Daily Papers

LLM-based agentic coding assistants lack persistent memory: they lose coherence across sessions, forget project conventions, and repeat known mistakes. Recent studies characterize how developers configure agents through manifest files, but an open challenge remains how to scale such configurations for large, multi-agent projects. This paper presents a three-component codified context infrastructure developed during construction of a 108,000-line C# distributed system: (1) a hot-memory constitution encoding conventions, retrieval hooks, and orchestration protocols; (2) 19 specialized domain-expert agents; and (3) a cold-memory knowledge base of 34 on-demand specification documents. Quantitative metrics on infrastructure growth and interaction patterns across 283 development sessions are reported alongside four observational case studies illustrating how codified context propagates across sessions to prevent failures and maintain consistency. The framework is published as an open-source companion repository.

Domain experts across engineering, healthcare, and education follow strict standards for producing quality content such as technical manuals, medication instructions, and children's reading materials. However, current works in controllable text generation have yet to explore using these standards as references for control. Towards this end, we introduce Standardize, a retrieval-style in-context learning-based framework to guide large language models to align with expert-defined standards. Focusing on English language standards in the education domain as a use case, we consider the Common European Framework of Reference for Languages (CEFR) and Common Core Standards (CCS) for the task of open-ended content generation. Our findings show that models can gain 40% to 100% increase in precise accuracy for Llama2 and GPT-4, respectively, demonstrating that the use of knowledge artifacts extracted from standards and integrating them in the generation process can effectively guide models to produce better standard-aligned content.

The Model Context Protocol (MCP) has recently emerged as a standardized interface for connecting language models with external tools and data. As the ecosystem rapidly expands, the lack of a structured, comprehensive view of existing MCP artifacts presents challenges for research. To bridge this gap, we introduce MCPCorpus, a large-scale dataset containing around 14K MCP servers and 300 MCP clients. Each artifact is annotated with 20+ normalized attributes capturing its identity, interface configuration, GitHub activity, and metadata. MCPCorpus provides a reproducible snapshot of the real-world MCP ecosystem, enabling studies of adoption trends, ecosystem health, and implementation diversity. To keep pace with the rapid evolution of the MCP ecosystem, we provide utility tools for automated data synchronization, normalization, and inspection. Furthermore, to support efficient exploration and exploitation, we release a lightweight web-based search interface. MCPCorpus is publicly available at: https://github.com/Snakinya/MCPCorpus.

Autonomous AI agents increasingly depend on external knowledge stores, yet most retrieval pipelines provide relevance without durable guarantees of provenance, version identity, integrity, traceability, or point-in-time reconstruction. We formalize this as context governance and present ContextNest, an open specification and reference implementation for governed AI-consumable knowledge vaults. ContextNest does not replace Retrieval-Augmented Generation (RAG); it supplies the governance layer beneath retrieval, determining which artifacts are approved, current, attributable, and integrity-verified before retrieval systems operate over them. The specification combines typed Markdown documents with metadata, deterministic set-algebraic selectors, contextnest:// URI references, SHA-256 hash-chained version histories, graph-level checkpoints, source nodes for live data through the Model Context Protocol (MCP), and audit traces of agent context consumption. These mechanisms let organizations reconstruct which knowledge versions informed an agent output and whether those versions were AI-eligible when consumed. We report first empirical results from two controlled experiments. In a stale-version attack isolating the governance-versus-retrieval failure mode, governed selection strictly Pareto-dominates BM25 sparse retrieval, with higher answer-quality pass rate (97% versus 93-90%) at about one-third the input-token cost. In a retrieval-determinism experiment over a 1,060-document corpus, deterministic selectors and BM25 return stable document sets across repeated identical queries (Jaccard 1.0), while a dense+HNSW baseline is non-deterministic on 80% of queries (mean Jaccard 0.611, worst case 0.210). These results suggest that context governance addresses failure modes retrieval quality alone is not designed to resolve. We release a core engine, CLI, and MCP server under open licenses.

Generative AI (GenAI) has reshaped software system design by introducing foundation models as pre-trained subsystems that redefine architectures and operations. The emerging challenge is no longer model fine-tuning but context engineering-how systems capture, structure, and govern external knowledge, memory, tools, and human input to enable trustworthy reasoning. Existing practices such as prompt engineering, retrieval-augmented generation (RAG), and tool integration remain fragmented, producing transient artefacts that limit traceability and accountability. This paper proposes a file-system abstraction for context engineering, inspired by the Unix notion that 'everything is a file'. The abstraction offers a persistent, governed infrastructure for managing heterogeneous context artefacts through uniform mounting, metadata, and access control. Implemented within the open-source AIGNE framework, the architecture realises a verifiable context-engineering pipeline, comprising the Context Constructor, Loader, and Evaluator, that assembles, delivers, and validates context under token constraints. As GenAI becomes an active collaborator in decision support, humans play a central role as curators, verifiers, and co-reasoners. The proposed architecture establishes a reusable foundation for accountable and human-centred AI co-work, demonstrated through two exemplars: an agent with memory and an MCP-based GitHub assistant. The implementation within the AIGNE framework demonstrates how the architecture can be operationalised in developer and industrial settings, supporting verifiable, maintainable, and industry-ready GenAI systems.

Spec-driven development (SDD) with AI coding agents provides a structured workflow, but agents often remain "context blind" in large, evolving repositories, leading to hallucinated APIs and architectural violations. We present Spec Kit Agents, a multi-agent SDD pipeline (with PM and developer roles) that adds phase-level, context-grounding hooks. Read-only probing hooks ground each stage (Specify, Plan, Tasks, Implement) in repository evidence, while validation hooks check intermediate artifacts against the environment. We evaluate 128 runs covering 32 features across five repositories. Context-grounding hooks improve judged quality by +0.15 on a 1-5 composite LLM-as-judge score (+3.0 percent of the full score; Wilcoxon signed-rank, p < 0.05) while maintaining 99.7-100 percent repository-level test compatibility. We further evaluate the framework on SWE-bench Lite, where augmentation hooks improve baseline by 1.7 percent, achieving 58.2 percent Pass@1.

The Model Context Protocol (MCP), introduced by Anthropic in November 2024, defines a standardized interface for connecting large language models (LLMs) to external tools, data sources, and services. Within months of release, hundreds of community-built MCP servers appeared on GitHub, but no software-maintenance literature has yet described how the ecosystem is being structured in production. This industry experience paper catalogues five recurring MCP server architectural patterns observed across an enumerated corpus of fifteen independently developed servers (five production servers from the ANSYR voice AI platform plus ten public servers from the official MCP registry): Resource Gateway, Tool Orchestrator, Stateful Session Server, Proxy Aggregator, and Domain-Specific Adapter. Each pattern is described in the structured form of Gamma et al.: context, problem, solution, and consequences. We also document four anti-patterns and a set of cross-cutting concerns around authentication, versioning, and observability. The quantitative evaluation contributes three measurements: inter-rater reliability of the taxonomy across two independent LLM raters on 54 held-out servers (Cohen's kappa = 0.76), which also localizes three pattern-boundary ambiguities; transport overhead measured end-to-end on loopback and modeled for cross-host paths; and a tool-count study showing tool-selection accuracy drops below 90% between 10 and 15 tools per context for Claude Haiku 4.5 and between 20 and 30 tools for Sonnet 4. Code, corpus, and prompts are released as a replication package.

Large Language Model agents increasingly operate external systems through programmatic interfaces, yet practitioners lack empirical guidance on how to structure the context these agents consume. Using SQL generation as a proxy for programmatic agent operations, we present a systematic study of context engineering for structured data, comprising 9,649 experiments across 11 models, 4 formats (YAML, Markdown, JSON, Token-Oriented Object Notation [TOON]), and schemas ranging from 10 to 10,000 tables. Our findings challenge common assumptions. First, architecture choice is model-dependent: file-based context retrieval improves accuracy for frontier-tier models (Claude, GPT, Gemini; +2.7%, p=0.029) but shows mixed results for open source models (aggregate -7.7%, p<0.001), with deficits varying substantially by model. Second, format does not significantly affect aggregate accuracy (chi-squared=2.45, p=0.484), though individual models, particularly open source, exhibit format-specific sensitivities. Third, model capability is the dominant factor, with a 21 percentage point accuracy gap between frontier and open source tiers that dwarfs any format or architecture effect. Fourth, file-native agents scale to 10,000 tables through domain-partitioned schemas while maintaining high navigation accuracy. Fifth, file size does not predict runtime efficiency: compact or novel formats can incur a token overhead driven by grep output density and pattern unfamiliarity, with the magnitude depending on model capability. These findings provide practitioners with evidence-based guidance for deploying LLM agents on structured systems, demonstrating that architectural decisions should be tailored to model capability rather than assuming universal best practices.

The Model Context Protocol (MCP) is a standardized interface designed to enable seamless interaction between AI models and external tools and resources, breaking down data silos and facilitating interoperability across diverse systems. This paper provides a comprehensive overview of MCP, focusing on its core components, workflow, and the lifecycle of MCP servers, which consists of three key phases: creation, operation, and update. We analyze the security and privacy risks associated with each phase and propose strategies to mitigate potential threats. The paper also examines the current MCP landscape, including its adoption by industry leaders and various use cases, as well as the tools and platforms supporting its integration. We explore future directions for MCP, highlighting the challenges and opportunities that will influence its adoption and evolution within the broader AI ecosystem. Finally, we offer recommendations for MCP stakeholders to ensure its secure and sustainable development as the AI landscape continues to evolve.

Model Context Protocol (MCP) servers contain a collection of thousands of open-source standardized tools, linking LLMs to external systems; however, existing datasets and benchmarks lack realistic, human-like user queries, remaining a critical gap in evaluating the tool usage and ecosystems of MCP servers. Existing datasets often do contain tool descriptions but fail to represent how different users portray their requests, leading to poor generalization and inflated reliability of certain benchmarks. This paper introduces the first large-scale MCP dataset featuring diverse, high-quality diverse user queries generated specifically to match 2800 tools across 308 MCP servers, developing on the MCP Zero dataset. Each tool is paired with multiple unique user personas that we have generated, to capture varying levels of user intent ranging from precise task requests, and ambiguous, exploratory commands, reflecting the complexity of real-world interaction patterns.

Coding agents repeatedly search, navigate, and retain context from evolving repositories, but disconnected indexes, language servers, and task-local histories force repeated discovery and obscure lifecycle costs. CodeNib builds reusable lexical, dense, and structural views per repository commit, maps outputs to repository-relative source ranges, maintains selected views across edits, and serves ranked search, symbol navigation, and bounded context through one runtime. Across 100 snapshots, we map quality-cost frontiers across the repository-context lifecycle. When outputs match an independent rebuild, graph and vector updates are 8.7times and 25.4times faster at the median. On the static-navigation subset matching normalized live-server locations (63% of 1,000 requests), the median per-request live/static latency ratio is 4.7times. Across five models, selected context policies preserve localization with 50--87% fewer trajectory tokens than paired grep/read. Together, these results support multi-view repository-context serving with explicit, operation-specific validity boundaries.

Large language model (LLM)-powered agents are increasingly used to plan and execute scientific workflows, yet most research cyberinfrastructure (CI) exposes heterogeneous APIs and implements security models that present barriers for use by agents. We report on our experience using the Model Context Protocol (MCP) as a unifying interface that makes research capabilities discoverable, invokable, and composable. Our approach is pragmatic: we implement thin MCP servers over mature services, including Globus Transfer, Compute, and Search; status APIs exposed by computing facilities; Octopus event fabric; and domain-specific tools such as Garden and Galaxy. We use case studies in computational chemistry, bioinformatics, quantum chemistry, and filesystem monitoring to illustrate how this MCP-oriented architecture can be used in practice. We distill lessons learned and outline open challenges in evaluation and trust for agent-led science.

LLMs' capabilities are enhanced by using function calls to integrate various data sources or API results into the context window. Typical tools include search, web crawlers, maps, financial data, file systems, and browser usage, etc. Integrating these data sources or functions requires a standardized method. The Model Context Protocol (MCP) provides a standardized way to supply context to LLMs. However, the evaluation of LLMs and AI Agents' MCP tool use abilities suffer from several issues. First, there's a lack of comprehensive datasets or benchmarks to evaluate various MCP tools. Second, the diverse formats of response from MCP tool call execution further increase the difficulty of evaluation. Additionally, unlike existing tool-use benchmarks with high success rates in functions like programming and math functions, the success rate of real-world MCP tool is not guaranteed and varies across different MCP servers. Furthermore, the LLMs' context window also limits the number of available tools that can be called in a single run, because the textual descriptions of tool and the parameters have long token length for an LLM to process all at once. To help address the challenges of evaluating LLMs' performance on calling MCP tools, we propose MCPToolBench++, a large-scale, multi-domain AI Agent tool use benchmark. As of July 2025, this benchmark is build upon marketplace of over 4k MCP servers from more than 40 categories, collected from the MCP marketplaces and GitHub communities. The datasets consist of both single-step and multi-step tool calls across different categories. We evaluated SOTA LLMs with agentic abilities on this benchmark and reported the results.

Large language models are increasingly used within larger systems ("LLM agents"). These make a sequence of LLM calls, each call providing the LLM with a combination of instructions, observations, and interaction history. The design of the encoded information and its structure play a central role in the quality of the resulting system, leading to efforts spent on context engineering. It is therefore critical to communicate the composition of the LLM context in a system, and how it evolves over time. Yet, no standard exists for doing so: context construction is typically conveyed through informal prose, ad hoc diagrams, or direct inspection of code, none of which precisely capture how a prompt evolves across interaction steps or how two context representation strategies differ. To remedy this, we introduce the Agentic Context Description Language (ACDL), a language for specifying the structure and dynamics of LLM input contexts in a precise, readable, and standard manner, along with visualizations. ACDL provides constructs for specifying context aspects such as role message sequences, dynamic content, time-indexed references, and conditional or iterative structure, capturing the full architecture of a prompt independently of any particular implementation. ACDL diagrams can be hand drawn on a whiteboard, or written in formal language which can then be rendered. We describe the language, demonstrate it by documenting several existing systems and their variants, and encourage the community to adopt it for describing LLM systems context, both in day-to-day communication and in papers. Tooling, examples and documentation are available at www.acdlang.org.

The performance of Large Language Models (LLMs) is fundamentally determined by the contextual information provided during inference. This survey introduces Context Engineering, a formal discipline that transcends simple prompt design to encompass the systematic optimization of information payloads for LLMs. We present a comprehensive taxonomy decomposing Context Engineering into its foundational components and the sophisticated implementations that integrate them into intelligent systems. We first examine the foundational components: context retrieval and generation, context processing and context management. We then explore how these components are architecturally integrated to create sophisticated system implementations: retrieval-augmented generation (RAG), memory systems and tool-integrated reasoning, and multi-agent systems. Through this systematic analysis of over 1300 research papers, our survey not only establishes a technical roadmap for the field but also reveals a critical research gap: a fundamental asymmetry exists between model capabilities. While current models, augmented by advanced context engineering, demonstrate remarkable proficiency in understanding complex contexts, they exhibit pronounced limitations in generating equally sophisticated, long-form outputs. Addressing this gap is a defining priority for future research. Ultimately, this survey provides a unified framework for both researchers and engineers advancing context-aware AI.

The Model Context Protocol (MCP) standardizes how AI agents discover and invoke external tools, with over 10,000 active servers and 97 million monthly SDK downloads as of early 2026. Yet MCP does not yet standardize how agents safely operate those tools at production scale. Three protocol-level primitives remain missing: identity propagation, adaptive tool budgeting, and structured error semantics. This paper identifies these gaps through field lessons from an enterprise deployment of an AI agent platform integrated with a major cloud provider's MCP servers (client name redacted). We propose three mechanisms to fill them: (1) the Context-Aware Broker Protocol (CABP), which extends JSON-RPC with identity-scoped request routing via a six-stage broker pipeline; (2) Adaptive Timeout Budget Allocation (ATBA), which frames sequential tool invocation as a budget allocation problem over heterogeneous latency distributions; and (3) the Structured Error Recovery Framework (SERF), which provides machine-readable failure semantics that enable deterministic agent self-correction. We organize production failure modes into five design dimensions (server contracts, user context, timeouts, errors, and observability), document concrete failure vignettes, and present a production readiness checklist. All three algorithms are formalized as testable hypotheses with reproducible experimental methodology. Field observations demonstrate that while MCP provides a solid protocol foundation, reliable agent tool integration requires infrastructure-level mechanisms that the specification does not yet address.

The rapid expansion of interconnected devices, autonomous systems, and AI applications has created severe fragmentation in adaptive transport systems, where diverse protocols and context sources remain isolated. This survey provides the first systematic investigation of the Model Context Protocol (MCP) as a unifying paradigm, highlighting its ability to bridge protocol-level adaptation with context-aware decision making. Analyzing established literature, we show that existing efforts have implicitly converged toward MCP-like architectures, signaling a natural evolution from fragmented solutions to standardized integration frameworks. We propose a five-category taxonomy covering adaptive mechanisms, context-aware frameworks, unification models, integration strategies, and MCP-enabled architectures. Our findings reveal three key insights: traditional transport protocols have reached the limits of isolated adaptation, MCP's client-server and JSON-RPC structure enables semantic interoperability, and AI-driven transport demands integration paradigms uniquely suited to MCP. Finally, we present a research roadmap positioning MCP as a foundation for next-generation adaptive, context-aware, and intelligent transport infrastructures.

The Model Context Protocol (MCP) plays a crucial role in extending the capabilities of Large Language Models (LLMs) by enabling integration with external tools and data sources. However, the standard MCP specification presents significant security vulnerabilities, notably Tool Poisoning and Rug Pull attacks. This paper introduces the Enhanced Tool Definition Interface (ETDI), a security extension designed to fortify MCP. ETDI incorporates cryptographic identity verification, immutable versioned tool definitions, and explicit permission management, often leveraging OAuth 2.0. We further propose extending MCP with fine-grained, policy-based access control, where tool capabilities are dynamically evaluated against explicit policies using a dedicated policy engine, considering runtime context beyond static OAuth scopes. This layered approach aims to establish a more secure, trustworthy, and controllable ecosystem for AI applications interacting with LLMs and external tools.

We introduce Context Language Models (CLMs), language models that natively manage their own context. We implement this by treating the context as a file and allowing the model to make unrestricted updates to this file. This allows the model to learn what is most important to maintain in context, and naturally extends to multi-agent systems where multiple agent contexts coexist as files. Building CLMs zero-shot with existing models outperforms SOTA context management strategies across a variety of tasks: 11.4% higher accuracy with 21.5% fewer FLOPs on BrowseComp-Plus, 5% higher scores with 59% fewer FLOPs on 12-hour EdgeBench, and 65% greater improvement with the same compute on a 24-hour multi-repository agent-swarm task. Moreover, by shifting context management from external harness control to intrinsic model behavior, CLMs naturally enable both in-context and parametric learning of context-management strategies. We show that CLMs can be steered with natural-language instructions evolved through a standard skill-optimization loop, improving held-out accuracy by up to 35.9 points on a context-management task while reducing compute. We also introduce an online reinforcement learning method for CLMs, improving Qwen3.5-9B performance on BrowseComp-Plus by 47.6% while using 12% fewer FLOPs. Finally, we co-design Suffix Cache Reuse for CLM serving, further reducing server-side compute by 35% relative to standard SGLang at matched performance.

Long-horizon tool agents are bottlenecked by how their context grows toward the limits of the context window. Recent systems make context management agent- or system-controlled, but they either learn a compression policy that discards evidence or manage context in a layer the agent never sees. We argue both leave a more basic gap unaddressed. Frontier language models are proprioceptively blind to their own context. From the prompt alone they cannot see how large, how old, or how used each block is, the signals a keep-or-drop decision needs. We hypothesize that competent context management is already latent in capable models, and that what is missing is not a learned policy but an interface exposing this state. We introduce VISTA (Visible Internal State for Tool Agents), a training-free, model-agnostic layer that represents working memory as typed, addressable blocks, surfaces a runtime dashboard of per-block token usage, recency, and access history, and archives blocks as recoverable full-fidelity payloads. On LOCA-Bench, BrowseComp-Plus, and GAIA, the same untrained interface transfers across million-, 100K-, and 10K-scale trajectories. On LOCA-Bench it improves four backbones and lifts Gemini-3-Flash from 22.7 to 50.7%. The lift grows with context pressure and transfers across backbones. Ablations further confirm that the dashboard matters beyond archive and recovery tools.

As artificial intelligence (AI) systems evolve from stateless chatbots to autonomous multi-step agents, prompt engineering (PE), the discipline of crafting individual queries, proves necessary but insufficient. This paper introduces context engineering (CE) as a standalone discipline concerned with designing, structuring, and managing the entire informational environment in which an AI agent makes decisions. Drawing on vendor architectures (Google ADK, Anthropic, LangChain), current academic work (ACE framework, Google DeepMind's intelligent delegation), enterprise research (Deloitte, 2026; KPMG, 2026), and the author's experience building a multi-agent system, the paper proposes five context quality criteria: relevance, sufficiency, isolation, economy, and provenance, and frames context as the agent's operating system. Two higher-order disciplines follow. Intent engineering (IE) encodes organizational goals, values, and trade-off hierarchies into agent infrastructure. Specification engineering (SE) creates a machine-readable corpus of corporate policies and standards enabling autonomous operation of multi-agent systems at scale. Together these four disciplines form a cumulative pyramid maturity model of agent engineering, in which each level subsumes the previous one as a necessary foundation. Enterprise data reveals a gap: while 75% of enterprises plan agentic AI deployment within two years (Deloitte, 2026), deployment has surged and retreated as organizations confront scaling complexity (KPMG, 2026). The Klarna case illustrates a dual deficit, contextual and intentional. Whoever controls the agent's context controls its behavior; whoever controls its intent controls its strategy; whoever controls its specifications controls its scale.

Real-world tasks often require models to learn from task-specific context rather than relying only on pre-trained knowledge. While recent work has highlighted this capability as context learning, existing evaluations mainly focus on textual contexts. In many practical settings, however, the context to be learned from is multimodal: scientific findings are conveyed through figures and tables, financial indicators are scattered across converted reports, and spatial decisions depend on maps, scenes, or web pages. We introduce CLBench-V, a benchmark for multimodal context learning that addresses the difficulty of localizing where context use breaks down by organizing tasks around three dimensions: context grounding, new information application, and new knowledge learning. CLBench-V combines converted public benchmarks with newly constructed datasets spanning domains such as science, finance, long-document understanding, spatial reasoning, and web-based visual question answering. To reduce the cost of constructing domain-specific context-learning tasks, we further use automated construction and filtering procedures for our newly built datasets. Across 3,443 instances and six recent multimodal models, the best overall score is only 0.2847, indicating that multimodal context learning remains far from saturated. Moreover, InternVL3.5-30B-A3B performs best on context grounding and new knowledge learning, while Qwen3.5-Plus performs best on new information application. We further analyze judge reliability, context length, image count, and representative failure cases. Code is available at https://github.com/IamLihua/CLBench-V.

Providing Large Language Models with relevant contextual knowledge at inference time has been shown to greatly improve the quality of their generations. This is often achieved by prepending informative passages of text, or 'contexts', retrieved from external knowledge bases to their input. However, processing additional contexts online incurs significant computation costs that scale with their length. State Space Models (SSMs) offer a promising solution by allowing a database of contexts to be mapped onto fixed-dimensional states from which to start the generation. A key challenge arises when attempting to leverage information present across multiple contexts, since there is no straightforward way to condition generation on multiple independent states in existing SSMs. To address this, we leverage a simple mathematical relation derived from SSM dynamics to compose multiple states into one that efficiently approximates the effect of concatenating raw context tokens. Since the temporal ordering of contexts can often be uninformative, we enforce permutation-invariance by efficiently averaging states obtained via our composition algorithm across all possible context orderings. We evaluate our resulting method on WikiText and MSMARCO in both zero-shot and fine-tuned settings, and show that we can match the strongest performing baseline while enjoying on average 5.4x speedup.

Recent advances demonstrate that multimodal large language models (MLLMs) exhibit strong multimodal in-context learning (ICL) capabilities, enabling them to adapt to novel vision-language tasks from a few contextual examples. However, existing ICL approaches face challenges in reconciling scalability with robustness across diverse tasks and noisy contextual examples: manually selecting examples produces clean contexts but is labor-intensive and task-specific, while similarity-based retrieval improves scalability but could introduce irrelevant or structurally inconsistent samples that degrade ICL performance. To address these limitations, we propose ContextNav, the first agentic framework that integrates the scalability of automated retrieval with the quality and adaptiveness of human-like curation, enabling noise-robust and dynamically optimized contextualization for multimodal ICL. ContextNav unifies context management and noise-robust contextualization within a closed-loop workflow driven by graph-based orchestration. Specifically, it builds a resource-aware multimodal embedding pipeline, maintains a retrievable vector database, and applies agentic retrieval and structural alignment to construct noise-resilient contexts. An Operational Grammar Graph (OGG) further supports adaptive workflow planning and optimization, enabling the agent to refine its operational strategies based on downstream ICL feedback. Experimental results demonstrate that ContextNav achieves state-of-the-art performance across various datasets, underscoring the promise of agentic workflows for advancing scalable and robust contextualization in multimodal ICL.

Context faithfulness is essential for reliable reasoning in context-dependent scenarios. However, large language models often struggle to ground their outputs in the provided context, resulting in irrelevant responses. Inspired by the emergent expert specialization observed in mixture-of-experts architectures, this work investigates whether certain experts exhibit specialization in context utilization, offering a potential pathway toward targeted optimization for improved context faithfulness. To explore this, we propose Router Lens, a method that accurately identifies context-faithful experts. Our analysis reveals that these experts progressively amplify attention to relevant contextual information, thereby enhancing context grounding. Building on this insight, we introduce Context-faithful Expert Fine-Tuning (CEFT), a lightweight optimization approach that selectively fine-tunes context-faithful experts. Experiments across a wide range of benchmarks and models demonstrate that CEFT matches or surpasses the performance of full fine-tuning while being significantly more efficient.

Large Language Models (LLMs) show great capabilities in a wide range of applications, but serving them efficiently becomes increasingly challenging as requests (prompts) become more complex. Context caching improves serving performance by reusing Key-Value (KV) vectors, the intermediate representations of tokens that are repeated across requests. However, existing context caching requires exact prefix matches across requests, limiting reuse cases in settings such as few-shot learning and retrieval-augmented generation, where immutable content (e.g., documents) remains unchanged across requests but is preceded by varying prefixes. Position-Independent Caching (PIC) addresses this issue by enabling modular reuse of the KV vectors regardless of prefixes. We formalize PIC and advance prior work by introducing EPIC, a serving system incorporating our new LegoLink algorithm, which mitigates the inappropriate "attention sink" effect at every document beginning, to maintain accuracy with minimal computation. Experiments show that EPIC achieves up to 8x improvements in Time-To-First-Token (TTFT) and 7x throughput gains over existing systems, with negligible or no accuracy loss.

A research idea may be novel, coherent, and scientifically plausible, yet its proposed method may remain insufficiently specified for faithful implementation. We study the codification readiness of implementation-facing research-method specifications, defined by whether they provide sufficient methodological information for a competent implementer or coding agent to construct the intended method without unsupported assumptions. We construct evidence-grounded specifications and their supported resolutions from papers, codebases, issue threads, and reproduction artifacts. We introduce IdeaAMBIG, a benchmark of 660 evidence-grounded instances: 163 real-world gaps from reproducibility reports and GitHub issues, and 497 controlled synthetic gaps injected into codification-ready references. IdeaAMBIG evaluates three capabilities: codification-readiness assessment, defect localization, and clarification action generation. Defect localization receives only the specification, whereas clarification additionally receives the annotated defect. Across 13 LLMs, the best model achieves 9.6% Macro Defect Recovery Rate on real-world instances but 80.6% Macro Clarification Action Success Rate when given the defect. In an oracle study, supplying the gold resolution raises the downstream codification-ready rate from 14% to 98%. Across all evaluated models, defect localization is the main bottleneck, with stronger clarification given the defect.

The Model Context Protocol (MCP) has emerged as a de facto standard for integrating Large Language Models with external tools, yet no formal security analysis of the protocol specification exists. We present the first rigorous security analysis of MCP's architectural design, identifying three fundamental protocol-level vulnerabilities: (1) absence of capability attestation allowing servers to claim arbitrary permissions, (2) bidirectional sampling without origin authentication enabling server-side prompt injection, and (3) implicit trust propagation in multi-server configurations. We implement MCPBench, a novel framework bridging existing agent security benchmarks to MCP-compliant infrastructure, enabling direct measurement of protocol-specific attack surfaces. Through controlled experiments on 847 attack scenarios across five MCP server implementations, we demonstrate that MCP's architectural choices amplify attack success rates by 23--41\% compared to equivalent non-MCP integrations. We propose MCPSec, a backward-compatible protocol extension adding capability attestation and message authentication, reducing attack success rates from 52.8\% to 12.4\% with median latency overhead of 8.3ms per message. Our findings establish that MCP's security weaknesses are architectural rather than implementation-specific, requiring protocol-level remediation.

Context engineering has emerged as a pivotal paradigm for unlocking the potential of Large Language Models (LLMs) in Software Engineering (SE) tasks, enabling performance gains at test time without model fine-tuning. Despite its success, existing research lacks a systematic taxonomy of SE-specific context types and a dedicated benchmark to quantify the heterogeneous effects of different contexts across core SE workflows. To address this gap, we propose CL4SE (Context Learning for Software Engineering), a comprehensive benchmark featuring a fine-grained taxonomy of four SE-oriented context types (interpretable examples, project-specific context, procedural decision-making context, and positive & negative context), each mapped to a representative task (code generation, code summarization, code review, and patch correctness assessment). We construct high-quality datasets comprising over 13,000 samples from more than 30 open-source projects and evaluate five mainstream LLMs across nine metrics. Extensive experiments demonstrate that context learning yields an average performance improvement of 24.7% across all tasks. Specifically, procedural context boosts code review performance by up to 33% (Qwen3-Max), mixed positive-negative context improves patch assessment by 30% (DeepSeek-V3), project-specific context increases code summarization BLEU by 14.78% (GPT-Oss-120B), and interpretable examples enhance code generation PASS@1 by 5.72% (DeepSeek-V3). CL4SE establishes the first standardized evaluation framework for SE context learning, provides actionable empirical insights into task-specific context design, and releases a large-scale dataset to facilitate reproducible research in this domain.

The automation of scientific discovery represents a critical milestone in Artificial Intelligence (AI) research. However, existing agentic systems for science suffer from two fundamental limitations: rigid, pre-programmed workflows that cannot adapt to intermediate findings, and inadequate context management that hinders long-horizon research. We present freephdlabor, an open-source multiagent framework featuring fully dynamic workflows determined by real-time agent reasoning and a \textit{modular architecture} enabling seamless customization -- users can modify, add, or remove agents to address domain-specific requirements. The framework provides comprehensive infrastructure including automatic context compaction, workspace-based communication to prevent information degradation, memory persistence across sessions, and non-blocking human intervention mechanisms. These features collectively transform automated research from isolated, single-run attempts into continual research programs that build systematically on prior explorations and incorporate human feedback. By providing both the architectural principles and practical implementation for building customizable co-scientist systems, this work aims to facilitate broader adoption of automated research across scientific domains, enabling practitioners to deploy interactive multiagent systems that autonomously conduct end-to-end research -- from ideation through experimentation to publication-ready manuscripts.

The Model Context Protocol has emerged as a transformative standard for connecting large language models to external data sources and tools, rapidly gaining adoption across major AI providers and development platforms. However, existing benchmarks are overly simplistic and fail to capture real application challenges such as long-horizon reasoning and large, unfamiliar tool spaces. To address this critical gap, we introduce MCP-Universe, the first comprehensive benchmark specifically designed to evaluate LLMs in realistic and hard tasks through interaction with real-world MCP servers. Our benchmark encompasses 6 core domains spanning 11 different MCP servers: Location Navigation, Repository Management, Financial Analysis, 3D Design, Browser Automation, and Web Searching. To ensure rigorous evaluation, we implement execution-based evaluators, including format evaluators for agent format compliance, static evaluators for time-invariant content matching, and dynamic evaluators that automatically retrieve real-time ground truth for temporally sensitive tasks. Through extensive evaluation of leading LLMs, we find that even SOTA models such as GPT-5 (43.72%), Grok-4 (33.33%) and Claude-4.0-Sonnet (29.44%) exhibit significant performance limitations. In addition, our benchmark poses a significant long-context challenge for LLM agents, as the number of input tokens increases rapidly with the number of interaction steps. Moreover, it introduces an unknown-tools challenge, as LLM agents often lack familiarity with the precise usage of the MCP servers. Notably, enterprise-level agents like Cursor cannot achieve better performance than standard ReAct frameworks. Beyond evaluation, we open-source our extensible evaluation framework with UI support, enabling researchers and practitioners to seamlessly integrate new agents and MCP servers while fostering innovation in the rapidly evolving MCP ecosystem.

With the rise of LLMs, a large number of Model Context Protocol (MCP) services have emerged since the end of 2024. However, the effectiveness and efficiency of MCP servers have not been well studied. To study these questions, we propose an evaluation framework, called MCPBench. We selected several widely used MCP server and conducted an experimental evaluation on their accuracy, time, and token usage. Our experiments showed that the most effective MCP, Bing Web Search, achieved an accuracy of 64%. Importantly, we found that the accuracy of MCP servers can be substantially enhanced by involving declarative interface. This research paves the way for further investigations into optimized MCP implementations, ultimately leading to better AI-driven applications and data retrieval solutions.

Persistent context files (AGENTS.md, CLAUDE.md) are standard practice for guiding AI coding agents, yet evidence for their effectiveness is contradictory. We present a controlled ablation of context-injection strategy across two frontier agents (Claude Code and Codex), 17 real tasks from 3 repositories (15 shared + 2 Codex-only), and 288 evaluated runs with gold-test evaluation. Context strategy does not measurably move correctness on either agent (bounded to <=10-15pp via equivalence testing). A failure-mode triage reveals why: agents fail on implementation skill---feature design, pattern selection, exact wiring---not missing repository knowledge that a context file could supply; a manipulation probe confirms the real AGENTS.md never converts a near-miss to a pass on either agent. We further show that borderline task difficulty is agent-specific (Spearman rho=0.75), offering a candidate explanation for prior contradictions: single-agent studies draw tasks from different agents' informative bands. We release all code, data, and analysis.

The Model Context Protocol (MCP) is an emerging standard designed to enable seamless interaction between Large Language Model (LLM) applications and external tools or resources. Within a short period, thousands of MCP services have already been developed and deployed. However, the client-server integration architecture inherent in MCP may expand the attack surface against LLM Agent systems, introducing new vulnerabilities that allow attackers to exploit by designing malicious MCP servers. In this paper, we present the first systematic study of attack vectors targeting the MCP ecosystem. Our analysis identifies four categories of attacks, i.e., Tool Poisoning Attacks, Puppet Attacks, Rug Pull Attacks, and Exploitation via Malicious External Resources. To evaluate the feasibility of these attacks, we conduct experiments following the typical steps of launching an attack through malicious MCP servers: upload-download-attack. Specifically, we first construct malicious MCP servers and successfully upload them to three widely used MCP aggregation platforms. The results indicate that current audit mechanisms are insufficient to identify and prevent the proposed attack methods. Next, through a user study and interview with 20 participants, we demonstrate that users struggle to identify malicious MCP servers and often unknowingly install them from aggregator platforms. Finally, we demonstrate that these attacks can trigger harmful behaviors within the user's local environment-such as accessing private files or controlling devices to transfer digital assets-by deploying a proof-of-concept (PoC) framework against five leading LLMs. Additionally, based on interview results, we discuss four key challenges faced by the current security ecosystem surrounding MCP servers. These findings underscore the urgent need for robust security mechanisms to defend against malicious MCP servers.

Accurate mapping of the built asset information to established data classification systems and taxonomies is crucial for effective asset management, whether for compliance at project handover or ad-hoc data integration scenarios. Due to the complex nature of built asset data, which predominantly comprises technical text elements, this process remains largely manual and reliant on domain expert input. Recent breakthroughs in contextual text representation learning (text embedding), particularly through pre-trained large language models, offer promising approaches that can facilitate the automation of cross-mapping of the built asset data. However, no comprehensive evaluation has yet been conducted to assess these models' ability to effectively represent the complex semantics specific to built asset technical terminology. This study presents a comparative benchmark of state-of-the-art text embedding models to evaluate their effectiveness in aligning built asset information with domain-specific technical concepts. Our proposed datasets are derived from two renowned built asset data classification dictionaries. The results of our benchmarking across six proposed datasets, covering three tasks of clustering, retrieval, and reranking, highlight the need for future research on domain adaptation techniques. The benchmarking resources are published as an open-source library, which will be maintained and extended to support future evaluations in this field.

The operational efficacy of large language models relies heavily on their inference-time context. This has established Context Engineering (CE) as a formal discipline for optimizing these inputs. Current CE methods rely on manually crafted harnesses, such as rigid generation-reflection workflows and predefined context schemas. They impose structural biases and restrict context optimization to a narrow, intuition-bound design space. To address this, we introduce Meta Context Engineering (MCE), a bi-level framework that supersedes static CE heuristics by co-evolving CE skills and context artifacts. In MCE iterations, a meta-level agent refines engineering skills via agentic crossover, a deliberative search over the history of skills, their executions, and evaluations. A base-level agent executes these skills, learns from training rollouts, and optimizes context as flexible files and code. We evaluate MCE across five disparate domains under offline and online settings. MCE demonstrates consistent performance gains, achieving 5.6--53.8% relative improvement over state-of-the-art agentic CE methods (mean of 16.9%), while maintaining superior context adaptability, transferability, and efficiency in both context usage and training.

As Model Context Protocol (MCP) introduces an easy-to-use ecosystem for users and developers, it also brings underexplored safety risks. Its decentralized architecture, which separates clients and servers, poses unique challenges for systematic safety analysis. This paper proposes a novel framework to enhance MCP safety. Guided by the MAESTRO framework, we first analyze the missing safety mechanisms in MCP, and based on this analysis, we propose the Model Contextual Integrity Protocol (MCIP), a refined version of MCP that addresses these gaps. Next, we develop a fine-grained taxonomy that captures a diverse range of unsafe behaviors observed in MCP scenarios. Building on this taxonomy, we develop benchmark and training data that support the evaluation and improvement of LLMs' capabilities in identifying safety risks within MCP interactions. Leveraging the proposed benchmark and training data, we conduct extensive experiments on state-of-the-art LLMs. The results highlight LLMs' vulnerabilities in MCP interactions and demonstrate that our approach substantially improves their safety performance.

Context compression improves long-context efficiency but may introduce faithfulness issues through an information bottleneck. Existing evaluations rely on QA metrics, but a reader can still answer correctly from an unfaithful compression, so these metrics underestimate such loss. To bridge this gap, we introduce KEEP-Bench, a diagnostic benchmark that directly assesses compression faithfulness with 4,102 cases across three challenging settings that require keeping evidence for plausible reference resolutions, explicit qualifiers, and minority perspectives. Experiments show that even with tailored prompting, the strongest models remain unreliable: despite context windows exceeding 100K tokens and inputs averaging only 3.1K tokens, the best open-weight model (31B) preserves all required evidence in only 66.8% of cases, and the best proprietary model in only 61.6%. Performance also varies sharply across evidence structures, so conclusions from limited structures may be biased. We further introduce a metric, Evidence Preservation Return (EPR), to relate evidence recall to inference FLOPs, and find that it peaks at moderate scales (4B-8B), where recall remains low. Additional output budget mainly benefits already strong models and widens capability gaps, yet the stronger preservation of these models comes at a steep computational cost. These findings highlight the importance for future work to investigate compressors with strong information preservation under a small computation budget, rather than relying on a large output budget or model scaling.

Large Language Model (LLM) coding agents have achieved strong results on software engineering tasks, yet repository exploration remains a major bottleneck: locating relevant code consumes substantial token budget and pollutes the agent's context with irrelevant snippets. In most agents, the same model explores the repository and solves the task, leaving exploratory reads and searches in the solver's history. We present FastContext, a dedicated exploration subagent that separates repository exploration from solving. Invoked on demand, FastContext issues parallel tool calls and returns concise file paths and line ranges as focused context. FastContext is powered by specialized exploration models spanning 4B--30B parameters. We bootstrap them from strong reference-model trajectories and refine them with task-grounded rewards for broad first-turn search, multi-turn evidence gathering, and precise citation generation. Across SWE-bench Multilingual, SWE-bench Pro, and SWE-QA, integrating FastContext into Mini-SWE-Agent improves end-to-end resolution rates up to 5.5\% while reducing coding-agent token consumption up to 60\%, with marginal overhead. These results show that repository exploration can be separated from solving and handled effectively by specialized models. Code and data: https://github.com/microsoft/fastcontext

Retrieval-augmented generation is becoming agentic. A search harness writes queries, reads results, reformulates, and decides when to stop. This largely solves accuracy: a harness with only BM25/grep and MiniMax M3 answers 85% of BrowseComp-Plus and 91% on multi-hop FRAMES in our runs, without compiled or vector indexes. It exposes a context problem: an undisciplined loop repeats queries, rereads documents, and fills the window with unused passages. The missing layer is knowledge compilation: a configurable ingestion pipeline where LLMs enrich documents with context no chunk contains alone--navigation hierarchies with claim-evidence leaves, entity graphs, timelines, mind maps, ontologies, wikis, and memory. Compilation is not a better retriever: under a competent harness, structural artifacts gave no detectable accuracy gain on FRAMES, and a PageIndex-style outline degraded at scale. It is a supply layer. A navigation tree whose leaves are claim-evidence pairs--the mechanism we measure--cuts query tokens by 91% when evidence suffices and adds 1.9% when it does not, a 38% average reduction; this implies a 2% break-even sufficiency rate and a measured rate near 43%. A decision gate cuts latency from 140 s to 30 s, though substitution's token saving is bought with retrieval rounds and carries its own latency cost. Other artifacts--ontology, graph, wiki, timeline, mind map, memory--pay off in deployment (governance, integration, onboarding, temporal orientation, continuity) where accuracy benchmarks cannot see them. We describe RAGFlow's pipeline and harness (open source at https://github.com/infiniflow/ragflow), which turns the loop into five disciplined stations and keeps the context entering the model the smallest sufficient set; together they form an agent-native database: a store that hands the agent compiled, governed context instead of a ranked list of passages.

We present AIOS 1.0, a novel platform designed to advance computer-use agent (CUA) capabilities through environmental contextualization. While existing approaches primarily focus on building more powerful agent frameworks or enhancing agent models, we identify a fundamental limitation: the semantic disconnect between how language models understand the world and how computer interfaces are structured. AIOS 1.0 addresses this challenge by transforming computers into contextual environments that language models can natively comprehend, implementing a Model Context Protocol (MCP) server architecture to abstract computer states and actions. This approach effectively decouples interface complexity from decision complexity, enabling agents to reason more effectively about computing environments. To demonstrate our platform's effectiveness, we introduce LiteCUA, a lightweight computer-use agent built on AIOS 1.0 that achieves a 14.66% success rate on the OSWorld benchmark, outperforming several specialized agent frameworks despite its simple architecture. Our results suggest that contextualizing computer environments for language models represents a promising direction for developing more capable computer-use agents and advancing toward AI that can interact with digital systems. The source code of LiteCUA is available at https://github.com/agiresearch/LiteCUA, and it is also integrated into the AIOS main branch as part of AIOS at https://github.com/agiresearch/AIOS.

The Model Context Protocol (MCP) introduces a standard specification that defines how Foundation Model (FM)-based agents should interact with external systems by invoking tools. However, to understand a tool's purpose and features, FMs rely on natural-language tool descriptions, making these descriptions a critical component in guiding FMs to select the optimal tool for a given (sub)task and to pass the right arguments to the tool. While defects or smells in these descriptions can misguide FM-based agents, their prevalence and consequences in the MCP ecosystem remain unclear. Hence, we examine 856 tools spread across 103 MCP servers empirically, assess their description quality, and their impact on agent performance. We identify six components of tool descriptions from the literature, develop a scoring rubric utilizing these components, and then formalize tool description smells based on this rubric. By operationalizing this rubric through an FM-based scanner, we find that 97.1% of the analyzed tool descriptions contain at least one smell, with 56% failing to state their purpose clearly. While augmenting these descriptions for all components improves task success rates by a median of 5.85 percentage points and improves partial goal completion by 15.12%, it also increases the number of execution steps by 67.46% and regresses performance in 16.67% of cases. These results indicate that achieving performance gains is not straightforward; while execution cost can act as a trade-off, execution context can also impact. Furthermore, component ablations show that compact variants of different component combinations often preserve behavioral reliability while reducing unnecessary token overhead, enabling more efficient use of the FM context window and lower execution costs.

The most important architectural problem in AI is not the size of the model but the absence of a layer that carries forward what the model has come to understand. Sessions end. Context windows fill. Memory APIs return flat facts that the model has to reinterpret from scratch on every read. The result is intelligence that is powerful per session and amnesiac across time. This position paper argues that the layer which fixes this, the continuity layer, is the most consequential piece of infrastructure the field has not yet built, and that the engineering work to build it has begun in public. The formal evaluation framework for the property described here is the ATANT benchmark (arXiv:2604.06710), published separately with evaluation results on a 250-story corpus; a companion paper (arXiv:2604.10981) positions this framework against existing memory, long-context, and agentic-memory benchmarks. The paper defines continuity as a system property with seven required characteristics, distinct from memory and from retrieval; describes a storage primitive (Decomposed Trace Convergence Memory) whose write-time decomposition and read-time reconstruction produce that property; maps the engineering architecture to the theological pattern of kenosis and the symbolic pattern of Alpha and Omega, and argues this mapping is structural rather than metaphorical; proposes a four-layer development arc from external SDK to hardware node to long-horizon human infrastructure; examines why the physics limits now constraining the model layer make the continuity layer newly consequential; and argues that the governance architecture (privacy implemented as physics rather than policy, founder-controlled class shares on non-negotiable architectural commitments) is inseparable from the product itself.

The proliferation of Large Language Models (LLMs) has created a significant integration challenge in the AI agent ecosystem, often called the "N times M problem," where N models require custom integrations for M tools. This fragmentation stifles innovation and creates substantial development overhead. While the Model Context Protocol (MCP) has emerged as a standard to resolve this, its adoption is hindered by the manual effort required to convert the vast universe of existing software into MCP-compliant services. This is especially true for the millions of open-source repositories on GitHub, the world's largest collection of functional code. This paper introduces Code2MCP, a highly automated, agentic framework designed to transform any GitHub repository into a functional MCP service with minimal human intervention. Our system employs a multi-stage workflow that automates the entire process, from code analysis and environment configuration to service generation and deployment. A key innovation of our framework is an LLM-driven, closed-loop "Run--Review--Fix" cycle, which enables the system to autonomously debug and repair the code it generates. Code2MCP produces not only deployable services but also comprehensive technical documentation, acting as a catalyst to accelerate the MCP ecosystem by systematically unlocking the world's largest open-source code repository and automating the critical last mile of tool integration. The code is open-sourced at https://github.com/DEFENSE-SEU/MCP-Github-Agent.

Despite the huge success of Large Language Models (LLMs) in coding assistants like GitHub Copilot, these models struggle to understand the context present in the repository (e.g., imports, parent classes, files with similar names, etc.), thereby producing inaccurate code completions. This effect is more pronounced when using these assistants for repositories that the model has not seen during training, such as proprietary software or work-in-progress code projects. Recent work has shown the promise of using context from the repository during inference. In this work, we extend this idea and propose RepoFusion, a framework to train models to incorporate relevant repository context. Experiments on single-line code completion show that our models trained with repository context significantly outperform much larger code models as CodeGen-16B-multi (sim73times larger) and closely match the performance of the sim 70times larger StarCoderBase model that was trained with the Fill-in-the-Middle objective. We find these results to be a novel and compelling demonstration of the gains that training with repository context can bring. We carry out extensive ablation studies to investigate the impact of design choices such as context type, number of contexts, context length, and initialization within our framework. Lastly, we release Stack-Repo, a dataset of 200 Java repositories with permissive licenses and near-deduplicated files that are augmented with three types of repository contexts. Additionally, we are making available the code and trained checkpoints for our work. Our released resources can be found at https://huggingface.co/RepoFusion.

Data-intensive applications, ranging from large-scale retrieval systems to advanced data pipelines, are increasingly bottlenecked by the processing of highly redundant text corpora. We present Merlin, a local-first, agnostic, high-throughput deduplication and context optimization engine designed to mitigate these inefficiencies. Utilizing a highly optimized, SIMD-friendly open-addressing flat hash set combined with xxHash3-64, Merlin performs rapid, byte-exact deduplication of text passages and data chunks. While broadly applicable to any text-processing workflow, its impact is particularly pronounced in Large Language Model (LLM) ecosystems, such as Retrieval-Augmented Generation (RAG). Our empirical evaluations demonstrate an input reduction ranging from 13.9% in low-redundancy datasets to over 71% in high-redundancy pipelines, maintaining absolute data fidelity. Furthermore, we detail the system's integration architecture via the Model Context Protocol (MCP), enabling secure, zero-network-interception deployment across major IDEs and autonomous agents. This paper outlines the core algorithmic design, performance benchmarks, and the architectural principles required to process data at sustained speeds of up to 8.7 GB/s.

We demonstrate CEDAR, an application for automating data science (DS) tasks with an agentic setup. Solving DS problems with LLMs is an underexplored area that has immense market value. The challenges are manifold: task complexities, data sizes, computational limitations, and context restrictions. We show that these can be alleviated via effective context engineering. We first impose structure into the initial prompt with DS-specific input fields, that serve as instructions for the agentic system. The solution is then materialized as an enumerated sequence of interleaved plan and code blocks generated by separate LLM agents, providing a readable structure to the context at any step of the workflow. Function calls for generating these intermediate texts, and for corresponding Python code, ensure that data stays local, and only aggregate statistics and associated instructions are injected into LLM prompts. Fault tolerance and context management are introduced via iterative code generation and smart history rendering. The viability of our agentic data scientist is demonstrated using canonical Kaggle challenges.

In-context learning (ICL) is the standard method for low-resource classification, yet its efficacy in specialized domains remains largely unexplored. We address the challenge of classifying semantically complex, multi-party B2B conversations, where traditional ICL encounters significant limitations, especially as context length increases due to the concatenation of multiple few-shot examples. We introduce the Call Playbook dataset, featuring five classification tasks derived from real-world B2B conversations targeting core sales concepts. To bridge the gap between performance and practical utility, we propose novel knowledge extraction methods that distill verbose examples into compact, interpretable representations of structured classification criteria and precise task descriptions. Our approach achieves a 99\% reduction in token usage and improves macro-averaged AUC by up to 7\% over traditional ICL. Notably, it remains robust as context grows, unlike advanced token compression baselines which degrade by over 9 F1 points. Importantly, our framework enables direct refinement of classification logic, addressing critical needs for transparency, efficiency, and user interaction in real-world NLP applications.

As Large Language Model (LLM) agents increasingly execute complex, autonomous software engineering tasks, developers rely on natural language instruction files such as AGENTS.md to express project-specific coding conventions, tooling restrictions, and architectural boundaries. However, because these instructions remain passive text, agents frequently violate documented constraints due to context window saturation or conflicting local context. In autonomous settings without real-time human supervision, such violations rapidly compound into technical debt. To ground autonomous agents in repository constraints, we introduce ContextCov, a framework that transforms passive natural language instructions into executable guardrails. Unlike prompt-only or reflection-only compliance approaches, ContextCov compiles documented constraints into three complementary checks: static AST queries for code patterns, runtime shell shims that intercept prohibited commands, and architectural validators that enforce structural rules. Acting as an automated, continuous reviewer, ContextCov intercepts agent actions and returns immediate, reproducible violation traces, enabling self-correction before non-compliant changes are finalized. We evaluate ContextCov on SWE-bench Lite (12 repositories, 300 tasks). Compared to prompt-only and LLM reflection baselines, ContextCov achieves 88.3% constraint compliance (vs. 67.0% and 50.3%) with 3.4x lower feedback cost, while maintaining functional correctness. The source code and evaluation results are available at https://github.com/reSHARMA/ContextCov.

The Model Context Protocol (MCP) has emerged as a standardized interface enabling seamless integration between Large Language Models (LLMs) and external data sources and tools. While MCP significantly reduces development complexity and enhances agent capabilities, its openness and extensibility introduce critical security vulnerabilities that threaten system trustworthiness and user data protection. This paper systematically analyzes the security landscape of MCP-based systems, identifying three principal threat categories: (1) agent hijacking attacks stemming from protocol design deficiencies; (2) traditional web vulnerabilities in MCP servers; and (3) supply chain security. To address these challenges, we comprehensively survey existing defense strategies, examining both proactive server-side scanning approaches, ranging from layered detection pipelines and agentic auditing frameworks to zero-trust registry systems, and runtime interaction monitoring solutions that provide continuous oversight and policy enforcement. Our analysis reveals that MCP security fundamentally represents a paradigm shift where the attack surface extends from traditional code execution to semantic interpretation of natural language metadata, necessitating novel defense mechanisms tailored to this unique threat model.

Context engineering has become central to building reliable AI agents, yet it remains largely unmeasured. Agents do not fail in isolation: their behavior is shaped by the instructions, tools, memory, retrieved knowledge, guardrails, and untrusted inputs accumulated in their context. When this context is weak, agents drift, hallucinate, misuse tools, ignore constraints, become vulnerable to injection, and waste tokens. This paper validates context-engineering quality as an independent leading indicator of agent reliability. We implement the measurement in ProofAgent-Harness, an open-source infrastructure for AI agent evaluation that uses multi-juror, consensus-based scoring. The harness assesses context across seven criteria: role clarity, guardrail coverage, instruction consistency, tool schema quality, grounding sufficiency, injection hardening, and token efficiency. Crucially, the context score is isolated from behavioral metrics and release decisions, enabling a non-circular validation. Through a controlled context-quality study across regulated agent domains, holding frontier LLM agents fixed and varying only their operating context, we show that context-quality criteria consistently predict their corresponding behavioral outcomes. Grounding sufficiency predicts hallucination resistance, guardrail coverage predicts manipulation resistance, instruction consistency predicts instruction following, and tool-schema quality predicts tool use. These findings establish context measurement as a validated preflight signal for agent reliability and position context engineering as an auditable layer of agent evaluation and governance.

Large Language Models (LLMs) have demonstrated impressive quality when applied to predictive tasks such as relevance ranking and semantic search. However, deployment of such LLMs remains prohibitively expensive for industry applications with strict latency and throughput requirements. In this work, we present lessons and efficiency insights from developing a purely text-based decoder-only Small Language Model (SLM) for a semantic search application at LinkedIn. Particularly, we discuss model compression techniques such as pruning that allow us to reduce the model size by up to 40% while maintaining the accuracy. Additionally, we present context compression techniques that allow us to reduce the input context length by up to 10x with minimal loss of accuracy. Finally, we present practical lessons from optimizing the serving infrastructure for deploying such a system on GPUs at scale, serving millions of requests per second. Taken together, this allows us to increase our system's throughput by 10x in a real-world deployment, while meeting our quality bar.

Multimodal large language models (MLLMs) have demonstrated promising results in a variety of tasks that combine vision and language. As these models become more integral to research and applications, conducting comprehensive evaluations of their capabilities has grown increasingly important. However, most existing benchmarks fail to consider that, in certain situations, images need to be interpreted within a broader context. In this work, we introduce a new benchmark, named as CODIS, designed to assess the ability of models to use context provided in free-form text to enhance visual comprehension. Our findings indicate that MLLMs consistently fall short of human performance on this benchmark. Further analysis confirms that these models struggle to effectively extract and utilize contextual information to improve their understanding of images. This underscores the pressing need to enhance the ability of MLLMs to comprehend visuals in a context-dependent manner. View our project website at https://thunlp-mt.github.io/CODIS.

Tabular in-context learning (ICL) has recently achieved state-of-the-art (SOTA) performance on several tabular prediction tasks. Previously restricted to classification problems on small tables, recent advances such as TabPFN and TabICL have extended its use to larger datasets. While being architecturally efficient and well-adapted to tabular data structures, current table-native ICL architectures, being trained exclusively on synthetic data, do not fully leverage the rich semantics and world knowledge contained in real-world tabular data. On another end of this spectrum, tabular ICL models based on pretrained large language models such as TabuLa-8B integrate deep semantic understanding and world knowledge but are only able to make use of a small amount of context due to inherent architectural limitations. With the aim to combine the best of both these worlds, we introduce ConTextTab, integrating semantic understanding and alignment into a table-native ICL framework. By employing specialized embeddings for different data modalities and by training on large-scale real-world tabular data, our model is competitive with SOTA across a broad set of benchmarks while setting a new standard on the semantically rich CARTE benchmark.

Large language models (LLMs) are evolving into agentic systems that reason, plan, and operate external tools. The Model Context Protocol (MCP) is a key enabler of this transition, offering a standardized interface for connecting LLMs with heterogeneous tools and services. Yet MCP's openness and multi-server workflows introduce new safety risks that existing benchmarks fail to capture, as they focus on isolated attacks or lack real-world coverage. We present MCP-SafetyBench, a comprehensive benchmark built on real MCP servers that supports realistic multi-turn evaluation across five domains: browser automation, financial analysis, location navigation, repository management, and web search. It incorporates a unified taxonomy of 20 MCP attack types spanning server, host, and user sides, and includes tasks requiring multi-step reasoning and cross-server coordination under uncertainty. Using MCP-SafetyBench, we systematically evaluate leading open- and closed-source LLMs, revealing that all models remain vulnerable to MCP attacks, with a notable safety-utility trade-off. Our results highlight the urgent need for stronger defenses and establish MCP-SafetyBench as a foundation for diagnosing and mitigating safety risks in real-world MCP deployments.

Context utilisation, the ability of Language Models (LMs) to incorporate relevant information from the provided context when generating responses, remains largely opaque to users, who cannot determine whether models draw from parametric memory or provided context, nor identify which specific context pieces inform the response. Highlight explanations (HEs) offer a natural solution as they can point the exact context pieces and tokens that influenced model outputs. However, no existing work evaluates their effectiveness in accurately explaining context utilisation. We address this gap by introducing the first gold standard HE evaluation framework for context attribution, using controlled test cases with known ground-truth context usage, which avoids the limitations of existing indirect proxy evaluations. To demonstrate the framework's broad applicability, we evaluate four HE methods -- three established techniques and MechLight, a mechanistic interpretability approach we adapt for this task -- across four context scenarios, four datasets, and five LMs. Overall, we find that MechLight performs best across all context scenarios. However, all methods struggle with longer contexts and exhibit positional biases, pointing to fundamental challenges in explanation accuracy that require new approaches to deliver reliable context utilisation explanations at scale.

LLM-based coding agents have shown strong performance on automated issue resolution benchmarks, yet existing evaluations largely focus on final task success, providing limited insight into how agents retrieve and use code context during problem solving. We introduce ContextBench, a process-oriented evaluation of context retrieval in coding agents. ContextBench consists of 1,136 issue-resolution tasks from 66 repositories across eight programming languages, each augmented with human-annotated gold contexts. We further implement an automated evaluation framework that tracks agent trajectories and measures context recall, precision, and efficiency throughout issue resolution. Using ContextBench, we evaluate four frontier LLMs and five coding agents. Our results show that sophisticated agent scaffolding yields only marginal gains in context retrieval ("The Bitter Lesson" of coding agents), LLMs consistently favor recall over precision, and substantial gaps exist between explored and utilized context. ContextBench augments existing end-to-end benchmarks with intermediate gold-context metrics that unbox the issue-resolution process. These contexts offer valuable intermediate signals for guiding LLM reasoning in software tasks.

Systems based on Large Language Models (LLMs) have become formidable tools for automating research and software production. However, their governance remains a challenge when technical requirements demand absolute consistency, auditability, and predictable control over cost and latency. Recent literature highlights two phenomena that aggravate this scenario: the stochastic variance inherent in the model's judgment (often treated as "systemic noise") and the substantial degradation of context utilization in long inputs, with critical losses when decisive information is diluted in the middle of the prompt. This article proposes PARCER as an engineering response to these limitations. The framework acts as a declarative "operational contract" in YAML, transforming unstructured interactions into versioned and executable artifacts. PARCER imposes strict governance structured into seven operational phases, introducing decision hygiene practices inspired by legal judgments to mitigate noise, adaptive token budgeting, formalized recovery routes (fallbacks) for context preservation, and systemic observability via OpenTelemetry. The objective of this work is to present the conceptual and technical architecture of PARCER, positioning it as a necessary transition from simple "prompt engineering" to "context engineering with governable governance".

Multi-agent systems represent a significant advancement in artificial intelligence, enabling complex problem-solving through coordinated specialized agents. However, these systems face fundamental challenges in context management, coordination efficiency, and scalable operation. This paper introduces a comprehensive framework for advancing multi-agent systems through Model Context Protocol (MCP), addressing these challenges through standardized context sharing and coordination mechanisms. We extend previous work on AI agent architectures by developing a unified theoretical foundation, advanced context management techniques, and scalable coordination patterns. Through detailed implementation case studies across enterprise knowledge management, collaborative research, and distributed problem-solving domains, we demonstrate significant performance improvements compared to traditional approaches. Our evaluation methodology provides a systematic assessment framework with benchmark tasks and datasets specifically designed for multi-agent systems. We identify current limitations, emerging research opportunities, and potential transformative applications across industries. This work contributes to the evolution of more capable, collaborative, and context-aware artificial intelligence systems that can effectively address complex real-world challenges.

The Model Context Protocol (MCP) is rapidly becoming the standard interface for Large Language Models (LLMs) to discover and invoke external tools. However, existing evaluations often fail to capture the complexity of real-world scenarios, relying on restricted toolsets, simplistic workflows, or subjective LLM-as-a-judge metrics. We introduce MCP-Atlas, a large-scale benchmark for evaluating tool-use competency, comprising 36 real MCP servers and 220 tools. It includes 1,000 tasks designed to assess tool-use competency in realistic, multi-step workflows. Tasks use natural language prompts that avoid naming specific tools or servers, requiring agents to identify and orchestrate 3-6 tool calls across multiple servers. We score tasks using a claims-based rubric that awards partial credit based on the factual claims satisfied in the model's final answer, complemented by internal diagnostics on tool discovery, parameterization, syntax, error recovery, and efficiency. Evaluation results on frontier models reveal that top models achieve pass rates exceeding 50%, with primary failures arising from inadequate tool usage and task understanding. We release the task schema, containerized harness, and a 500-task public subset of the benchmark dataset to facilitate reproducible comparisons and advance the development of robust, tool-augmented agents.

Agentic coding tools receive goals written in natural language as input, break them down into specific tasks, and write or execute the actual code with minimal human intervention. Central to this process are agent context files ("READMEs for agents") that provide persistent, project-level instructions. In this paper, we conduct the first large-scale empirical study of 2,303 agent context files from 1,925 repositories to characterize their structure, maintenance, and content. We find that these files are not static documentation but complex, difficult-to-read artifacts that evolve like configuration code, maintained through frequent, small additions. Our content analysis of 16 instruction types shows that developers prioritize functional context, such as build and run commands (62.3%), implementation details (69.9%), and architecture (67.7%). We also identify a significant gap: non-functional requirements like security (14.5%) and performance (14.5%) are rarely specified. These findings indicate that while developers use context files to make agents functional, they provide few guardrails to ensure that agent-written code is secure or performant, highlighting the need for improved tooling and practices.

Software testing is a critical aspect of software development, yet generating test cases remains a routine task for engineers. This paper presents a benchmark, CLOVER, to evaluate models' capabilities in generating and completing test cases under specific conditions. Spanning from simple assertion completions to writing test cases that cover specific code blocks across multiple files, these tasks are based on 12 python repositories, analyzing 845 problems with context lengths ranging from 4k to 128k tokens. Utilizing code testing frameworks, we propose a method to construct retrieval contexts using coverage information. While models exhibit comparable performance with short contexts, notable differences emerge with 16k contexts. Notably, models like GPT-4o and Claude 3.5 can effectively leverage relevant snippets; however, all models score below 35\% on the complex Task III, even with the oracle context provided, underscoring the benchmark's significance and the potential for model improvement. The benchmark is containerized for code execution across tasks, and we will release the code, data, and construction methodologies.

Recent research has developed several LLM architectures suitable for inference on end-user devices, such as the Mixture of Lookup Experts (MoLE)~jie_mixture_2025. A key feature of MoLE is that each token id is associated with a dedicated group of experts. For a given input, only the experts corresponding to the input token id will be activated. Since the communication overhead of loading this small number of activated experts into RAM during inference is negligible, expert parameters can be offloaded to storage, making MoLE suitable for resource-constrained devices. However, MoLE's context-independent expert selection mechanism, based solely on input ids, may limit model performance. To address this, we propose the Mixture of Lookup Key-Value Experts (MoLKV) model. In MoLKV, each expert is structured as a key-value pair. For a given input, the input-derived query interacts with the cached key-value experts from the current sequence, generating a context-aware expert output. This context-aware mechanism alleviates the limitation of MoLE, and experimental results demonstrate that MoLKV achieves significantly lower validation loss in small-scale evaluations.

Deep research is emerging as a representative long-horizon task for large language model (LLM) agents. However, long trajectories in deep research often exceed model context limits, compressing token budgets for both evidence collection and report writing, and preventing effective test-time scaling. We introduce FS-Researcher, a file-system-based, dual-agent framework that scales deep research beyond the context window via a persistent workspace. Specifically, a Context Builder agent acts as a librarian which browses the internet, writes structured notes, and archives raw sources into a hierarchical knowledge base that can grow far beyond context length. A Report Writer agent then composes the final report section by section, treating the knowledge base as the source of facts. In this framework, the file system serves as a durable external memory and a shared coordination medium across agents and sessions, enabling iterative refinement beyond the context window. Experiments on two open-ended benchmarks (DeepResearch Bench and DeepConsult) show that FS-Researcher achieves state-of-the-art report quality across different backbone models. Further analyses demonstrate a positive correlation between final report quality and the computation allocated to the Context Builder, validating effective test-time scaling under the file-system paradigm. The code and data are anonymously open-sourced at https://github.com/Ignoramus0817/FS-Researcher.

Foundation model development attracts a rapidly expanding body of contributors, scientists, and applications. To help shape responsible development practices, we introduce the Foundation Model Development Cheatsheet: a growing collection of 250+ tools and resources spanning text, vision, and speech modalities. We draw on a large body of prior work to survey resources (e.g. software, documentation, frameworks, guides, and practical tools) that support informed data selection, processing, and understanding, precise and limitation-aware artifact documentation, efficient model training, advance awareness of the environmental impact from training, careful model evaluation of capabilities, risks, and claims, as well as responsible model release, licensing and deployment practices. We hope this curated collection of resources helps guide more responsible development. The process of curating this list, enabled us to review the AI development ecosystem, revealing what tools are critically missing, misused, or over-used in existing practices. We find that (i) tools for data sourcing, model evaluation, and monitoring are critically under-serving ethical and real-world needs, (ii) evaluations for model safety, capabilities, and environmental impact all lack reproducibility and transparency, (iii) text and particularly English-centric analyses continue to dominate over multilingual and multi-modal analyses, and (iv) evaluation of systems, rather than just models, is needed so that capabilities and impact are assessed in context.

The Model Context Protocol (MCP) has emerged as a universal standard that enables AI agents to seamlessly connect with external tools, significantly enhancing their functionality. However, while MCP brings notable benefits, it also introduces significant vulnerabilities, such as Tool Poisoning Attacks (TPA), where hidden malicious instructions exploit the sycophancy of large language models (LLMs) to manipulate agent behavior. Despite these risks, current academic research on MCP security remains limited, with most studies focusing on narrow or qualitative analyses that fail to capture the diversity of real-world threats. To address this gap, we present the MCP Attack Library (MCPLIB), which categorizes and implements 31 distinct attack methods under four key classifications: direct tool injection, indirect tool injection, malicious user attacks, and LLM inherent attack. We further conduct a quantitative analysis of the efficacy of each attack. Our experiments reveal key insights into MCP vulnerabilities, including agents' blind reliance on tool descriptions, sensitivity to file-based attacks, chain attacks exploiting shared context, and difficulty distinguishing external data from executable commands. These insights, validated through attack experiments, underscore the urgency for robust defense strategies and informed MCP design. Our contributions include 1) constructing a comprehensive MCP attack taxonomy, 2) introducing a unified attack framework MCPLIB, and 3) conducting empirical vulnerability analysis to enhance MCP security mechanisms. This work provides a foundational framework, supporting the secure evolution of MCP ecosystems.

Recent developments in long-context large language models have attracted considerable attention. Yet, their real-world applications are often hindered by ineffective context information use. This work shows that structuring training data to increase semantic interdependence is an effective strategy for optimizing context utilization. To this end, we introduce Structured Packing for Long Context (SPLiCe), a method for creating training examples by using information retrieval methods to collate mutually relevant documents into a single training context. We empirically validate SPLiCe on large 3B and 7B models, showing perplexity improvements and better long-context utilization on downstream tasks. Remarkably, already relatively short fine-tuning with SPLiCe is enough to attain these benefits. Additionally, the comprehensive study of SPLiCe reveals intriguing transfer effects such as training on code data leading to perplexity improvements on text data.

Coding agents powered by large language models (LLMs) repeatedly alternate between model inference and tool calls, creating long-lived sessions with reusable key-value (KV) states and asynchronous request resumptions. Logical readiness, however, does not ensure efficient admission in a shared serving system. Through direct trace analysis and trace-driven replay, we identify two mismatches: reusable KV states reside across storage tiers and incur unequal computational costs for state preparation, while requests with heterogeneous context lengths can decode inefficiently together. Our central insight is that exploiting admission flexibility can improve serving performance while preserving request progress. We present Coda, a coding-agent serving system that realizes this insight through a readiness-informed admission layer incorporating two mechanisms. Tiered-Aging state admission exploits bounded flexibility in admission order to improve admission efficiency and preserve request progress. Compatibility-Aware execution admission exploits flexibility in attention grouping within each model iteration to reduce mixed-context interference and improve shared decoding efficiency. For multi-worker configurations, Coda introduces a separate routing layer that considers KV-state residency, worker load, and request-to-worker context-length compatibility to guide efficient request placement. We evaluate Coda across different models and workloads against state-of-the-art coding-agent serving systems and vLLM. Across the single-worker and multi-worker experiments, Coda improves output-token and SLO-compliant throughput by 20.3% and 70.5% on average, with peak gains of 29.3% and 140.2%.

LLM-based Software Engineering agents face a critical bottleneck: context length limitations cause failures on complex, long-horizon tasks. One promising solution is to encode context as continuous embeddings rather than discrete tokens, enabling denser information storage. We apply the recently proposed In-Context Autoencoder for this purpose. While the method performs well on single-shot common-knowledge and code-understanding tasks, our experiments demonstrate that it fails on multi-step agentic coding tasks. In this paper, we explore this phenomenon and discuss possible factors contributing to this failure.

The Model Context Protocol (MCP), introduced by Anthropic, provides a standardized framework for artificial intelligence (AI) systems to interact with external data sources and tools in real-time. While MCP offers significant advantages for AI integration and capability extension, it introduces novel security challenges that demand rigorous analysis and mitigation. This paper builds upon foundational research into MCP architecture and preliminary security assessments to deliver enterprise-grade mitigation frameworks and detailed technical implementation strategies. Through systematic threat modeling and analysis of MCP implementations and analysis of potential attack vectors, including sophisticated threats like tool poisoning, we present actionable security patterns tailored for MCP implementers and adopters. The primary contribution of this research lies in translating theoretical security concerns into a practical, implementable framework with actionable controls, thereby providing essential guidance for the secure enterprise adoption and governance of integrated AI systems.

Tool calling has emerged as a critical capability for AI agents to interact with the real world and solve complex tasks. While the Model Context Protocol (MCP) provides a powerful standardized framework for tool integration, there is a significant gap in benchmarking how well AI agents can effectively solve multi-step tasks using diverse MCP tools in realistic, dynamic scenarios. In this work, we present LiveMCP-101, a benchmark of 101 carefully curated real-world queries, refined through iterative LLM rewriting and manual review, that require coordinated use of multiple MCP tools including web search, file operations, mathematical reasoning, and data analysis. Moreover, we introduce a novel evaluation approach that leverages ground-truth execution plans rather than raw API outputs, better reflecting the evolving nature of real-world environments. Experiments show that even frontier LLMs achieve a success rate below 60\%, highlighting major challenges in tool orchestration. Detailed ablations and error analysis further reveal distinct failure modes and inefficiencies in token usage, pointing to concrete directions for advancing current models. LiveMCP-101 sets a rigorous standard for evaluating real-world agent capabilities, advancing toward autonomous AI systems that reliably execute complex tasks through tool use.

The Model Context Protocol (MCP) replaces static, developer-controlled API integrations with more dynamic, user-driven agent systems, which also introduces new security risks. As MCP adoption grows across community servers and major platforms, organizations encounter threats that existing AI governance frameworks (such as NIST AI RMF and ISO/IEC 42001) do not yet cover in detail. We focus on three types of adversaries that take advantage of MCP s flexibility: content-injection attackers that embed malicious instructions into otherwise legitimate data; supply-chain attackers who distribute compromised servers; and agents who become unintentional adversaries by over-stepping their role. Based on early incidents and proof-of-concept attacks, we describe how MCP can increase the attack surface through data-driven exfiltration, tool poisoning, and cross-system privilege escalation. In response, we propose a set of practical controls, including per-user authentication with scoped authorization, provenance tracking across agent workflows, containerized sandboxing with input/output checks, inline policy enforcement with DLP and anomaly detection, and centralized governance using private registries or gateway layers. The aim is to help organizations ensure that unvetted code does not run outside a sandbox, tools are not used beyond their intended scope, data exfiltration attempts are detectable, and actions can be audited end-to-end. We close by outlining open research questions around verifiable registries, formal methods for these dynamic systems, and privacy-preserving agent operations.

The Model Context Protocol (MCP) has become a common interface for connecting large language model (LLM) agents to external tools, but its reliance on stateless, eager schema injection imposes a hidden per-turn overhead the MCP Tax or Tools Tax that practitioner reports place between roughly 10k and 60k tokens in typical multi-server deployments. This payload inflates the key-value cache, is associated with reasoning degradation as context utilization approaches published fracture points around 70%, and turns token budgets into a recurring operational cost. We introduce Tool Attention, a middleware-layer mechanism that generalizes the "Attention Is All You Need" paradigm from self-attention over tokens to gated attention over tools. Tool Attention combines (i) an Intent Schema Overlap (ISO) score from sentence embeddings, (ii) a state-aware gating function enforcing preconditions and access scopes, and (iii) a two-phase lazy schema loader that keeps a compact summary pool in context and promotes full JSON schemas only for top-k gated tools. We evaluate on a simulated 120-tool, six-server benchmark whose per-server token counts are calibrated to public audits of real MCP deployments. In this simulation, Tool Attention directly reduces measured per-turn tool tokens by 95.0% (47.3k -> 2.4k) and raises effective context utilization (a token-ratio quantity) from 24% to 91%. End-to-end figures for task success, latency, cost, and reasoning quality are reported as projections derived from the measured token counts combined with published deployment telemetry; they are not measured on live LLM agents, and we mark projected values explicitly throughout. Taken together, the results support a simple thesis: protocol-level efficiency, not raw context length, is a binding constraint on scalable gentic systems. The code for this work is accessible at https://github.com/asadani/tool-attention

This paper introduces long-context Granite code models that support effective context windows of up to 128K tokens. Our solution for scaling context length of Granite 3B/8B code models from 2K/4K to 128K consists of a light-weight continual pretraining by gradually increasing its RoPE base frequency with repository-level file packing and length-upsampled long-context data. Additionally, we also release instruction-tuned models with long-context support which are derived by further finetuning the long context base models on a mix of permissively licensed short and long-context instruction-response pairs. While comparing to the original short-context Granite code models, our long-context models achieve significant improvements on long-context tasks without any noticeable performance degradation on regular code completion benchmarks (e.g., HumanEval). We release all our long-context Granite code models under an Apache 2.0 license for both research and commercial use.

Large language models are prominently used in real-world applications, often tasked with reasoning over large volumes of documents. An exciting development in this space is models boasting extended context capabilities, with some accommodating over 2 million tokens. Such long context model capabilities remain uncertain in production systems, motivating the need to benchmark their performance on real world use cases. We address this challenge by proposing SWiM, an evaluation framework that addresses the limitations of standard tests. Testing the framework on eight long context models, we find that even strong models such as GPT-4 and Claude 3 Opus degrade in performance when information is present in the middle of the context window (lost-in-the-middle effect). Next, in addition to our benchmark, we propose medoid voting, a simple, but effective training-free approach that helps alleviate this effect, by generating responses a few times, each time randomly permuting documents in the context, and selecting the medoid answer. We evaluate medoid voting on single document QA tasks, achieving up to a 24% lift in accuracy.

The proliferation of Large Language Models (LLMs) has catalyzed a shift towards autonomous agents capable of complex reasoning and tool use. However, current agent architectures are frequently constructed using imperative, ad hoc patterns. This results in brittle systems plagued by difficulties in state management, error handling, and concurrency. This paper introduces Monadic Context Engineering (MCE), a novel architectural paradigm leveraging the algebraic structures of Functors, Applicative Functors, and Monads to provide a formal foundation for agent design. MCE treats agent workflows as computational contexts where cross-cutting concerns, such as state propagation, short-circuiting error handling, and asynchronous execution, are managed intrinsically by the algebraic properties of the abstraction. We demonstrate how Monads enable robust sequential composition, how Applicatives provide a principled structure for parallel execution, and crucially, how Monad Transformers allow for the systematic composition of these capabilities. This layered approach enables developers to construct complex, resilient, and efficient AI agents from simple, independently verifiable components. We further extend this framework to describe Meta-Agents, which leverage MCE for generative orchestration, dynamically creating and managing sub-agent workflows through metaprogramming. Project Page: https://github.com/yifanzhang-pro/monadic-context-engineering.

AI agent systems increasingly rely on reusable non-LLM engineering infrastructure that packages tool mediation, context handling, delegation, safety control, and orchestration. Yet the architectural design decisions in this surrounding infrastructure remain understudied. This paper presents a protocol-guided, source-grounded empirical study of 70 publicly available agent-system projects, addressing three questions: which design-decision dimensions recur across projects, which co-occurrences structure those decisions, and which typical architectural patterns emerge. Methodologically, we contribute a transparent investigation procedure for analyzing heterogeneous agent-system corpora through source-code and technical-material reading. Empirically, we identify five recurring design dimensions (subagent architecture, context management, tool systems, safety mechanisms, and orchestration) and find that the corpus favors file-persistent, hybrid, and hierarchical context strategies; registry-oriented tool systems remain dominant while MCP- and plugin-oriented extensions are emerging; and intermediate isolation is common but high-assurance audit is rare. Cross-project co-occurrence analysis reveals that deeper coordination pairs with more explicit context services, stronger execution environments with more structured governance, and formalized tool-registration boundaries with broader ecosystem ambitions. We synthesize five recurring architectural patterns spanning lightweight tools, balanced CLI frameworks, multi-agent orchestrators, enterprise systems, and scenario-verticalized projects. The result provides an evidence-based account of architectural regularities in agent-system engineering, with grounded guidance for framework designers, selectors, and researchers.

Agentic AI systems built around large language models (LLMs) are moving away from closed, single-model frameworks and toward open ecosystems that connect a variety of agents, external tools, and resources. The Model Context Protocol (MCP) has emerged as a standard to unify tool access, allowing agents to discover, invoke, and coordinate with tools more flexibly. However, as MCP becomes more widely adopted, it also brings a new set of security and privacy challenges. These include risks such as unauthorized access, tool poisoning, prompt injection, privilege escalation, and supply chain attacks, any of which can impact different parts of the protocol workflow. While recent research has examined possible attack surfaces and suggested targeted countermeasures, there is still a lack of systematic, protocol-level security improvements for MCP. To address this, we introduce the Secure Model Context Protocol (SMCP), which builds on MCP by adding unified identity management, robust mutual authentication, ongoing security context propagation, fine-grained policy enforcement, and comprehensive audit logging. In this paper, we present the main components of SMCP, explain how it helps reduce security risks, and illustrate its application with practical examples. We hope that this work will contribute to the development of agentic systems that are not only powerful and adaptable, but also secure and dependable.

Long-horizon search agents must manage a rapidly growing working context as they reason, call tools, and observe information. Naively accumulating all intermediate content can overwhelm the agent, increasing costs and the risk of errors. We propose that effective context management should be adaptive: parts of the agent's trajectory are maintained at different levels of detail depending on their current relevance to the task. To operationalize this principle, we introduce Context-ReAct, a general agentic paradigm for elastic context orchestration that integrates reasoning, context management, and tool use in a unified loop. Context-ReAct provides five atomic operations: Skip, Compress, Rollback, Snippet and Delete, which allow the agent to dynamically reshape its working context, preserving important evidence, summarizing resolved information, discarding unhelpful branches, and controlling context size. We prove that the Compress operator is expressively complete, while the other specialized operators provide efficiency and fidelity guarantees that reduce generation cost and hallucination risk. Building on this paradigm, we develop LongSeeker, a long-horizon search agent fine-tuned from Qwen3-30B-A3B on 10k synthesized trajectories. Across four representative search benchmarks, LongSeeker achieves 61.5% on BrowseComp and 62.5% on BrowseComp-ZH, substantially outperforming Tongyi DeepResearch (43.2% and 46.7%) and AgentFold (36.2% and 47.3%). These results highlight the potential of adaptive context management, showing that agents can achieve more reliable and efficient long-horizon reasoning by actively shaping their working memory.

Deployed LLM agents rely on agentic context, the model-external textual control content assembled by an operational harness. In this work, the mutable component of that context is a persistent system-level instruction that is updated from operational experience while the model, tools, and harness remain fixed. Over long evolution horizons, flat-text maintenance makes verification increasingly difficult as accumulated instructions grow and interact. We propose Graph-Regularized Agentic Context Evolution (GRACE), which maintains the persistent instruction component as a typed semantic graph and validates proposed updates within the local typed neighborhoods of modified nodes. Accepted graph updates are reconstructed as incremental edits to the textual instruction checkpoint used at deployment. We evaluate GRACE within a fixed telecom agent harness derived from τ^2-bench under a controlled distribution-shift protocol. Across five independent replications, GRACE improves strict reliability, measured by pass^3, from the Gemini 2.5 Flash zero-shot value of 0.091 to 0.673pm0.136 at the final checkpoint. This exceeds a Gemini 3.1 Pro zero-shot reference of 0.242 on the same held-out set, while the flat-text HCE baseline finishes at 0.191pm0.051. These results identify two requirements for reliable long-horizon context evolution, a structural substrate that makes verification local and a consolidation mechanism that keeps accumulated instruction content usable.

Broad textual understanding and in-context learning require language models that utilize full document contexts. Due to the implementation challenges associated with directly training long-context models, many methods have been proposed for extending models to handle long contexts. However, owing to differences in data and model classes, it has been challenging to compare these approaches, leading to uncertainty as to how to evaluate long-context performance and whether it differs from standard evaluation. We implement a controlled protocol for extension methods with a standardized evaluation, utilizing consistent base models and extension data. Our study yields several insights into long-context behavior. First, we reaffirm the critical role of perplexity as a general-purpose performance indicator even in longer-context tasks. Second, we find that current approximate attention methods systematically underperform across long-context tasks. Finally, we confirm that exact fine-tuning based methods are generally effective within the range of their extension, whereas extrapolation remains challenging. All codebases, models, and checkpoints will be made available open-source, promoting transparency and facilitating further research in this critical area of AI development.

The Needle-in-a-Haystack (NIAH) benchmark is widely used to evaluate Large Language Models' (LLMs) ability to understand long contexts (LC). It evaluates the capability to identify query-relevant context within extensive query-irrelevant passages. Although this method serves as a widely accepted standard for evaluating long-context understanding, our findings suggest it may overestimate the true LC capability of LLMs. We demonstrate that even state-of-the-art models such as GPT-4o struggle to intactly incorporate given contexts made up of solely query-relevant ten sentences. In response, we introduce a novel benchmark, NeedleChain, where the context consists entirely of query-relevant information, requiring the LLM to fully grasp the input to answer correctly. Our benchmark allows for flexible context length and reasoning order, offering a more comprehensive analysis of LLM performance. Additionally, we propose an extremely simple yet compelling strategy to improve LC understanding capability of LLM: ROPE Contraction. Our experiments with various advanced LLMs reveal a notable disparity between their ability to process large contexts and their capacity to fully understand them. Source code and datasets are available at https://github.com/hyeonseokk/NeedleChain

Ensuring faithfulness to context in large language models (LLMs) and retrieval-augmented generation (RAG) systems is crucial for reliable deployment in real-world applications, as incorrect or unsupported information can erode user trust. Despite advancements on standard benchmarks, faithfulness hallucination-where models generate responses misaligned with the provided context-remains a significant challenge. In this work, we introduce FaithEval, a novel and comprehensive benchmark tailored to evaluate the faithfulness of LLMs in contextual scenarios across three diverse tasks: unanswerable, inconsistent, and counterfactual contexts. These tasks simulate real-world challenges where retrieval mechanisms may surface incomplete, contradictory, or fabricated information. FaithEval comprises 4.9K high-quality problems in total, validated through a rigorous four-stage context construction and validation framework, employing both LLM-based auto-evaluation and human validation. Our extensive study across a wide range of open-source and proprietary models reveals that even state-of-the-art models often struggle to remain faithful to the given context, and that larger models do not necessarily exhibit improved faithfulness.Project is available at: https://github.com/SalesforceAIResearch/FaithEval.

Large language model (LLM)-based AI agents extend LLM capabilities by enabling access to tools such as data sources, APIs, search engines, code sandboxes, and even other agents. While this empowers agents to perform complex tasks, LLMs may invoke unintended tool interactions and introduce risks, such as leaking sensitive data or overwriting critical records, which are unacceptable in enterprise contexts. Current approaches to mitigate these risks, such as model-based safeguards, enhance agents' reliability but cannot guarantee system safety. Methods like information flow control (IFC) and temporal constraints aim to provide guarantees but often require extensive human annotation. We propose a process that starts with applying System-Theoretic Process Analysis (STPA) to identify hazards in agent workflows, derive safety requirements, and formalize them as enforceable specifications on data flows and tool sequences. To enable this, we introduce a capability-enhanced Model Context Protocol (MCP) framework that requires structured labels on capabilities, confidentiality, and trust level. Together, these contributions aim to shift LLM-based agent safety from ad hoc reliability fixes to proactive guardrails with formal guarantees, while reducing dependence on user confirmation and making autonomy a deliberate design choice.

Enterprise software organizations accumulate critical institutional knowledge - architectural decisions, deployment procedures, compliance policies, incident playbooks - yet this knowledge remains trapped in formats designed for human interpretation. The bottleneck to effective agentic software development is not model capability but knowledge architecture. When any knowledge consumer - an autonomous AI agent, a newly onboarded engineer, or a senior developer - encounters an enterprise task without institutional context, the result is guesswork, correction cascades, and a disproportionate tax on senior engineers who must manually supply what others cannot infer. This paper introduces Knowledge Activation, a framework that specializes AI Skills - the open standard for agent-consumable knowledge - into structured, governance-aware Atomic Knowledge Units (AKUs) for institutional knowledge delivery. Rather than retrieving documents for interpretation, AKUs deliver action - ready specifications encoding what to do, which tools to use, what constraints to respect, and where to go next - so that agents act correctly and engineers receive institutionally grounded guidance without reconstructing organizational context from scratch. AKUs form a composable knowledge graph that agents traverse at runtime - compressing onboarding, reducing cross - team friction, and eliminating correction cascades. The paper formalizes the resource constraints that make this architecture necessary, specifies the AKU schema and deployment architecture, and grounds long - term maintenance in knowledge commons practice. Organizations that architect their institutional knowledge for the agentic era will outperform those that invest solely in model capability.

Agents based on large language models have recently shown strong potential on real-world software engineering (SWE) tasks that require long-horizon interaction with repository-scale codebases. However, most existing agents rely on append-only context maintenance or passively triggered compression heuristics, which often lead to context explosion, semantic drift, and degraded reasoning in long-running interactions. We propose CAT, a new context management paradigm that elevates context maintenance to a callable tool integrated into the decision-making process of agents. CAT formalizes a structured context workspace consisting of stable task semantics, condensed long-term memory, and high-fidelity short-term interactions, and enables agents to proactively compress historical trajectories into actionable summaries at appropriate milestones. To support context management for SWE-agents, we propose a trajectory-level supervision framework, CAT-GENERATOR, based on an offline data construction pipeline that injects context-management actions into complete interaction trajectories. Using this framework, we train a context-aware model, SWE-Compressor. Experiments on SWE-Bench-Verified demonstrate that SWE-Compressor reaches a 57.6% solved rate and significantly outperforms ReAct-based agents and static compression baselines, while maintaining stable and scalable long-horizon reasoning under a bounded context budget.

Large Language Models (LLMs) have shown promise in automating code generation and software engineering tasks, yet they often struggle with complex, multi-file projects due to context limitations and knowledge gaps. We propose a novel context engineering workflow that combines multiple AI components: an Intent Translator (GPT-5) for clarifying user requirements, an Elicit-powered semantic literature retrieval for injecting domain knowledge, NotebookLM-based document synthesis for contextual understanding, and a Claude Code multi-agent system for code generation and validation. Our integrated approach leverages intent clarification, retrieval-augmented generation, and specialized sub-agents orchestrated via Claude's agent framework. We demonstrate that this method significantly improves the accuracy and reliability of code assistants in real-world repositories, yielding higher single-shot success rates and better adherence to project context than baseline single-agent approaches. Qualitative results on a large Next.js codebase show the multi-agent system effectively plans, edits, and tests complex features with minimal human intervention. We compare our system with recent frameworks like CodePlan, MASAI, and HyperAgent, highlighting how targeted context injection and agent role decomposition lead to state-of-the-art performance. Finally, we discuss the implications for deploying LLM-based coding assistants in production, along with lessons learned on context management and future research directions.

The Model Context Protocol (MCP) (MCP Community, 2025) has emerged as a widely used framework for enabling LLM-based agents to communicate with external tools and services. The original MCP implementation (Anthropic, 2024) relies on a Large Language Model (LLM) to decompose tasks and issue instructions to servers. In particular, the agents, models, and servers are stateless and do not have access to a global context. However, in tasks involving LLM-driven coordination, it is natural that a Shared Context Store (SCS) could improve the efficiency and coherence of multi-agent workflows by reducing redundancy and enabling knowledge transfer between servers. Thus, in this work, we design and assess the performance of a Context-Aware MCP (CA-MCP) that offloads execution logic to specialized MCP servers that read from and write to a shared context memory, allowing them to coordinate more autonomously in real time. In this design, context management serves as the central mechanism that maintains continuity across task executions by tracking intermediate states and shared variables, thereby enabling persistent collaboration among agents without repeated prompting. We present experiments showing that the CA-MCP can outperform the traditional MCP by reducing the number of LLM calls required for complex tasks and decreasing the frequency of response failures when task conditions are not satisfied. In particular, we conducted experiments on the TravelPlanner (Yang et al., 2024) and REALM-Bench (Geng & Chang, 2025) benchmark datasets and observed statistically significant results indicating the potential advantages of incorporating a shared context store via CA-MCP in LLM-driven multi-agent systems.

Recent advancements in code-fluent Large Language Models (LLMs) enabled the research on repository-level code editing. In such tasks, the model navigates and modifies the entire codebase of a project according to request. Hence, such tasks require efficient context retrieval, i.e., navigating vast codebases to gather relevant context. Despite the recognized importance of context retrieval, existing studies tend to approach repository-level coding tasks in an end-to-end manner, rendering the impact of individual components within these complicated systems unclear. In this work, we decouple the task of context retrieval from the other components of the repository-level code editing pipelines. We lay the groundwork to define the strengths and weaknesses of this component and the role that reasoning plays in it by conducting experiments that focus solely on context retrieval. We conclude that while the reasoning helps to improve the precision of the gathered context, it still lacks the ability to identify its sufficiency. We also outline the ultimate role of the specialized tools in the process of context gathering. The code supplementing this paper is available at https://github.com/JetBrains-Research/ai-agents-code-editing.

The Model Context Protocol (MCP) has rapidly established itself as a standard interface for enabling LLM-based agents to interact with external tools and services. As MCP servers are increasingly entrusted with security-sensitive operations, understanding their real-world risks has become critical. In practice, due to the absence of large-scale runtime MCP servers, such understanding largely relies on security scanners applied to a small number of cases, yet the reliability of these assessments remains unclear. In this study, we revisit how MCP security is measured. We present MCPZoo, the largest collection of MCP servers for dynamic analysis to date. MCPZoo is constructed through a multi-agent framework for transforming in-the-wild static repositories into dynamic services. The framework emulates how human experts build, diagnose, and iteratively repair deployment and runtime defects by combining environment inference with feedback-driven refinement. To ensure practical interactivity at runtime, the servers are validated via real protocol interactions. As a result, MCPZoo contains 64,611 unique MCP servers (113,927 in total), with more than 37,288 supporting dynamic analysis. Leveraging MCPZoo, we conduct the first ecosystem-scale measurement of MCP servers and the scanners that analyze them. While existing scanners report that 96.89% of servers are risky, we find that these signals are unreliable. In particular, manual validation shows that less than 50% of sampled alerts are true positives, and scanner outputs exhibit clear inconsistency across scanners. Overall, MCPZoo enables large-scale, reproducible measurement of MCP server security and exposes limitations of current scanning practices. We further release a public query interface to support practical risk assessment of MCP servers.

Communicating complex system designs or scientific processes through text alone is inefficient and prone to ambiguity. A system that automatically generates scientific architecture diagrams from text with high semantic fidelity can be useful in multiple applications like enterprise architecture visualization, AI-driven software design, and educational content creation. Hence, in this paper, we focus on leveraging language models to perform semantic understanding of the input text description to generate intermediate code that can be processed to generate high-fidelity architecture diagrams. Unfortunately, no clean large-scale open-access dataset exists, implying lack of any effective open models for this task. Hence, we contribute a comprehensive dataset, \system, comprising scientific architecture images, their corresponding textual descriptions, and associated DOT code representations. Leveraging this resource, we fine-tune a suite of small language models, and also perform in-context learning using GPT-4o. Through extensive experimentation, we show that models significantly outperform existing baseline models like DiagramAgent and perform at par with in-context learning-based generations from GPT-4o. We make the code, data and models publicly available.

How do language models use information provided as context when generating a response? Can we infer whether a particular generated statement is actually grounded in the context, a misinterpretation, or fabricated? To help answer these questions, we introduce the problem of context attribution: pinpointing the parts of the context (if any) that led a model to generate a particular statement. We then present ContextCite, a simple and scalable method for context attribution that can be applied on top of any existing language model. Finally, we showcase the utility of ContextCite through three applications: (1) helping verify generated statements (2) improving response quality by pruning the context and (3) detecting poisoning attacks. We provide code for ContextCite at https://github.com/MadryLab/context-cite.

Context lengths for models have grown rapidly, from thousands to millions of tokens in just a few years. The extreme context sizes of modern long-context models have made it difficult to construct realistic long-context benchmarks -- not only due to the cost of collecting million-context tasks but also in identifying realistic scenarios that require significant contexts. We identify code comprehension and repair as a natural testbed and challenge task for long-context models and introduce LongCodeBench (LCB), a benchmark to test LLM coding abilities in long-context scenarios. Our benchmark tests both the comprehension and repair capabilities of LCLMs in realistic and important settings by drawing from real-world GitHub issues and constructing QA (LongCodeQA) and bug fixing (LongSWE-Bench) tasks. We carefully stratify the complexity of our benchmark, enabling us to evaluate models across different scales -- ranging from Qwen2.5 14B Instruct to Google's flagship Gemini model. We find that long-context remains a weakness for all models, with performance drops such as from 29% to 3% for Claude 3.5 Sonnet, or from 70.2% to 40% for Qwen2.5.

Agent communication protocols are becoming critical infrastructure for large language model (LLM) systems that must use tools, coordinate with other agents, and operate across heterogeneous environments. This work presents a human-inspired perspective on this emerging landscape by organizing agent communication into three layers: communication, syntactic, and semantic. Under this framework, we systematically analyze 18 representative protocols and compare how they support reliable transport, structured interaction, and meaning-level coordination. Our analysis shows a clear imbalance in current protocol design. Most protocols provide increasingly mature support for transport, streaming, schema definition, and lifecycle management, but offer limited protocol-level mechanisms for clarification, context alignment, and verification. As a result, semantic responsibilities are often pushed into prompts, wrappers, or application-specific orchestration logic, creating hidden interoperability and maintenance costs. To make this gap actionable, we further identify major forms of technical debt in today's protocol ecosystem and distill practical guidance for selecting protocols under different deployment settings. We conclude by outlining a research agenda for interoperable, secure, and semantically robust agent ecosystems that move beyond message passing toward shared understanding.

Language models of code (LMs) work well when the surrounding code in the vicinity of generation provides sufficient context. This is not true when it becomes necessary to use types or functionality defined in another module or library, especially those not seen during training. LMs suffer from limited awareness of such global context and end up hallucinating, e.g., using types defined in other files incorrectly. Recent work tries to overcome this issue by retrieving global information to augment the local context. However, this bloats the prompt or requires architecture modifications and additional training. Integrated development environments (IDEs) assist developers by bringing the global context at their fingertips using static analysis. We extend this assistance, enjoyed by developers, to the LMs. We propose a notion of monitors that use static analysis in the background to guide the decoding. Unlike a priori retrieval, static analysis is invoked iteratively during the entire decoding process, providing the most relevant suggestions on demand. We demonstrate the usefulness of our proposal by monitoring for type-consistent use of identifiers whenever an LM generates code for object dereference. To evaluate our approach, we curate PragmaticCode, a dataset of open-source projects with their development environments. On models of varying parameter scale, we show that monitor-guided decoding consistently improves the ability of an LM to not only generate identifiers that match the ground truth but also improves compilation rates and agreement with ground truth. We find that LMs with fewer parameters, when guided with our monitor, can outperform larger LMs. With monitor-guided decoding, SantaCoder-1.1B achieves better compilation rate and next-identifier match than the much larger text-davinci-003 model. The datasets and code will be released at https://aka.ms/monitors4codegen .

Large Language Models (LLMs) have shown impressive capabilities in downstream software engineering tasks such as Automated Program Repair (APR). In particular, there has been a lot of research on repository-level issue-resolution benchmarks such as SWE-Bench. Although there has been significant progress on this topic, we notice that in the process of solving such issues, existing agentic systems tend to hyper-localize on immediately suspicious lines of code and fix them in isolation, without a deeper understanding of the issue semantics, code semantics, or execution semantics. Consequently, many existing systems generate patches that overfit to the user issue, even when a more general fix is preferable. To address this limitation, we introduce SemAgent, a novel workflow-based procedure that leverages issue, code, and execution semantics to generate patches that are complete - identifying and fixing all lines relevant to the issue. We achieve this through a novel pipeline that (a) leverages execution semantics to retrieve relevant context, (b) comprehends issue-semantics via generalized abstraction, (c) isolates code-semantics within the context of this abstraction, and (d) leverages this understanding in a two-stage architecture: a repair stage that proposes fine-grained fixes, followed by a reviewer stage that filters relevant fixes based on the inferred issue-semantics. Our evaluations show that our methodology achieves a solve rate of 44.66% on the SWEBench-Lite benchmark beating all other workflow-based approaches, and an absolute improvement of 7.66% compared to our baseline, which lacks such deep semantic understanding. We note that our approach performs particularly well on issues requiring multi-line reasoning (and editing) and edge-case handling, suggesting that incorporating issue and code semantics into APR pipelines can lead to robust and semantically consistent repairs.

Retrieval-augmented Generation (RAG) extends large language models (LLMs) with external knowledge but faces key challenges: restricted effective context length and redundancy in retrieved documents. Pure compression-based approaches reduce input size but often discard fine-grained details essential for factual accuracy. We propose SARA, a unified RAG framework that balances local precision and global knowledge coverage under tight context budgets. SARA combines natural-language text snippets with semantic compression vectors to jointly enhance context efficiency and answer correctness. It represents contexts at two complementary levels: 1) fine-grained natural-language spans that preserve critical entities and numerical values, and 2) compact, interpretable vectors that summarize high-level semantics. An iterative evidence-selection module employs the compression vectors for dynamic reranking of contexts. Across 9 datasets and 5 open-source LLMs spanning 3 model families (Mistral, Llama, and Gemma), SARA consistently improves answer relevance (+17.71), answer correctness (+13.72), and semantic similarity (+15.53), demonstrating the importance of integrating textual and compressed representations for robust, context-efficient RAG.

Current long-context benchmarks primarily focus on retrieval-based tests, requiring Large Language Models (LLMs) to locate specific information within extensive input contexts, such as the needle-in-a-haystack (NIAH) benchmark. Long-context generation refers to the ability of a language model to generate coherent and contextually accurate text that spans across lengthy passages or documents. While recent studies show strong performance on NIAH and other retrieval-based long-context benchmarks, there is a significant lack of benchmarks for evaluating long-context generation capabilities. To bridge this gap and offer a comprehensive assessment, we introduce a synthetic benchmark, LongGenBench, which allows for flexible configurations of customized generation context lengths. LongGenBench advances beyond traditional benchmarks by redesigning the format of questions and necessitating that LLMs respond with a single, cohesive long-context answer. Upon extensive evaluation using LongGenBench, we observe that: (1) both API accessed and open source models exhibit performance degradation in long-context generation scenarios, ranging from 1.2% to 47.1%; (2) different series of LLMs exhibit varying trends of performance degradation, with the Gemini-1.5-Flash model showing the least degradation among API accessed models, and the Qwen2 series exhibiting the least degradation in LongGenBench among open source models.

Managing extensive context remains a critical bottleneck for Large Language Models (LLMs), particularly in applications like long-document question answering and autonomous agents where lengthy inputs incur high computational costs and introduce noise. Existing compression techniques often disrupt local coherence through discrete token removal or rely on implicit latent encoding that suffers from positional bias and incompatibility with closed-source APIs. To address these limitations, we introduce the EDU-based Context Compressor, a novel explicit compression framework designed to preserve both global structure and fine-grained details. Our approach reformulates context compression as a structure-then-select process. First, our LingoEDU transforms linear text into a structural relation tree of Elementary Discourse Units (EDUs) which are anchored strictly to source indices to eliminate hallucination. Second, a lightweight ranking module selects query-relevant sub-trees for linearization. To rigorously evaluate structural understanding, we release StructBench, a manually annotated dataset of 248 diverse documents. Empirical results demonstrate that our method achieves state-of-the-art structural prediction accuracy and significantly outperforms frontier LLMs while reducing costs. Furthermore, our structure-aware compression substantially enhances performance across downstream tasks ranging from long-context tasks to complex Deep Search scenarios.

Establishing whether language models can use contextual information in a human-plausible way is important to ensure their safe adoption in real-world settings. However, the questions of when and which parts of the context affect model generations are typically tackled separately, and current plausibility evaluations are practically limited to a handful of artificial benchmarks. To address this, we introduce Plausibility Evaluation of Context Reliance (PECoRe), an end-to-end interpretability framework designed to quantify context usage in language models' generations. Our approach leverages model internals to (i) contrastively identify context-sensitive target tokens in generated texts and (ii) link them to contextual cues justifying their prediction. We use PECoRe to quantify the plausibility of context-aware machine translation models, comparing model rationales with human annotations across several discourse-level phenomena. Finally, we apply our method to unannotated generations to identify context-mediated predictions and highlight instances of (im)plausible context usage in model translations.

Data availability limits the scope of any given task. In machine translation, historical models were incapable of handling longer contexts, so the lack of document-level datasets was less noticeable. Now, despite the emergence of long-sequence methods, we remain within a sentence-level paradigm and without data to adequately approach context-aware machine translation. Most large-scale datasets have been processed through a pipeline that discards document-level metadata. In this work, we reconstruct document-level information for three (ParaCrawl, News Commentary, and Europarl) large datasets in German, French, Spanish, Italian, Polish, and Portuguese (paired with English). We then introduce a document-level filtering technique as an alternative to traditional bitext filtering. We present this filtering with analysis to show that this method prefers context-consistent translations rather than those that may have been sentence-level machine translated. Last we train models on these longer contexts and demonstrate improvement in document-level translation without degradation of sentence-level translation. We release our dataset, ParaDocs, and resulting models as a resource to the community.

While language models (LMs) have proven remarkably adept at generating code, many programs are challenging for LMs to generate using their parametric knowledge alone. Providing external contexts such as library documentation can facilitate generating accurate and functional code. Despite the success of retrieval-augmented generation (RAG) in various text-oriented tasks, its potential for improving code generation remains under-explored. In this work, we conduct a systematic, large-scale analysis by asking: in what scenarios can retrieval benefit code generation models? and what challenges remain? We first curate a comprehensive evaluation benchmark, CodeRAG-Bench, encompassing three categories of code generation tasks, including basic programming, open-domain, and repository-level problems. We aggregate documents from five sources for models to retrieve contexts: competition solutions, online tutorials, library documentation, StackOverflow posts, and GitHub repositories. We examine top-performing models on CodeRAG-Bench by providing contexts retrieved from one or multiple sources. While notable gains are made in final code generation by retrieving high-quality contexts across various settings, our analysis reveals room for improvement -- current retrievers still struggle to fetch useful contexts especially with limited lexical overlap, and generators fail to improve with limited context lengths or abilities to integrate additional contexts. We hope CodeRAG-Bench serves as an effective testbed to encourage further development of advanced code-oriented RAG methods.

Current clinical agent built on small LLMs, such as TxAgent suffer from a Context Utilization Failure, where models successfully retrieve biomedical evidence due to supervised finetuning but fail to ground their diagnosis in that information. In this work, we propose the Executor-Analyst Framework, a modular architecture that decouples the syntactic precision of tool execution from the semantic robustness of clinical reasoning. By orchestrating specialized TxAgents (Executors) with long-context foundation models (Analysts), we mitigate the reasoning deficits observed in monolithic models. Beyond simple modularity, we demonstrate that a Stratified Ensemble strategy significantly outperforms global pooling by preserving evidentiary diversity, effectively addressing the information bottleneck. Furthermore, our stress tests reveal critical scaling insights: (1) a Context-Performance Paradox, where extending reasoning contexts beyond 12k tokens introduces noise that degrades accuracy; and (2) the Curse of Dimensionality in action spaces, where expanding toolsets necessitates hierarchical retrieval strategies. Crucially, our approach underscores the potential of training-free architectural engineering, achieving state-of-the-art performance on CURE-Bench without the need for expensive end-to-end finetuning. This provides a scalable, agile foundation for the next generation of trustworthy AI-driven therapeutics. Code has been released on https://github.com/June01/CureAgent.

When reading long-form text, human cognition is complex and structurized. While large language models (LLMs) process input contexts through a causal and sequential perspective, this approach can potentially limit their ability to handle intricate and complex inputs effectively. To enhance LLM's cognition capability, this paper presents a novel concept of context structurization. Specifically, we transform the plain, unordered contextual sentences into well-ordered and hierarchically structurized elements. By doing so, LLMs can better grasp intricate and extended contexts through precise attention and information-seeking along the organized structures. Extensive evaluations are conducted across various model architectures and sizes (including a series of auto-regressive LLMs as well as BERT-like masking models) on a diverse set of NLP tasks (e.g., context-based question-answering, exhaustive hallucination evaluation, and passage-level dense retrieval). Empirical results show consistent and significant performance gains afforded by a single-round structurization. In particular, we boost the open-sourced LLaMA2-70B model to achieve comparable performance against GPT-3.5-Turbo as the hallucination evaluator. Besides, we show the feasibility of distilling advanced LLMs' language processing abilities to a smaller yet effective StruXGPT-7B to execute structurization, addressing the practicality of our approach. Code is available at https://github.com/alibaba/struxgpt.

Information seeking is a fundamental requirement for humans. However, existing LLM agents rely heavily on open-web search, which exposes two fundamental weaknesses: online content is noisy and unreliable, and many real-world tasks require precise, domain-specific knowledge unavailable from the web. The emergence of the Model Context Protocol (MCP) now allows agents to interface with thousands of specialized tools, seemingly resolving this limitation. Yet it remains unclear whether agents can effectively leverage such tools -- and more importantly, whether they can integrate them with general-purpose search to solve complex tasks. Therefore, we introduce InfoMosaic-Bench, the first benchmark dedicated to multi-source information seeking in tool-augmented agents. Covering six representative domains (medicine, finance, maps, video, web, and multi-domain integration), InfoMosaic-Bench requires agents to combine general-purpose search with domain-specific tools. Tasks are synthesized with InfoMosaic-Flow, a scalable pipeline that grounds task conditions in verified tool outputs, enforces cross-source dependencies, and filters out shortcut cases solvable by trivial lookup. This design guarantees both reliability and non-triviality. Experiments with 14 state-of-the-art LLM agents reveal three findings: (i) web information alone is insufficient, with GPT-5 achieving only 38.2% accuracy and 67.5% pass rate; (ii) domain tools provide selective but inconsistent benefits, improving some domains while degrading others; and (iii) 22.4% of failures arise from incorrect tool usage or selection, highlighting that current LLMs still struggle with even basic tool handling.

Recent agentic search systems have made substantial progress by emphasising deep, multi-step reasoning. However, this focus often overlooks the challenges of wide-scale information synthesis, where agents must aggregate large volumes of heterogeneous evidence across many sources. As a result, most existing large language model agent systems face severe limitations in data-intensive settings, including context saturation, cascading error propagation, and high end-to-end latency. To address these challenges, we present \framework, a hierarchical framework based on principle of near-decomposability, containing a strategic Host, multiple Managers and parallel Workers. By leveraging aggregation and reflection mechanisms at the Manager layer, our framework enforces strict context isolation to prevent saturation and error propagation. Simultaneously, the parallelism in worker layer accelerates the speed of overall task execution, mitigating the significant latency. Our evaluation on two complementary benchmarks demonstrates both efficiency ( 3-5 times speed-up) and effectiveness, achieving a 8.4% success rate on WideSearch-en and 52.9% accuracy on BrowseComp-zh. The code is released at https://github.com/agent-on-the-fly/InfoSeeker

On-the-fly retrieval of relevant knowledge has proven an essential element of reliable systems for tasks such as open-domain question answering and fact verification. However, because retrieval systems are not perfect, generation models are required to generate outputs given partially or entirely irrelevant passages. This can cause over- or under-reliance on context, and result in problems in the generated output such as hallucinations. To alleviate these problems, we propose FILCO, a method that improves the quality of the context provided to the generator by (1) identifying useful context based on lexical and information-theoretic approaches, and (2) training context filtering models that can filter retrieved contexts at test time. We experiment on six knowledge-intensive tasks with FLAN-T5 and LLaMa2, and demonstrate that our method outperforms existing approaches on extractive question answering (QA), complex multi-hop and long-form QA, fact verification, and dialog generation tasks. FILCO effectively improves the quality of context, whether or not it supports the canonical output.

Byte-based machine translation systems have shown significant potential in massively multilingual settings. Unicode encoding, which maps each character to specific byte(s), eliminates the emergence of unknown words, even in new languages. This avoids out-of-vocabulary risk in multilingual translation and enables broad language scalability. However, byte-level tokenization results in sequences that are hard to interpret due to limited semantic information per byte. Local contextualization has proven effective in assigning initial semantics to tokens, improving sentence comprehension. Nevertheless, variations in encoding rules across languages necessitate an adaptive approach for effective contextualization. To this end, we propose Mixture of Contextualization Experts (MoCE), adaptively selecting and mixing attention heads, which are treated as contextualization experts. This enhances the flexibility of contextualization scales and allows models to search for better contextualization combinations. Experiment results show that our method outperforms existing methods without extensive manual adjustment of hyper-parameters and surpasses subword-based models with fewer parameters in Ted-59 dataset. Our code is available at https://github.com/ictnlp/MoCE.

We propose a new long-context financial benchmark, FailSafeQA, designed to test the robustness and context-awareness of LLMs against six variations in human-interface interactions in LLM-based query-answer systems within finance. We concentrate on two case studies: Query Failure and Context Failure. In the Query Failure scenario, we perturb the original query to vary in domain expertise, completeness, and linguistic accuracy. In the Context Failure case, we simulate the uploads of degraded, irrelevant, and empty documents. We employ the LLM-as-a-Judge methodology with Qwen2.5-72B-Instruct and use fine-grained rating criteria to define and calculate Robustness, Context Grounding, and Compliance scores for 24 off-the-shelf models. The results suggest that although some models excel at mitigating input perturbations, they must balance robust answering with the ability to refrain from hallucinating. Notably, Palmyra-Fin-128k-Instruct, recognized as the most compliant model, maintained strong baseline performance but encountered challenges in sustaining robust predictions in 17% of test cases. On the other hand, the most robust model, OpenAI o3-mini, fabricated information in 41% of tested cases. The results demonstrate that even high-performing models have significant room for improvement and highlight the role of FailSafeQA as a tool for developing LLMs optimized for dependability in financial applications. The dataset is available at: https://huggingface.co/datasets/Writer/FailSafeQA

The emergence of open data portals necessitates more attention to protecting sensitive data before datasets get published and exchanged. While an abundance of methods for suppressing sensitive data exist, the conceptualization of sensitive data and methods to detect it, focus particularly on personal data that, if disclosed, may be harmful or violate privacy. We observe the need for refining and broadening our definitions of sensitive data, and argue that the sensitivity of data depends on its context. Based on this definition, we introduce two mechanisms for contextual sensitive data detection that consider the broader context of a dataset at hand. First, we introduce type contextualization, which first detects the semantic type of particular data values, then considers the overall context of the data values within the dataset or document. Second, we introduce domain contextualization which determines sensitivity of a given dataset in the broader context based on the retrieval of relevant rules from documents that specify data sensitivity (e.g., data topic and geographic origin). Experiments with these mechanisms, assisted by large language models (LLMs), confirm that: 1) type-contextualization significantly reduces the number of false positives for type-based sensitive data detection and reaches a recall of 94% compared to 63% with commercial tools, and 2) domain-contextualization leveraging sensitivity rule retrieval is effective for context-grounded sensitive data detection in non-standard data domains such as humanitarian datasets. Evaluation with humanitarian data experts also reveals that context-grounded LLM explanations provide useful guidance in manual data auditing processes, improving consistency. We open-source mechanisms and annotated datasets for contextual sensitive data detection at https://github.com/trl-lab/sensitive-data-detection.

Previous work has showcased the intriguing capability of large language models (LLMs) in retrieving facts and processing context knowledge. However, only limited research exists on the layer-wise capability of LLMs to encode knowledge, which challenges our understanding of their internal mechanisms. In this paper, we devote the first attempt to investigate the layer-wise capability of LLMs through probing tasks. We leverage the powerful generative capability of ChatGPT to construct probing datasets, providing diverse and coherent evidence corresponding to various facts. We employ mathcal V-usable information as the validation metric to better reflect the capability in encoding context knowledge across different layers. Our experiments on conflicting and newly acquired knowledge show that LLMs: (1) prefer to encode more context knowledge in the upper layers; (2) primarily encode context knowledge within knowledge-related entity tokens at lower layers while progressively expanding more knowledge within other tokens at upper layers; and (3) gradually forget the earlier context knowledge retained within the intermediate layers when provided with irrelevant evidence. Code is publicly available at https://github.com/Jometeorie/probing_llama.

Language-model (LM) harnesses enable LMs to operate effectively over long contexts using additional compute. However, existing long-context evaluations are insufficient for distinguishing modern harnesses, reflected by saturated accuracy across harnesses and largely similar evaluation costs. In this paper, we introduce a benchmark for evaluating both the effectiveness and efficiency of long-context harnesses. Our tasks require diverse retrieval strategies, including lexical search and semantic matching, together with strategic and adaptive reasoning over global and local context. Much of the context is semantically relevant but only a small subset is useful at each step, creating both a challenging search problem and different accuracy--cost tradeoffs across processing strategies. For example, one task requires identifying every person satisfying several conditions using evidence scattered across documents; strategically checking the most selective condition first can narrow the search before verifying the remaining conditions. We evaluate multiple families of frontier language models with four state-of-the-art harnesses. Our benchmarks remain challenging even for strong model--harness combinations: the best reaches 68\% macro-average accuracy across four evaluation suites. More importantly, we find that the same underlying model can exhibit markedly different efficiency under different harnesses. Our results establish efficiency as an important axis for long-context evaluation and provide a testbed for developing harnesses that process context strategically rather than exhaustively.

The Model Context Protocol (MCP) enables large language models to invoke external tools through natural-language descriptions, forming the foundation of many AI agent applications. However, MCP does not enforce consistency between documented tool behavior and actual code execution, even though MCP Servers often run with broad system privileges. This gap introduces a largely unexplored security risk. We study how mismatches between externally presented tool descriptions and underlying implementations systematically shape the mental models and decision-making behavior of intelligent agents. Specifically, we present the first large-scale study of description-code inconsistency in the MCP ecosystem. We design an automated static analysis framework and apply it to 10,240 real-world MCP Servers across 36 categories. Our results show that while most servers are highly consistent, approximately 13% exhibit substantial mismatches that can enable undocumented privileged operations, hidden state mutations, or unauthorized financial actions. We further observe systematic differences across application categories, popularity levels, and MCP marketplaces. Our findings demonstrate that description-code inconsistency is a concrete and prevalent attack surface in MCP-based AI agents, and motivate the need for systematic auditing and stronger transparency guarantees in future agent ecosystems.

Recent advancements in large language models (LLM) capable of processing extremely long texts highlight the need for a dedicated evaluation benchmark to assess their long-context capabilities. However, existing methods, like the needle-in-a-haystack test, do not effectively assess whether these models fully utilize contextual information, raising concerns about the reliability of current evaluation techniques. To thoroughly examine the effectiveness of existing benchmarks, we introduce a new metric called information coverage (IC), which quantifies the proportion of the input context necessary for answering queries. Our findings indicate that current benchmarks exhibit low IC; although the input context may be extensive, the actual usable context is often limited. To address this, we present ETHIC, a novel benchmark designed to assess LLMs' ability to leverage the entire context. Our benchmark comprises 2,648 test instances spanning four long-context tasks with high IC scores in the domains of books, debates, medicine, and law. Our evaluations reveal significant performance drops in contemporary LLMs, highlighting a critical challenge in managing long contexts. Our benchmark is available at https://github.com/dmis-lab/ETHIC.

Large Language Models (LLMs) have demonstrated exceptional capabilities across diverse tasks. However, their deployment in long context scenarios remains hindered by computational inefficiency and information redundancy. Context compression methods address these challenges by significantly reducing input length and eliminating redundancy. We propose COMI, a coarse-to-fine adaptive context compression framework that jointly optimizes for semantic relevance and diversity under high compression rates. We introduce Marginal Information Gain (MIG), a metric defined as the relevance of a unit to the input query minus its semantic redundancy with other units, guiding the compression process to prioritize information that is both relevant and low redundant. The framework operates in two stages: (1) Coarse-Grained Group Reallocation, where the context is partitioned into groups and dynamically assigned compression rates based on inter-group MIG, ensuring compression budgets align with information value distribution; and (2) Fine-Grained Token Merging, where tokens within each group are fused via an intra-group MIG-based weighting mechanism, thereby preserving key semantics while avoiding the accumulation of redundancy. Extensive experiments across question-answering (e.g., NaturalQuestions, 2WikiMQA, HotpotQA and NarrativeQA), summarization (e.g., MultiNews) with various backbones (e.g., LLaMA-2-7B, Qwen2-7B) show that COMI outperforms existing baselines by a large margin, e.g., approximately 25-point Exact Match (EM) improvement under 32x compression constraint with Qwen2-7B on NaturalQuestions.

The Model Context Protocol (MCP) is rapidly emerging as a pivotal open standard, designed to enhance agent-tool integration and interoperability, and is positioned to unlock a new era of powerful, interconnected, and genuinely utilitarian agentic AI. However, despite MCP's growing adoption, existing benchmarks often fail to capture real-world agent performance within this new paradigm, leading to a distorted perception of their true operational value and an inability to reliably differentiate proficiencies. To bridge this critical evaluation gap, we introduce MCP-AgentBench -- a comprehensive benchmark specifically engineered to rigorously assess language agent capabilities in MCP-mediated tool interactions. Core contributions of MCP-AgentBench include: the establishment of a robust MCP testbed comprising 33 operational servers with 188 distinct tools; the development of a benchmark featuring 600 systematically designed queries distributed across 6 distinct categories of varying interaction complexity; and the introduction of MCP-Eval, a novel outcome-oriented evaluation methodology prioritizing real-world task success. Through extensive empirical evaluation of leading language agents, we provide foundational insights. MCP-AgentBench aims to equip the research community with a standardized and reliable framework to build, validate, and advance agents capable of fully leveraging MCP's transformative benefits, thereby accelerating progress toward truly capable and interoperable AI systems.

Although Foundation Models (FMs), such as GPT-4, are increasingly used in domains like finance and software engineering, reliance on textual interfaces limits these models' real-world interaction. To address this, FM providers introduced tool calling-triggering a proliferation of frameworks with distinct tool interfaces. In late 2024, Anthropic introduced the Model Context Protocol (MCP) to standardize this tool ecosystem, which has become the de facto standard with over eight million weekly SDK downloads. Despite its adoption, MCP's AI-driven, non-deterministic control flow introduces new risks to sustainability, security, and maintainability, warranting closer examination. Towards this end, we present the first large-scale empirical study of MCP servers. Using state-of-the-art health metrics and a hybrid analysis pipeline, combining a general-purpose static analysis tool with an MCP-specific scanner, we evaluate 1,899 open-source MCP servers to assess their health, security, and maintainability. Despite MCP servers demonstrating strong health metrics, we identify eight distinct vulnerabilities - only three overlapping with traditional software vulnerabilities. Additionally, 7.2% of servers contain general vulnerabilities and 5.5% exhibit MCP-specific tool poisoning. Regarding maintainability, while 66% exhibit code smells, 14.4% contain nine bug patterns overlapping with traditional open-source software projects. These findings highlight the need for MCP-specific vulnerability detection techniques while reaffirming the value of traditional analysis and refactoring practices.

We introduce SWE-PRBench, a benchmark of 350 pull requests with human-annotated ground truth for evaluating AI code review quality. Evaluated against an LLM-as-judge framework validated at kappa=0.75, 8 frontier models detect only 15-31% of human-flagged issues on the diff-only configuration, demonstrating that AI code review remains far below human expert performance despite strong results on code generation benchmarks. Pull requests are drawn from active open-source repositories, filtered from 700 candidates using a Repository Quality Score, and evaluated under three frozen context configurations: diff only (config_A), diff with file content (config_B), and full context (config_C), enabling systematic ablation of context provision strategies. All 8 models degrade monotonically from config_A to config_C, even when context is provided via structured semantic layers including AST-extracted function context and import graph resolution. The dominant mechanism is a collapse of Type2_Contextual issue detection at config_B, consistent with attention dilution in long contexts: a structured 2,000-token diff-with-summary prompt outperforms a 2,500-token full-context prompt enriched with execution context, behaviour mapping, and test signatures across all 8 models. The top four models are statistically indistinguishable (mean score 0.147-0.153) while a clear tier gap separates them from the remaining four (mean score <= 0.113). Dataset, contexts, annotations, and evaluation harness are released publicly.

Orchestrated multi-agent systems represent the next stage in the evolution of artificial intelligence, where autonomous agents collaborate through structured coordination and communication to achieve complex, shared objectives. This paper consolidates and formalizes the technical composition of such systems, presenting a unified architectural framework that integrates planning, policy enforcement, state management, and quality operations into a coherent orchestration layer. Another primary contribution of this work is the in-depth technical delineation of two complementary communication protocols - the Model Context Protocol, which standardizes how agents access external tools and contextual data, and the Agent2Agent protocol, which governs peer coordination, negotiation, and delegation. Together, these protocols establish an interoperable communication substrate that enables scalable, auditable, and policy-compliant reasoning across distributed agent collectives. Beyond protocol design, the paper details how orchestration logic, governance frameworks, and observability mechanisms collectively sustain system coherence, transparency, and accountability. By synthesizing these elements into a cohesive technical blueprint, this paper provides comprehensive treatments of orchestrated multi-agent systems - bridging conceptual architectures with implementation-ready design principles for enterprise-scale AI ecosystems.

Reliable responses from large language models (LLMs) require adherence to user instructions and retrieved information. While alignment techniques help LLMs align with human intentions and values, improving context-faithfulness through alignment remains underexplored. To address this, we propose Context-DPO, the first alignment method specifically designed to enhance LLMs' context-faithfulness. We introduce ConFiQA, a benchmark that simulates Retrieval-Augmented Generation (RAG) scenarios with knowledge conflicts to evaluate context-faithfulness. By leveraging faithful and stubborn responses to questions with provided context from ConFiQA, our Context-DPO aligns LLMs through direct preference optimization. Extensive experiments demonstrate that our Context-DPO significantly improves context-faithfulness, achieving 35% to 280% improvements on popular open-source models. Further analysis demonstrates that Context-DPO preserves LLMs' generative capabilities while providing interpretable insights into context utilization. Our code and data are released at https://github.com/byronBBL/Context-DPO