Protocol

Federated differentially private protocols can communicate over many adaptive rounds and reuse each client's local samples. Existing lower bound arguments for federated DP are often restricted to noninteractive protocols or fresh batch decompositions, so the fundamental information-theoretic limit of estimation under fully interactive protocols remains unknown. We establish a federated van Trees inequality for parameter estimation under squared \ell_2 loss from any complete public transcript satisfying a clientwise zCDP constraint at the sample level. A scalar trace form covers homogeneous experiments, while a matrix form preserves directional Fisher geometry in heterogeneous experiments where different clients are informative in different subspaces. Together with existing upper bounds for the corresponding problems, these results identify the minimax rates for various statistical problems including mean estimation, linear regression, nonparametric regression, and functional mean estimation over the full class of interactive public-transcript protocols. For these problems, arbitrary public interaction and repeated sample reuse do not improve the rate over simpler restricted protocols. The key technical ingredient in our paper is a contraction inequality for the Fisher information in the transcript: each client's contribution is bounded both by the Fisher information in its local experiment and by its total privacy budget.

We present AffectAI-Capture, a protocol for collecting synchronized multimodal data in four-person meeting-like interactions, combining eye tracking, wearable physiology, close-talk and room audio, multi-view video, event logging, and structured self-report. Sessions use fixed task blocks grounded in established group-interaction paradigms, while acquisition and post-processing are organized around a single authoritative event timeline and standardized outputs. We describe the experimental rationale, synchronization philosophy, data organization, and practical trade-offs. Pilot-level validation of audio quality and video synchronization has been conducted using controlled bench tests; full protocol sessions with participants remain ongoing work. The contribution is a reproducible protocol architecture linking task design, instrumentation, timing provenance, and data packaging for affective, behavioral, and meeting-analytics research.

Automating science laboratories enables faster, safer, more accurate, and more reproducible execution of protocols, accelerating the discovery and testing of new materials, drugs, and more. However, setting up and running autonomous labs requires coordinating numerous instruments and robots, forcing scientists to write code, manage configuration files, and navigate complex software infrastructure. We present an AI agent architecture that integrates large language models with laboratory orchestration, enabling scientists to interactively create and monitor automated lab protocols using natural language. Integrated into the Experiment Orchestration System (EOS), the AI agent operates under an agentic loop with automated validation and error correction, and supports the complete experimental lifecycle: creating protocols, running and monitoring both protocols and closed-loop optimization campaigns, and analyzing results. A visual graph editor renders protocols as interactive node-based diagrams synchronized with the AI agent's protocol representation, enabling seamless alternation between AI-assisted and manual protocol construction. Evaluated on three simulated automated labs spanning chemistry, biology, and materials science, the AI agent achieves a 97% first-attempt protocol generation success rate and an order of magnitude reduction in required interface actions.

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.

We present Portable Agent Memory, an open protocol and reference implementation for transferring persistent memory state across heterogeneous AI agents. Modern AI agents accumulate rich context -- episodic events,semantic knowledge, procedural skills, working state, and identity preferences -- but this context remains locked within vendor-specific runtimes. Portable Agent Memory addresses this through: (1) a five-component structured memory model with content-addressable entries linked by a Merkle-DAG provenance graph providing tamper-evidence; (2) capability-based access control enabling selective, scoped disclosure of memory segments; (3) an injection-resistant rehydration protocol that adapts recalled content to heterogeneous target models while mitigating indirect prompt injection; and (4) a JSON-first serialization format with optional CBOR compaction for efficient transport. We provide a Python SDK with 54 passing tests, agent skills for multiple platforms, and demonstrate cross-model memory transfer between GPT-4, Claude, Gemini, and Llama architectures. The protocol is open-source under Apache 2.0.

We present TraceFix, a verification-first pipeline for Large Language Model (LLM) multi-agent coordination. An agent synthesizes a protocol topology as a structured intermediate representation (IR) from a task description, generates PlusCal coordination logic, and iteratively repairs the protocol using counterexamples from the TLA+ model checker (TLC) until verification succeeds. Verified process bodies are compiled into per-agent system prompts and executed under a runtime monitor that rejects out-of-topology coordination operations. On 48 tasks spanning 16 scenario families, all tasks reach full TLC verification; 62.5% pass on the first attempt and none requires more than four repair iterations. State spaces span six orders of magnitude yet verification completes in under 60 s for every task. A 3,456-run runtime comparison shows that topology-monitored execution achieves the highest task completion (89.4% average, 81.5% full) and that runtimes using the verified protocol degrade at roughly half the rate of prompt-only and chat-only baselines when model capability is reduced. A paired ablation under a fixed runtime shows that TLC-verified protocols cut deadlock/livelock (DL/LL) from 31.1% to 14.1%, with the largest separation under fault injection.

Autonomous AI agents already transact at production scale -- 69,000 bots, 165 million transactions, $50 million in volume on a single marketplace -- and any party can verify a signed credential without a central service. In an open agent world that covers most of what trust requires: there are no universal borders, and each party chooses for itself whom to deal with. Borders appear only where a closed space draws one -- a marketplace, a platform, or a consortium sets house rules. Whoever draws the border holds the authority to apply it, and may apply it as they choose, behind closed doors. This paper addresses the gap that opens there: when you rely on someone else's border, how do you check that they applied their own published rules -- taking no one's word for it, and handing the check to no new trusted party? Our answer is the Combined Evidence Protocol (CEP): a five-condition predicate any party recomputes from anchored data, turning "did the boundary-owner follow its own admission rules" into a fact anyone verifies rather than a claim anyone believes. The move that secures optimistic rollups secures this -- correctness rests on recomputation, so the measurement belongs to everyone and the oracle problem dissolves. Its load-bearing setting is a consortium of co-equal, mutually distrusting peers under a shared charter, each able to verify, independently, that the rules they jointly agreed are the rules being applied. CEP belongs to the family of trustless systems -- optimistic and zero-knowledge rollups, verifiable ML, self-sovereign-identity predicates. The infrastructure beneath it is live: a W3C VC + DID trust layer running since March 2026, anchored on Base L2, continuing arXiv:2605.06738 and standing on its own.

Most coding-agent benchmarks ask whether generated code behaves correctly. That remains essential, but repository-level engineering is increasingly agent-managed: one agent writes a repository, and later agents inspect, audit, or extend it as working context. In that setting, a generated repository is not only an answer to a task but also a communication artifact for future work. Even when strong agents nearly satisfy the visible behavioral objective, repositories can differ in how clearly they expose the intended behavior and design choices behind that behavior. We introduce BUILD-AND-FIND, a protocol for evaluating whether downstream agents can recover those intended choices from generated repositories, and how much inspection that recovery requires. For each task, a builder sees a hidden repository specification and creates a codebase; a finder sees only the codebase and a specification-traced multiple-choice question bank. The protocol separates behavioral correctness from artifact-side recovery and reports recovery accuracy, repeatability, implementation coverage, and inspection effort. Accuracy and stability act as gates: effort is interpreted only when recovery succeeds reliably. Among artifacts from which the same intent can be recovered, lower effort by the same finder suggests that the artifact makes that intent easier to locate. Question-only and spec-only controls quantify generic priors and specification access, while audits separate omitted claims from finder failures and check whether correct answers cite artifact evidence. In the released high-prior task pack, recovery accuracy is near saturation, so inspection effort and finder-specific effects provide the main panel-local comparison.

Recursive language-model loops often settle into recognizable attractor-like patterns. The practical question is how much injected text is needed to move a settled loop somewhere else, and whether that move lasts. We study this in 30-step recursive loops by separating the model from the context-update rule: append, replace, and dialog updates expose different histories to the same generator. The main result is that persistent redirection in append-mode recursive loops is memory-policy-conditioned. Under a 12,000-character tail clip, destination-coherent persistence plateaus near 16 percent and retained source-basin escape near 36 percent at dose 400; neither crosses 50 percent. Under a full-history protocol, retained source-basin escape crosses 50 percent near 400 tokens and saturates at 75-80 percent by 1,500 tokens; destination-coherent persistence first reaches 0.50 near 1,500 tokens (Wilson 95 percent CI [0.41, 0.61]). A four-step falsification battery (heterogeneity control, granularity sweep with hierarchical macro-merge, transition-entropy diagnostic, and long-horizon trajectory continuation) recasts the high-dose destination-coherent dip as a finite-horizon, endpoint-definition-sensitive feature rather than a stable structural asymmetry. Half the canonical magnitude is endpoint timing; the residual drops 73 percent from -0.143 at step 29 to -0.039 at step 79 under the frozen canonical cluster basis, bootstrap interval straddling zero. Replace-mode raw switching is near-saturated under the default protocol but largely reflects state-reset overwrite: insert-mode probes drop it to 12-32 percent. We report 37 experiments on gpt-4o-mini with within-vendor replication on gpt-4.1-nano. Recursive-loop evaluations should distinguish transient movement from durable escape, subtract stochastic floors, and treat context-update rules as safety-relevant design choices.

Tool-augmented reasoning has become a popular direction for LLM-based agents, and it is widely assumed to improve reasoning and reliability. However, we demonstrate that this consensus does not always hold: in the presence of semantic distractors, tool-augmented reasoning does not necessarily outperform native CoT. To explain this performance gap, we propose a Factorized Intervention Framework that isolates the cost of prompt formatting, the overhead of the tool-calling protocol, and the actual gain from executing tools. Our analysis reveals a critical tradeoff: under semantic noise, the gains from tools often fail to offset the "tool-use tax", which is the performance degradation introduced by the tool-calling protocol itself. To address this, we introduce G-STEP, a lightweight inference-time gate to mitigate protocol-induced errors. While this yields partial recovery, our findings suggest that more substantial improvements still require strengthening the model's intrinsic reasoning and tool-interaction capabilities.

Large language models are increasingly deployed as protocols: structured multi-call procedures that spend additional computation to transform a baseline answer into a final one. These protocols are evaluated only by end-to-end accuracy, giving limited insight into when they help, when they hurt, and whether their behavior transfers under distribution shift or composition. We propose a paired-outcome measurement interface for auditing a single protocol step on exact-match tasks. For each instance, the interface records a baseline correctness bit $E_0\in\{0,1\}$ and a post-step correctness bit $E_1\in\{0,1\}$, separating correction ($E_0=0\to E_1=1$) from corruption ($E_0=1\to E_1=0$) through two rates: $c=\Pr(E_1=1\mid E_0=0)$ and $γ=\Pr(E_1=0\mid E_0=1)$. These rates predict accuracy changes and define a reusable empirical interface testable across seeds, mixtures, and pipelines. We identify three failure mechanisms. Under mixture shift, pooled estimates of $(c,γ)$ become biased when calibration and deployment mixtures differ; conditioning on a difficulty proxy restores stability without additional model calls. Under presentation contamination, selection protocols alter the interface through stable presentation artifacts when candidate content is fixed. Under state insufficiency, the correctness bit may not carry enough history for multi-step pipelines to compose predictably; a Markov factorization test identifies when composition is valid and where additional state is needed. When a protocol step passes these diagnostics, it becomes an auditable module: gated by estimated gain, conditioned on a difficulty proxy to correct mixture bias, and composed into multi-step pipelines with predictable accuracy. We demonstrate these ideas on synthetic mathematical tasks and on GSM8K, where the calibrated interface correctly predicts when protocol steps should be activated or suppressed.

Recent advances in LLM based agent systems have shown promise in tackling complex, long horizon tasks. However, existing agent protocols (e.g., A2A and MCP) under specify cross entity lifecycle and context management, version tracking, and evolution safe update interfaces, which encourages monolithic compositions and brittle glue code. We introduce Autogenesis Protocol (AGP), a self evolution protocol that decouples what evolves from how evolution occurs. Its Resource Substrate Protocol Layer (RSPL) models prompts, agents, tools, environments, and memory as protocol registered resources with explicit state, lifecycle, and versioned interfaces. Its Self Evolution Protocol Layer (SEPL) specifies a closed loop operator interface for proposing, assessing, and committing improvements with auditable lineage and rollback. Building on AGP, we present Autogenesis System (AGS), a self-evolving multi-agent system that dynamically instantiates, retrieves, and refines protocol-registered resources during execution. We evaluate AGS on multiple challenging benchmarks that require long horizon planning and tool use across heterogeneous resources. The results demonstrate consistent improvements over strong baselines, supporting the effectiveness of agent resource management and closed loop self evolution. The code is available at https://github.com/DVampire/Autogenesis.

Existing infrastructure cannot deploy agents from different decision-making paradigms within the same environment, making fair cross-paradigm comparison under identical conditions impossible. We present MOSAIC, an open-source platform that enables heterogeneous agents (RL policies, LLMs, VLMs, and human operators) to act within shared reinforcement learning environments in ad-hoc team settings with reproducible results. MOSAIC introduces three contributions. (i) IPC-based worker protocol that wraps native and third-party frameworks as isolated subprocess workers, each executing its own training and inference logic unmodified and communicating through a versioned inter-process protocol. (ii) An operator abstraction that forms an agent-level interface by mapping workers to agent slots: each operator, regardless of whether it is backed by an RL policy, an LLM, or a human, conforms to a minimal universal interface. (iii) A deterministic cross-paradigm evaluation framework with two complementary modes: a manual mode that advances up to $N$ operators in lock-step under shared seeds for fine-grained visual inspection of behavioural differences; and a script mode that drives automated, long-running evaluation via declarative Python scripts for reproducible experiments. Our documentation is released at: https://mosaic-platform.readthedocs.io.

Understanding biomedical experiments provides a foundation for downstream tasks, e.g., laboratory automation, and facilitates effective cross-disciplinary communication. Two challenges, High Information Density (HID) and Multi-Step Reasoning (MSR), pose unique difficulties for precise experimental understanding. Extracting structured knowledge, e.g., Knowledge Graphs (KGs), is an effective approach to address the HID and MSR. However, existing biomedical datasets for structured knowledge information extraction are limited to a general or coarse-grained level, hindering fine-grained experimental understanding. To address this gap, we introduce Biomedical Protocol Information Extraction Dataset (BioPIE), a dataset providing procedure-centric KGs that capture entities, actions, and relations at a scale sufficient for reasoning across biomedical protocols. We evaluate information extraction methods on BioPIE and implement a question answering system leveraging the dataset for validation, demonstrating improved understanding performance on test sets as well as on the HID and MSR question sets.

Temporal cascade prediction is widely studied, yet its empirical foundations remain fragile. Most existing works report results under random cascade splits that mix past and future signals, rely on datasets with limited features and no downstream conversion labels, and compare increasingly complex models without systematically examining whether benchmark conclusions are protocol-dependent. This paper argues that the field should move from leakage-prone evaluation toward fidelity-aware benchmarking. We introduce a protocol suite and renewed evaluation standard for temporal cascade prediction, centered on the Full Temporal protocol, overlap-based leakage diagnostics, and analyses of performance inflation and temporal drift. To broaden the scope of benchmark tasks, we also present Taoke, a real-world e-commerce cascade dataset with rich promoter/product features and observed purchase conversions, enabling both first-stage popularity forecasting and second-stage conversion forecasting under a shared benchmark asset. Finally, we include CasTemp as a lightweight reference method and additionally probe a larger same-task internal extension to verify that this pipeline remains operational at substantially greater scale. Together, these components turn cascade prediction from a protocol-sensitive leaderboard exercise into a more reliable analysis and benchmarking problem, while still providing a practical reference pipeline for large-scale evaluation and conversion-aware modeling.

Medium Access Control (MAC) protocols, essential for wireless networks, are typically manually configured. While deep reinforcement learning (DRL)-based protocols enhance task-specified network performance, they suffer from poor generalizability and resilience, demanding costly retraining to adapt to dynamic environments. To overcome this limitation, we introduce a game-theoretic LLM-empowered multi-agent DRL (MARL) framework, in which the uplink transmission between a base station and a varying number of user equipments is modeled as a dynamic multi-follower Stackelberg game (MFSG), capturing the network's natural hierarchical structure. Within this game, LLM-driven agents, coordinated through proximal policy optimization (PPO), synthesize adaptive, semantic MAC protocols in response to network dynamics. Protocol action grammar (PAG) is employed to ensure the reliability and efficiency of this process. Under this system, we further analyze the existence and convergence behavior in terms of a Stackelberg equilibrium by studying the learning dynamics of LLM-empowered unified policies in response to changing followers. Simulations corroborate that our framework achieves a 77.6% greater throughput and a 65.2% fairness improvement over conventional baselines. Besides, our framework generalizes excellently to a fluctuating number of users without requiring retraining or architectural changes.

As large language models (LLMs) are increasingly deployed in sensitive everyday contexts -- offering personal advice, mental health support, and moral guidance -- understanding their behavior in navigating complex moral reasoning is essential. Most evaluations study this sociotechnical alignment through single-turn prompts, but it is unclear if these findings extend to multi-turn settings, and even less clear how they depend on the interaction protocols used to coordinate agentic systems. We address this gap using LLM debate to examine deliberative dynamics and value alignment in multi-turn settings by prompting subsets of three models (GPT-4.1, Claude 3.7 Sonnet, and Gemini 2.0 Flash) to collectively assign blame in 1,000 everyday dilemmas from Reddit's ``Am I the Asshole'' community. To test order effects and assess verdict revision, we use both synchronous (parallel responses) and round-robin (sequential responses) deliberation structures, mirroring how multi-agent systems are increasingly orchestrated in practice. Our findings show striking behavioral differences. In the synchronous setting, GPT-4.1 showed strong inertia (0.6-3.1% revision rates) while Claude 3.7 Sonnet and Gemini 2.0 Flash were far more flexible (28-41% revision rates). Value patterns also diverged: GPT-4.1 emphasized personal autonomy and direct communication (relative to its deliberation partners), while Claude 3.7 Sonnet and Gemini 2.0 Flash prioritized empathetic dialogue. We further find that deliberation format had a strong impact on model behavior: GPT-4.1 and Gemini 2.0 Flash stood out as highly conforming relative to Claude 3.7 Sonnet, with their verdict behavior strongly shaped by order effects. We provide additional results on open-source models (DeepSeek-V3.2 and Llama 3.1).