Model Context Protocol

Industrial asset operations workflows are latency-sensitive because a single user query may require coordination over sensor data, work orders, failure modes, forecasting tools, and domain-specific agents. We evaluate this problem on AssetOpsBench (AOB), an industrial agent benchmark whose plan-execute pipeline exposes repeated overhead from tool discovery, LLM planning, MCP tool execution, and final summarization. Existing LLM caching techniques such as KV-cache reuse and embedding-based semantic caching were designed for chatbot serving and break down when output validity depends on time, asset, or sensor parameters. We propose two complementary optimization layers for AOB plan-execute pipelines: a temporal semantic cache and a set of MCP workflow optimizations combining disk-backed tool-discovery caching and dependency-aware parallel step execution. MCP workflow optimizations corresponded to a 1.67x speedup and reduced median end-to-end latency by about 40.0% while the temporal-cache benchmark achieved a median of 30.6x speedup on cache hits. Beyond the speedup, our results expose a concrete failure mode of pure semantic caching for parameter-rich industrial queries, providing a critical analysis of how caching choices interact with evaluation correctness in MCP-backed agent benchmarks.

Large language models increasingly operate as autonomous agents that select and invoke tools from large registries. We identify a critical gap: when unauthorized tools are visible in an agent's context, models select them in adversarial scenarios -- even when explicitly instructed otherwise. We propose a governed MCP proxy that enforces attribute-based access control (ABAC) at two points: tool discovery, where unauthorized tools are removed from the model's context window, and tool invocation, where a second check blocks any unauthorized call. Across three models (Qwen 2.5 7B, Llama 3.1 8B, Claude Haiku 3.5) and 150 adversarial tasks spanning four attack categories, our proxy reduces unauthorized invocation rate (UIR) to 0% while adding under 50ms median latency. Prompt-based restrictions reduce UIR by only 11--18 percentage points, leaving substantial residual risk. Our results show that architectural enforcement -- not prompting -- is necessary for reliable tool access control in deployed agentic systems.

We present the Agentic AI Detection and Response (ADR) system, the first large-scale, production-proven enterprise framework for securing AI agents operating through the Model Context Protocol (MCP). We identify three persistent challenges in this domain: (1) limited observability -- existing Endpoint Detection and Response (EDR) tools see file writes but not the agent reasoning, prompts, or causal chains linking intent to execution; (2) insufficient robustness -- static defenses constrained by pre-defined rules fail to generalize across diverse attack techniques and enterprise contexts; and (3) high detection costs -- LLM-based inference is prohibitively expensive at scale. ADR addresses these challenges via three components: the ADR Sensor for high-fidelity agentic telemetry, the ADR Explorer for systematic pre-deployment red teaming and hard-example generation, and the ADR Detector for scalable, two-tier online detection combining fast triage with context-aware reasoning. Deployed at Uber for over ten months, ADR has sustained reliable detection in production with growing adoption reaching over 7,200 unique hosts and processing over 10,000 agent sessions daily, uncovering hundreds of credential exposures across 26 categories and enabling a shift-left prevention layer (97.2% precision, 206 detected credentials). To validate the approach and enable community adoption, we introduce ADR-Bench (302 tasks, 17 techniques, 133 MCP servers), where ADR achieves zero false positives while detecting 67% of attacks -- outperforming three state-of-the-art baselines (ALRPHFS, GuardAgent, LlamaFirewall) by 2--4x in F1-score. On AgentDojo (public prompt injection benchmark), ADR detects all attacks with only three false alarms out of 93 tasks.

We introduce ColPackAgent, an agent framework that autonomously runs Monte Carlo simulations of colloidal packing through a Model Context Protocol (MCP) tool server and an agent skill, whether as a standalone agent or inside an existing agent system. By harnessing the MCP server and agent skill, ColPackAgent executes a structured workflow for colloidal packing simulations, which are central to studies of phase behavior, self-assembly, and materials design. Without dedicated simulation tools and workflow instructions, general-purpose Large Language Model (LLM) agents tend to describe such workflows rather than execute them reliably. The MCP server exposes a custom-built colpack Python package that wraps HOOMD-blue hard-particle Monte Carlo, and the skill encodes a four-stage workflow contract. ColPackAgent can carry out the workflow interactively with human feedback, autonomously from an end-to-end prompt, or as autoresearch following a provided program file. We demonstrate the system in different modes with several colloidal packing simulation examples such as cube particles in 3D, a binary system of disks and capsules in 2D, and the 2D hard-disk freezing transition using autoresearch. We also compare model performance on this workflow across a panel of LLMs with 17 stage-specific prompts. This benchmark provides a stage-level check of how reliably different models follow the setup, planning, and analysis workflow. Together, these results show that pairing a domain Python package with MCP tools and a portable agent skill provides a practical route for turning a simulation toolkit into an agent-assisted research workflow.

Self-driving laboratories (SDLs) are attracting increasing attention as a means of accelerating scientific discovery; however, developing SDL software remains technically demanding. To improve accessibility, orchestration software frameworks have been proposed to coordinate SDL components, but many existing frameworks are primarily designed for human interaction and lack standardized interfaces for direct integration with AI agents. In this work, we propose an SDL software architecture based on the Model Context Protocol (MCP), in which all SDL functionalities are exposed through MCP servers. Following this design principle, we introduce NIMO Controller, an MCP-based SDL orchestrator that integrates the experimental planning software NIMO. It provides a visual programming interface automatically generated through MCP-based tool discovery, allowing human users to design experimental workflows without writing code. The same MCP backend is also accessible to AI agents, providing a unified interface through which both human users and AI agents can interact with SDL components. AI agents can invoke MCP tools directly or generate NIMO workflows from natural language instructions. We evaluated the agentic workflow generation performance of various LLMs and conducted a user study using a color-matching SDL.

Recent advances in Large Language Models (LLMs) have enabled agentic systems for complex, multi-step tasks; cybersecurity is emerging as a prominent application. To evaluate such agents, researchers widely adopt Capture The Flag (CTF) benchmarks. However, current CTF benchmarks reuse existing challenges, which exposes them to data contamination and potential cheating. Notably, we confirmed these issues in practice by integrating web search tools into an existing agent. To address these limitations, we present CTFusion, a streaming evaluation framework built on Live CTFs. To achieve this, CTFusion preserves per-agent independence under a single team account and reduces competition impact by forwarding only the first correct flag per challenge. Moreover, we implement CTFusion as a Model Context Protocol (MCP) server on the widely used CTFd platform, which offers broad applicability to diverse CTF events and agent types. Through experiments with three LLMs, two agents, and five Live CTFs, we demonstrate that existing CTF benchmarks can be unreliable in assessing LLM-based agents, while CTFusion can serve as a robust solution for evaluating cybersecurity agents. We release CTFusion as open source to foster future research in this area.

As Model Context Protocol adoption grows, securing tool invocations via meaningful user consent has become a critical challenge, as existing methods, broad always allow toggles or opaque LLM-based decisions, fail to account for dangerous call arguments and often lead to consent fatigue. In this work, we present Conleash, a client-side middleware that enforces boundary-scoped authorization by utilizing a risk lattice to auto-permit safe calls within known boundaries while escalating risks, a policy engine for user-defined invariants, and a refinement loop that converts user decisions into reusable rules. Evaluated on 984 real-world traces, Conleash achieved 98.2% accuracy, caught 99.4% of escalations, and added only 8.2 ms of overhead for policy verification; furthermore, in a user study where N=16, participants significantly preferred Conleash scoped permissions over traditional methods, citing higher trust and reduced prompting.

Current LLM agents are proficient at calling isolated APIs but struggle with the "last mile" of commercial software automation. In real-world scenarios, tools are not independent; they are atomic, interdependent, and prone to environmental noise. We introduce $\textbf{ComplexMCP}$, a benchmark designed to evaluate agents in these rigorous conditions. Built on the Model Context Protocol (MCP), $\textbf{ComplexMCP}$ provides over 300 meticulously tested tools derived from 7 stateful sandboxes, ranging from office suites to financial systems. Unlike existing datasets, our benchmark utilizes a seed-driven architecture to simulate dynamic environment states and unpredictable API failures, ensuring a deterministic yet diverse evaluation. We evaluate various LLMs across full-context and RAG paradigms, revealing a stark performance gap: even top-tier models fail to exceed a 60% success rate, far trailing human performance 90%. Granular trajectory analysis identifies three fundamental bottlenecks: (1) $\textbf{tool retrieval saturation}$ as action spaces scale; (2) $\textbf{over-confidence}$, where agents skip essential environment verifications; and (3) $\textbf{strategic defeatism}$, a tendency to rationalize failure rather than pursuing recovery. These findings underscore the insufficiency of current agents for interdependent workflows, positioning $\textbf{ComplexMCP}$ as a critical testbed for the next generation of resilient autonomous systems.

The Model Context Protocol (MCP) has become a widely adopted interface for LLM agents to invoke external tools, yet learned monitoring of MCP tool-call traffic remains underexplored. In this article, the proposed detector is presented as an attack detection framework for MCP tool-call traffic that encodes each agent session as a graph (tool calls as nodes, sequential and data-flow links as edges), enriches nodes with sentence-embedding features over arguments and responses, and classifies sessions as benign or attacked. Three GNN architectures (GAT, GCN, GraphSAGE), a no-graph MLP, and classical baselines (XGBoost, random forest, logistic regression, linear SVM) are evaluated, with the full architecture comparison conducted on RAS-Eval (task-stratified splits) and GraphSAGE retained as the GNN baseline on ATBench and a combined-source variant (both label-stratified). Three findings emerge. First, content-level features are essential: metadata-only detection plateaus around an AUROC of 0.64 regardless of architecture, while content embeddings push the AUROC above 0.89. Second, naive random-split evaluation inflates AUROC by up to 26 percentage points relative to task-disjoint splits, a memorization confound that prior agent-detection work has not addressed. Third, the detection signal resides primarily in the SBERT content embeddings: an AUROC of 0.975 was reached by tree ensembles on pooled embeddings, performing, for the most part, better than the neural architectures in the primary RAS-Eval setting including GNNs (0.917) and the MLP (0.896), and self-supervised pre-training does not deliver a label-efficiency advantage on this task.

In this paper, we describe early work on a specification inference tool for the Move Prover that combines a weakest-precondition (WP) analysis over Move bytecode with an agentic coding CLI such as Claude Code. Specification inference reduces the boilerplate of writing specifications in Move: in order to verify a high-level property such as a global state invariant, pre- and post-conditions for the supporting functions typically have to be written by hand, which is tedious. In our setting, a Model Context Protocol (MCP) service exposes the WP analysis and the prover itself to the coding agent. The WP analysis provides a sound, mechanical baseline for inference; the AI is used precisely where WP is weakest -- for loop invariants and high-level idiomatic specifications such as monotonicity, conservation, and structural invariants. The Move Prover serves as the oracle that decides whether the generated specs are valid, and the agent is equipped to generate proof hints and to refine the inferred specification until verification succeeds. The tool has been applied to a corpus of canonical Move code, including code that uses higher-order functions, dynamic dispatch, global state, references, and various forms of loops.

The Model Context Protocol (MCP) has unified the interface between Large Language Models (LLMs) and external tools, yet a fundamental gap remains in how agents conceptualize the environments within which they operate. Current paradigms are bifurcated: Task-level planning often ignores execution-time dynamics, while reactive execution lacks long-horizon foresight. We present MCP-Cosmos, a framework that infuses generative World Models (WM) into the MCP ecosystem to enable predictive task automation. By unifying three disparate technologies, namely MCP, World Model, and Agent, we demonstrate that a "Bring Your Own World Model" (BYOWM) strategy allows agents to simulate state transitions and refine plans in a latent space before execution. We conducted experiments using two strategies, namely ReAct and SPIRAL with 2 planning models and 3 representative world models over 20+ MCP-Bench tasks. We observed improvements in Agent's environment interaction KPI such as tool success rate and tool parameter accuracy. The framework also offers new metrics such as Execution Quality to generate new insights about the effectiveness of world models compared to baseline.

Recent agentic-robotics systems, from Code-asPolicies to modern vision-language-action (VLA) foundation models, presuppose that drivers, SDKs, or ROS-style primitives for the target hardware already exist. Writing those primitives is the dominant engineering cost of bringing up new hardware for agent control. We present Octopus Protocol, a system that collapses that cost to a single shell command. Given only raw OS access and a language-model API key, a coding agent executes a five-stage pipeline--PROBE, IDENTIFY, INTERFACE, SERVE, DEPLOY--to discover connected devices, infer their capabilities, generate a Model Context Protocol (MCP) server with typed tools, and deploy it as a live HTTP endpoint. A persistent daemon then monitors the system, heals broken code, and perceives physical state through the camera tools it generated for itself. Two architectural principles make this work: protocols are prompts, not code, and the coding agent is the runtime. We validate the system on three heterogeneous platforms (PC/WSL, Apple Silicon macOS, Raspberry Pi 4) and on a commercial 6-DOF robotic arm with USB camera feedback. One command onboards the hardware in ~10-15 minutes and exposes up to 30 MCP tools; an MCP-compliant client then performs closed-loop visual-motor control through tools no human wrote.

Large Language Models (LLMs) are increasingly explored as high-level reasoning engines for cyber-physical systems, yet their application to real-time UAV swarm management remains challenging due to heterogeneous interfaces, limited grounding, and the need for long-running closed-loop execution. This paper presents a mission-agnostic, agent-enhanced LLM framework for UAV swarm control, where users express mission objectives in natural language and the system autonomously executes them through grounded, real-time interactions. The proposed architecture combines an LLM-based Agent Core with a Model Context Protocol (MCP) gateway and a Web-of-Drones abstraction based on W3C Web of Things (WoT) standards. By exposing drones, sensors, and services as standardized WoT Things, the framework enables structured tool-based interaction, continuous state observation, and safe actuation without relying on code generation. We evaluate the framework using ArduPilot-based simulation across four swarm missions and six state-of-the-art LLMs. Results show that, despite strong reasoning abilities, current general-purpose LLMs still struggle to achieve reliable execution - even for simple swarm tasks - when operating without explicit grounding and execution support. Task-specific planning tools and runtime guardrails substantially improve robustness, while token consumption alone is not indicative of execution quality or reliability.

Production agent frameworks (OpenAI Function Calling, Anthropic Tool Use, MCP) transmit tool schemas as JSON, a format designed for machine parsing, not for interpretation by language models. For small models (4B-14B), this protocol mismatch accounts for the majority of tool-use failure at production catalog sizes. We present TSCG, a deterministic tool-schema compiler that resolves this mismatch at the API boundary, converting JSON schemas into token-efficient structured text without model access, fine-tuning, or runtime search. TSCG combines eight composable operators with a formal compression bound (>=51% on well-formed schemas). On TSCG-Agentic-Bench (about 19,000 calls, 12 models, 5 scenarios), TSCG restores Phi-4 14B from 0% to 84.4% accuracy at 20 tools (90.3% at 50 tools) and achieves 108-181% accuracy-retained ratio across three models on BFCL. Format-versus-compression decomposition (R^2=0.88 -> 0.03) establishes representation change as the dominant mechanism. Per-operator isolation across three frontier models reveals three distinct operator-response profiles: operator-hungry (Opus 4.7), operator-sensitive (GPT-5.2), and operator-robust (Sonnet 4), providing per-model deployment guidance. Scaling experiments show accuracy advantages persisting on heavy production MCP schemas (+5.0 pp at about 10,500 input tokens) despite saturation on light synthetic catalogs, with 52-57% token savings throughout. The synthetic benchmark generalizes to real MCP schemas within 0.1 accuracy points. TSCG ships as a 1,200-line zero-dependency TypeScript package.

Large language model (LLM) coding agents increasingly operate over repositories, terminals, tests, and execution traces across long software-engineering episodes. Persistent memory is useful, but static vector stores or generic retrieval-augmented generation (RAG) are insufficient for reinforcement-learning (RL) code development, where small details can alter Bellman targets, terminal masks, gradient flow, or validation claims. This paper presents RL Developer Memory, a local-first, Model Context Protocol (MCP)-native developer-memory architecture for RL coding agents. It treats memory selection as a logged contextual decision process: issue_match ranks candidates and records telemetry, issue_feedback maps raw labels to bounded rewards, and issue_record_resolution links verified resolutions to earlier retrieval events. A deterministic ranker remains deployed, while a contextual-bandit residual policy runs in shadow mode and can affect canary behavior only through conservative off-policy-evaluation (OPE) gates. RL/control memories require theory-to-code metadata and review-gated governance. The system is evaluated on a deterministic 200-case benchmark with RL algorithm bugs, hard negatives, review-gated RL/control cases, and low-risk failures. In the same-commit comparison, deterministic control and full shadow/OPE both achieve 80.0% expected-decision accuracy and 100.0% hard-negative suppression; the full configuration adds learning telemetry rather than accuracy gain. Static validation passed 11/11 checks; dynamic integration passed 10/10 cases. The evidence reports limits: active learned-policy deployment and official-client MCP interoperability are unsupported, live full-configuration latency regresses, and 40 residual non-RL failures remain. The contribution is an auditable memory-control architecture with explicit claim boundaries, not a universal coding-agent improvement claim.

Multi-server MCP agents create an information-flow control problem: faithful tool composition can turn individually benign read/write permissions into cross-boundary credential propagation -- a structural side effect of workflow topology, not necessarily malicious model behavior. We present MCPHunt, to our knowledge the first controlled benchmark that isolates non-adversarial, verbatim credential propagation across multi-server MCP trust boundaries, with three methodological contributions: (1) canary-based taint tracking that reduces propagation detection to objective string matching; (2) an environment-controlled coverage design with risky, benign, and hard-negative conditions that validates pipeline soundness and controls for credential-format confounds; (3) CRS stratification that disentangles task-mandated propagation (faithful execution of verbatim-transfer instructions) from policy-violating propagation (credentials included despite the option to redact). Across 3,615 main-benchmark traces from 5 models spanning 147 tasks and 9 mechanism families, policy-violating propagation rates reach 11.5--41.3% across all models. This propagation is pathway-specific (25x cross-mechanism range) and concentrated in browser-mediated data flows; hard-negative controls provide evidence that production-format credentials are not necessary -- prompt-directed cross-boundary data flow is sufficient. A prompt-mitigation study across 3 models reduces policy-violating propagation by up to 97% while preserving 80.5% utility, but effectiveness varies with instruction-following capability -- suggesting that prompt-level defenses alone may not suffice. Code, traces, and labeling pipeline are released under MIT and CC BY 4.0.

Enterprise software engineering is shifting away from deterministic CRUD/REST architectures toward AI-native systems where large language models act as cognitive orchestrators. This transition introduces a critical security tension: probabilistic LLMs weaken classical mechanisms for validation, access control, and formal testing. This paper proposes the design, formal validation, and empirical evaluation of a Semantic Gateway governed by the Model Context Protocol (MCP). The gateway reframes the enterprise API as a semantic surface where tools are dynamically discovered, authorized, and executed based on intent and policy enforcement. The central contribution rests on a paradigm shift: autonomous agents must not be validated as traditional software nor as simple API consumers, but as stochastic state-transition systems whose behavior must be abstracted, fuzzed, and audited through enabled-tool graphs. The architecture introduces a three-layer Zero-Trust security model comprising a pre-inference Semantic Firewall, deterministic Tool-Level RBAC, and out-of-band Cryptographic Human-in-the-Loop approval. Enabledness-Preserving Abstractions (EPAs) and greybox semantic fuzzing--originally developed for blockchain smart contract verification--are adapted to audit agent behavior in enterprise environments. Results demonstrate an 84.2% reduction in incidental code. Across 500,000 multi-turn fuzzing sequences, the methodology achieved a 100% discovery rate of hidden unauthorized state transitions, proving that dynamic formal verification is strictly necessary for secure agentic deployment.

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

The growth of agentic AI has drawn significant attention to function calling Large Language Models (LLMs), which are designed to extend the capabilities of AI-powered system by invoking external functions. Injection and jailbreaking attacks have been extensively explored to showcase the vulnerabilities of LLMs to user prompt manipulation. The expanded capabilities of agentic models introduce further vulnerabilities via their function calling interface. Recent work in LLM security showed that function calling can be abused, leading to data tampering and theft, causing disruptive behavior such as endless loops, or causing LLMs to produce harmful content in the style of jailbreaking attacks. This paper introduces a novel function hijacking attack (FHA) that manipulates the tool selection process of agentic models to force the invocation of an attacker-chosen function. While existing attacks focus on semantic preference of the model for function-calling tasks, we show that FHA is largely agnostic to the context semantics and remains effective across domains and function sets. We demonstrate that FHA generalizes to unseen queries and payload perturbations under a fixed target model, reaching 62.5% to 81.9% ASR on held-out queries across 4 function-calling LLMs (instructed and reasoning models), evaluated on the Berkeley Function Calling Leaderboard (BFCL). We further evaluate the cross-model transferability of FHA, showing that FHA can be transferred to other model sizes and families (11.2-27.6% ASR). Our findings further demonstrate the need for strong guardrails and modules for agentic systems.

Large language models are rapidly evolving into interactive coding agents capable of end-to-end web coding, yet existing benchmarks evaluate only narrow slices of this capability, typically text-conditioned generation with static-correctness metrics, leaving visual fidelity, interaction quality, and codebase-level reasoning largely unmeasured. We introduce WebCompass, a multimodal benchmark that provides unified lifecycle evaluation of web engineering capability. Recognizing that real-world web coding is an iterative cycle of generation, editing, and repair, WebCompass spans three input modalities (text, image, video) and three task types (generation, editing, repair), yielding seven task categories that mirror professional workflows. Through a multi-stage, human-in-the-loop pipeline, we curate instances covering 15 generation domains, 16 editing operation types, and 11 repair defect types, each annotated at Easy/Medium/Hard levels. For evaluation, we adopt a checklist-guided LLM-as-a-Judge protocol for editing and repair, and propose a novel Agent-as-a-Judge paradigm for generation that autonomously executes generated websites in a real browser, explores interactive behaviors via the Model Context Protocol (MCP), and iteratively synthesizes targeted test cases, closely approximating human acceptance testing. We evaluate representative closed-source and open-source models and observe that: (1) closed-source models remain substantially stronger and more balanced; (2) editing and repair exhibit distinct difficulty profiles, with repair preserving interactivity better but remaining execution-challenging; (3) aesthetics is the most persistent bottleneck, especially for open-source models; and (4) framework choice materially affects outcomes, with Vue consistently challenging while React and Vanilla/HTML perform more strongly depending on task type.

The Model Context Protocol (MCP) widens the prompt injection attack surface of large language model applications to tool descriptions, parameter schemas, and tool outputs. Defenses for it are appearing quickly, but their reported figures are not comparable: each is evaluated on a corpus of its authors' construction, under a decision convention that is rarely stated. This paper asks how much those choices decide, taking CASCADE, a fully local layered defense, as the case: three configurations on a frozen 5,000-sample corpus under a pinned revision and a fixed protocol, with that corpus audited in full. Four results follow. First, the aggregation convention dominates the headline metric: counting review referrals as positives reports an 11.70% false-positive rate where 1.51% of benign traffic would be denied without a human, and conceals that 68.5% of all traffic reaches a reviewer. Second, detection is not provenance-invariant: recall ranges from 86.20% on original material to 99.88% on template-generated material, and added false positives fall on original benign records at ten times the rate they fall on transformed ones. Third, the operating point that ran is not readable from the released configuration, which names four candidate thresholds, its deployment files selecting one that did not govern; it is recoverable from point masses the policy layer leaves in the score distribution, so record-level output is a stronger reproducibility guarantee than a parameter table. Fourth, a local review model invoked for 32.56% of requests at 2.51 s each changes no classification outcome: it returned 90 not-malicious verdicts and the policy stage admitted none, making that null a guard setting rather than a model property. The ablation is unsurprising -- the rule-based layer reaches 61.05% recall, the semantic stage 94.77% -- and that is what makes the other results the substance of the paper.

AI agents increasingly call external tools (file system, network, APIs) through the Model Context Protocol (MCP). These tool calls are the agent's syscalls: privileged operations with side effects on shared state, yet today's safety enforcement lives entirely in userspace, where a 10-line script can bypass it. I propose Governed MCP, a kernel-resident tool governance gateway built on a logit-based safety primitive (ProbeLogits). The gateway interposes on every MCP tool call in a 6-layer pipeline: schema validation, trust tier, rate limit, adversarial pre-filter, a ProbeLogits semantic gate (the load-bearing check), and constitutional policy match, with a Blake3-hashed audit chain. I implement Governed MCP in Anima OS, a bare-metal x86-64 kernel in ~286,000 lines of Rust. The five non-inference layers plus the audit append cost a measured 11.3 us per call; the ProbeLogits gate (one probe-prompt prefill plus a single logit read) costs 332-556 ms per classification across Qwen2.5-7B, Llama-3-8B, and Mistral-7B, 2.4-3.4x faster than a Llama Guard 3 pass on the same hardware. A silicon-measured ablation shows that removing the ProbeLogits layer collapses F1 from 0.789 to 0.357 (delta-F1 = -0.432): hand-rule firewalling alone is insufficient. Every WASM-to-system host function and every registered MCP tool is mediated by the kernel gateway, so the 10-line userspace bypass that defeats existing guardrail libraries is structurally impossible; a disclosed set of ring-3 syscall paths remains ungated pending future work. Multi-model validation across three architectures (HarmBench 98-99% non-copyright block, XSTest 98.5-100% unsafe recall, ToxicChat parity with Llama Guard 3) shows the underlying primitive is architecture-agnostic. Governed MCP demonstrates that tool-call governance is feasible as an OS primitive, not just an application-layer concern.

The emergence of large language model agents capable of invoking external tools has created urgent need for formal verification of agent protocols. Two paradigms dominate this space: Schema-Guided Dialogue (SGD), a research framework for zero-shot API generalization, and the Model Context Protocol (MCP), an industry standard for agent-tool integration. While both enable dynamic service discovery through schema descriptions, their formal relationship remains unexplored. We present the first process calculus formalization of SGD and MCP, proving they are structurally bisimilar under a well-defined mapping Phi. We demonstrate that the reverse mapping Phi-1 is partial and lossy, revealing critical gaps in MCP's expressivity. Through bidirectional analysis, we identify four principles - semantic completeness, explicit action boundaries, failure mode documentation, and inter-tool relationship declaration -- as necessary and sufficient conditions for full behavioral equivalence. We formalize these principles as type-system extensions MCP+, proving MCP+ is fully equivalent to SGD. Our work provides the first formal foundation for verified agent systems and establishes schema quality as a provable safety property. Practically, this means that the current MCP specification has expressiveness gaps compared to SGD and would benefit from the proposed extensions.

Large Language Models (LLMs) are increasingly deployed in tool-driven environments such as healthcare analytics, financial systems, retrieval-augmented generation (RAG), and multi-agent workflows. Although the Model Context Protocol (MCP) standardizes how LLM applications expose and invoke external tools, its baseline model does not require tool-use manifests to be cryptographically authenticated, freshness-checked, policy-bound, or independently auditable before execution. As a result, MCP pipelines may remain vulnerable to manifest tampering, unauthorized tool invocation, replay of stale requests, and weak accountability. This paper presents a manifest-level enforcement layer for MCP-based LLM pipelines. It treats each MCP tool-use manifest as a first-class security object whose canonical form must be policy-validated, freshness-checked, digitally signed, verified before execution, and linked to tamper-evident audit evidence. The framework binds tool invocation to verifiable manifest integrity and fail-closed authorization, separates user-visible request parameters from execution metadata, rejects non-compliant or stale manifests before execution, and records accepted invocations in a Merkle-based transparency log. Evaluation across GPT-5.3, LLaMA-3.5, and DeepSeek-V3 using up to 50,000 manifest instances shows near-linear scalability (R^2 = 0.998), bounded verification latency (<= 9.4 ms on edge devices), and rejection of expired, malformed, replayed, and policy-violating manifests, with rejection rates above 98.7%. Experiments in healthcare, finance, RAG, and multi-agent settings show that manifest-level cryptographic enforcement enables low-overhead, traceable, and auditable execution control for heterogeneous LLM-tool pipelines.

Large Language Models (LLMs) are increasingly serving as autonomous agents, and their utilization of external tools via the Model Context Protocol (MCP) is considered a future trend. Current MCP evaluation sets suffer from issues such as reliance on external MCP services and a lack of difficulty awareness. To address these limitations, we propose MCPAgentBench, a benchmark based on real-world MCP definitions designed to evaluate the tool-use capabilities of agents. We construct a dataset containing authentic tasks and simulated MCP tools. The evaluation employs a dynamic sandbox environment that presents agents with candidate tool lists containing distractors, thereby testing their tool selection and discrimination abilities. Furthermore, we introduce comprehensive metrics to measure both task completion rates and execution efficiency. Experiments conducted on state-of-the-art LLMs reveal significant performance differences in handling complex, multi-step tool invocations. All code is open-source at https://github.com/Brunestuder/MCPAgentBench.