed prompt engineering techniques have been proposed to improve problem solvers based on Large Language Models (LLMs), yielding many disparate code bases. We unify these approaches by describing LLM-based agents as computational graphs. The nodes implement functions to process multimodal data or query LLMs, and the edges describe the information flow between operations. Graphs can be recursively combined into larger composite graphs representing hierarchies of inter-agent collaboration (where edges connect operations of different agents). Our novel automatic graph optimizers (1) refine node-level LLM prompts (node optimization) and (2) improve agent orchestration by changing graph connectivity (edge optimization). Experiments demonstrate that our framework can be used to efficiently develop, integrate, and automatically improve various LLM agents. The code can be found at https://github.com/metauto-ai/gptswarm.

This work aims to tackle the challenging heterogeneous graph encoding problem in the text-to-SQL task. Previous methods are typically node-centric and merely utilize different weight matrices to parameterize edge types, which 1) ignore the rich semantics embedded in the topological structure of edges, and 2) fail to distinguish local and non-local relations for each node. To this end, we propose a Line Graph Enhanced Text-to-SQL (LGESQL) model to mine the underlying relational features without constructing meta-paths. By virtue of the line graph, messages propagate more efficiently through not only connections between nodes, but also the topology of directed edges. Furthermore, both local and non-local relations are integrated distinctively during the graph iteration. We also design an auxiliary task called graph pruning to improve the discriminative capability of the encoder. Our framework achieves state-of-the-art results (62.8% with Glove, 72.0% with Electra) on the cross-domain text-to-SQL benchmark Spider at the time of writing.

Large Language Models (LLMs) have demonstrated their potential in hardware design tasks, such as Hardware Description Language (HDL) generation and debugging. Yet, their performance in real-world, repository-level HDL projects with thousands or even tens of thousands of code lines is hindered. To this end, we propose HDLxGraph, a novel framework that integrates Graph Retrieval Augmented Generation (Graph RAG) with LLMs, introducing HDL-specific graph representations by incorporating Abstract Syntax Trees (ASTs) and Data Flow Graphs (DFGs) to capture both code graph view and hardware graph view. HDLxGraph utilizes a dual-retrieval mechanism that not only mitigates the limited recall issues inherent in similarity-based semantic retrieval by incorporating structural information, but also enhances its extensibility to various real-world tasks by a task-specific retrieval finetuning. Additionally, to address the lack of comprehensive HDL search benchmarks, we introduce HDLSearch, a multi-granularity evaluation dataset derived from real-world repository-level projects. Experimental results demonstrate that HDLxGraph significantly improves average search accuracy, debugging efficiency and completion quality by 12.04%, 12.22% and 5.04% compared to similarity-based RAG, respectively. The code of HDLxGraph and collected HDLSearch benchmark are available at https://github.com/Nick-Zheng-Q/HDLxGraph.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

Despite the rapid advancements in Vision-Language Models (VLMs), a critical gap remains in their ability to handle structured, controllable diagrammatic tasks essential for professional workflows. Existing methods predominantly rely on pixel-based synthesis, which operates in probabilistic pixel spaces and is inherently limited in editability and fidelity. Instead, we propose a new Diagram-as-Code paradigm with symbolic logic that leverages mxGraph Extensible Markup Language (XML) for precise diagram generation and editing. We present VCG-Bench, a unified benchmark for visual-centric mxGraph tasks. VCG-Bench comprises: (1) a taxonomized dataset of 1,449 diverse diagrams spanning 6 domains and 15 sub-domains, (2) a paradigm definition that integrates Generation (Vision-to-Code) and Editability (Code-to-Code), (3) a Tailored Evaluation Protocol employing multi-dimensional metrics such as mxGraph Execution Success Rate, Style Consistency Score (SCS), etc. Experimental results highlight the challenges faced by current State-of-the-Art (SOTA) VLMs in structured fidelity and instruction compliance, reflecting their vision and reasoning capabilities.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Graphs can be used to represent and reason about systems and a variety of metrics have been devised to quantify their global characteristics. However, little is currently known about how to construct a graph or improve an existing one given a target objective. In this work, we formulate the construction of a graph as a decision-making process in which a central agent creates topologies by trial and error and receives rewards proportional to the value of the target objective. By means of this conceptual framework, we propose an algorithm based on reinforcement learning and graph neural networks to learn graph construction and improvement strategies. Our core case study focuses on robustness to failures and attacks, a property relevant for the infrastructure and communication networks that power modern society. Experiments on synthetic and real-world graphs show that this approach can outperform existing methods while being cheaper to evaluate. It also allows generalization to out-of-sample graphs, as well as to larger out-of-distribution graphs in some cases. The approach is applicable to the optimization of other global structural properties of graphs.

Organized crime inflicts human suffering on a genocidal scale: the Mexican drug cartels have murdered 150,000 people since 2006, upwards of 700,000 people per year are "exported" in a human trafficking industry enslaving an estimated 40 million people. These nefarious industries rely on sophisticated money laundering schemes to operate. Despite tremendous resources dedicated to anti-money laundering (AML) only a tiny fraction of illicit activity is prevented. The research community can help. In this brief paper, we map the structural and behavioral dynamics driving the technical challenge. We review AML methods, current and emergent. We provide a first look at scalable graph convolutional neural networks for forensic analysis of financial data, which is massive, dense, and dynamic. We report preliminary experimental results using a large synthetic graph (1M nodes, 9M edges) generated by a data simulator we created called AMLSim. We consider opportunities for high performance efficiency, in terms of computation and memory, and we share results from a simple graph compression experiment. Our results support our working hypothesis that graph deep learning for AML bears great promise in the fight against criminal financial activity.

The growing importance of textual and relational systems has driven interest in enhancing large language models (LLMs) for graph-structured data, particularly Text-Attributed Graphs (TAGs), where samples are represented by textual descriptions interconnected by edges. While research has largely focused on developing specialized graph LLMs through task-specific instruction tuning, a comprehensive benchmark for evaluating LLMs solely through prompt design remains surprisingly absent. Without such a carefully crafted evaluation benchmark, most if not all, tailored graph LLMs are compared against general LLMs using simplistic queries (e.g., zero-shot reasoning with LLaMA), which can potentially camouflage many advantages as well as unexpected predicaments of them. To achieve more general evaluations and unveil the true potential of LLMs for graph tasks, we introduce Graph In-context Learning (GraphICL) Benchmark, a comprehensive benchmark comprising novel prompt templates designed to capture graph structure and handle limited label knowledge. Our systematic evaluation shows that general-purpose LLMs equipped with our GraphICL outperform state-of-the-art specialized graph LLMs and graph neural network models in resource-constrained settings and out-of-domain tasks. These findings highlight the significant potential of prompt engineering to enhance LLM performance on graph learning tasks without training and offer a strong baseline for advancing research in graph LLMs.

Intermediate Representations (IRs) play a critical role in compiler design and program analysis, yet their comprehension by Large Language Models (LLMs) remains underexplored. In this paper, we present an explorative empirical study evaluating the capabilities of six state-of-the-art LLMs: GPT-4, GPT-3, DeepSeek, Gemma 2, Llama 3, and Code Llama, in understanding IRs. Specifically, we assess model performance across four core tasks: control flow graph reconstruction, decompilation, code summarization, and execution reasoning. While LLMs exhibit competence in parsing IR syntax and identifying high-level structures, they consistently struggle with instruction-level reasoning, especially in control flow reasoning, loop handling, and dynamic execution. Common failure modes include misinterpreting branching instructions, omitting critical operations, and relying on heuristic reasoning rather than precise instruction-level logic. Our findings highlight the need for IR-specific enhancements in LLM design. We recommend fine-tuning on structured IR datasets and integrating control-flow-sensitive architectures to improve model effectiveness. All experimental data and source code are publicly available at

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

Program errors can occur in any type of programming, and can manifest in a variety of ways, such as unexpected output, crashes, or performance issues. And program error diagnosis can often be too abstract or technical for developers to understand, especially for beginners. The goal of this paper is to present a novel machine-learning approach for Multi-task Program Error Repair and Explanatory Diagnosis (mPRED). A pre-trained language model is used to encode the source code, and a downstream model is specifically designed to identify and repair errors. Programs and test cases will be augmented and optimized from several perspectives. Additionally, our approach incorporates a "chain of thoughts" method, which enables the models to produce intermediate reasoning explanations before providing the final correction. To aid in visualizing and analyzing the program structure, we use a graph neural network for program structure visualization. Overall, our approach offers a promising approach for repairing program errors across different programming languages and providing helpful explanations to programmers.

Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In this work, we design new, more stringent evaluation procedures for link prediction specific to dynamic graphs, which reflect real-world considerations, to better compare the strengths and weaknesses of methods. First, we create two visualization techniques to understand the reoccurring patterns of edges over time and show that many edges reoccur at later time steps. Based on this observation, we propose a pure memorization baseline called EdgeBank. EdgeBank achieves surprisingly strong performance across multiple settings because easy negative edges are often used in the current evaluation setting. To evaluate against more difficult negative edges, we introduce two more challenging negative sampling strategies that improve robustness and better match real-world applications. Lastly, we introduce six new dynamic graph datasets from a diverse set of domains missing from current benchmarks, providing new challenges and opportunities for future research. Our code repository is accessible at https://github.com/fpour/DGB.git.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.