Daily Papers

Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains formidable due to the complexity of multiple large, semi-structured files and the need for extensive domain expertise. Current automation approaches are often limited by either inflexible workflows that break down in edge cases or by fully autonomous agents that lack the necessary precision for rigorous scientific inquiry. GenoMAS charts a different course by presenting a team of LLM-based scientists that integrates the reliability of structured workflows with the adaptability of autonomous agents. GenoMAS orchestrates six specialized LLM agents through typed message-passing protocols, each contributing complementary strengths to a shared analytic canvas. At the heart of GenoMAS lies a guided-planning framework: programming agents unfold high-level task guidelines into Action Units and, at each juncture, elect to advance, revise, bypass, or backtrack, thereby maintaining logical coherence while bending gracefully to the idiosyncrasies of genomic data. On the GenoTEX benchmark, GenoMAS reaches a Composite Similarity Correlation of 89.13% for data preprocessing and an F_1 of 60.48% for gene identification, surpassing the best prior art by 10.61% and 16.85% respectively. Beyond metrics, GenoMAS surfaces biologically plausible gene-phenotype associations corroborated by the literature, all while adjusting for latent confounders. Code is available at https://github.com/Liu-Hy/GenoMAS.

Communicating state machines provide a formal foundation for distributed computation. Unfortunately, they are Turing-complete and, thus, challenging to analyse. In this paper, we classify restrictions on channels which have been proposed to work around the undecidability of verification questions. We compare half-duplex communication, existential B-boundedness, and k-synchronisability. These restrictions do not prevent the communication channels from growing arbitrarily large but still restrict the power of the model. Each restriction gives rise to a set of languages so, for every pair of restrictions, we check whether one subsumes the other or if they are incomparable. We investigate their relationship in two different contexts: first, the one of communicating state machines, and, second, the one of communication protocol specifications using high-level message sequence charts. Surprisingly, these two contexts yield different conclusions. In addition, we integrate multiparty session types, another approach to specify communication protocols, into our classification. We show that multiparty session type languages are half-duplex, existentially 1-bounded, and 1-synchronisable. To~show this result, we provide the first formal embedding of multiparty session types into high-level message sequence charts.

Large language model powered autonomous agents demand robust, standardized protocols to integrate tools, share contextual data, and coordinate tasks across heterogeneous systems. Ad-hoc integrations are difficult to scale, secure, and generalize across domains. This survey examines four emerging agent communication protocols: Model Context Protocol (MCP), Agent Communication Protocol (ACP), Agent-to-Agent Protocol (A2A), and Agent Network Protocol (ANP), each addressing interoperability in deployment contexts. MCP provides a JSON-RPC client-server interface for secure tool invocation and typed data exchange. ACP defines a general-purpose communication protocol over RESTful HTTP, supporting MIME-typed multipart messages and synchronous and asynchronous interactions. Its lightweight and runtime-independent design enables scalable agent invocation, while features like session management, message routing, and integration with role-based and decentralized identifiers (DIDs). A2A enables peer-to-peer task delegation using capability-based Agent Cards, supporting secure and scalable collaboration across enterprise agent workflows. ANP supports open network agent discovery and secure collaboration using W3C decentralized identifiers DIDs and JSON-LD graphs. The protocols are compared across multiple dimensions, including interaction modes, discovery mechanisms, communication patterns, and security models. Based on the comparative analysis, a phased adoption roadmap is proposed: beginning with MCP for tool access, followed by ACP for structured, multimodal messaging session-aware interaction and both online and offline agent discovery across scalable, HTTP-based deployments A2A for collaborative task execution, and extending to ANP for decentralized agent marketplaces. This work provides a comprehensive foundation for designing secure, interoperable, and scalable ecosystems of LLM-powered agents.

Extending Large Language Models (LLMs) to advanced applications requires reliable structured output generation. Existing methods which often rely on rigid JSON schemas, can lead to unreliable outputs, diminished reasoning capabilities, and increased computational overhead, limiting LLMs' adaptability for complex tasks. We introduce Meaning Typed Prompting (MTP), a technique for efficient structured output generation that integrates types, meanings, and abstractions, such as variables and classes, into the prompting process. By utilizing expressive type definitions, MTP enhances output clarity and reduces dependence on complex abstractions, simplifying development, and improving implementation efficiency. This enables LLMs to understand relationships and generate structured data more effectively. Empirical evaluations on multiple benchmarks demonstrate that MTP outperforms existing frameworks in accuracy, reliability, consistency, and token efficiency. We present Semantix, a framework that implements MTP, providing practical insights into its application.

The rapid development of large language models (LLMs) has led to the widespread deployment of LLM agents across diverse industries, including customer service, content generation, data analysis, and even healthcare. However, as more LLM agents are deployed, a major issue has emerged: there is no standard way for these agents to communicate with external tools or data sources. This lack of standardized protocols makes it difficult for agents to work together or scale effectively, and it limits their ability to tackle complex, real-world tasks. A unified communication protocol for LLM agents could change this. It would allow agents and tools to interact more smoothly, encourage collaboration, and triggering the formation of collective intelligence. In this paper, we provide the first comprehensive analysis of existing agent protocols, proposing a systematic two-dimensional classification that differentiates context-oriented versus inter-agent protocols and general-purpose versus domain-specific protocols. Additionally, we conduct a comparative performance analysis of these protocols across key dimensions such as security, scalability, and latency. Finally, we explore the future landscape of agent protocols by identifying critical research directions and characteristics necessary for next-generation protocols. These characteristics include adaptability, privacy preservation, and group-based interaction, as well as trends toward layered architectures and collective intelligence infrastructures. We expect this work to serve as a practical reference for both researchers and engineers seeking to design, evaluate, or integrate robust communication infrastructures for intelligent agents.

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.

Type-and-effect systems help the programmer to organize data and computational effects in a program. While for traditional type systems expressive variants with sophisticated inference algorithms have been developed and widely used in programming languages, type-and-effect systems did not yet gain widespread adoption. One reason for this is that type-and-effect systems are more complex and the existing inference algorithms make compromises between expressiveness, intuitiveness, and decidability. In this work, we present an effect inference algorithm for a type-and-effect system with subtyping, expressive higher-rank polymorphism, and intuitive set-like semantics of effects. In order to deal with scoping issues of higher-rank polymorphism, we delay solving of effect constraints by transforming them into formulae of propositional logic. We prove soundness and completeness of our algorithm with respect to a declarative type-and-effect system. All the presented results have been formalized in the Rocq proof assistant, and the algorithm has been successfully implemented in a realistic programming language.

Statically analyzing dynamically-typed code is a challenging endeavor, as even seemingly trivial tasks such as determining the targets of procedure calls are non-trivial without knowing the types of objects at compile time. Addressing this challenge, gradual typing is increasingly added to dynamically-typed languages, a prominent example being TypeScript that introduces static typing to JavaScript. Gradual typing improves the developer's ability to verify program behavior, contributing to robust, secure and debuggable programs. In practice, however, users only sparsely annotate types directly. At the same time, conventional type inference faces performance-related challenges as program size grows. Statistical techniques based on machine learning offer faster inference, but although recent approaches demonstrate overall improved accuracy, they still perform significantly worse on user-defined types than on the most common built-in types. Limiting their real-world usefulness even more, they rarely integrate with user-facing applications. We propose CodeTIDAL5, a Transformer-based model trained to reliably predict type annotations. For effective result retrieval and re-integration, we extract usage slices from a program's code property graph. Comparing our approach against recent neural type inference systems, our model outperforms the current state-of-the-art by 7.85% on the ManyTypes4TypeScript benchmark, achieving 71.27% accuracy overall. Furthermore, we present JoernTI, an integration of our approach into Joern, an open source static analysis tool, and demonstrate that the analysis benefits from the additional type information. As our model allows for fast inference times even on commodity CPUs, making our system available through Joern leads to high accessibility and facilitates security research.

We introduce Probabilistic Dependent Type Systems (PDTS) via a functional language based on a subsystem of intuitionistic type theory including dependent sums and products, which is expanded to include stochastic functions. We provide a sampling-based semantics for the language based on non-deterministic beta reduction. Further, we derive a probabilistic logic from the PDTS introduced as a direct result of the Curry-Howard isomorphism. The probabilistic logic derived is shown to provide a universal representation for finite discrete distributions.

Emerging Large Language Model (LLM) system patterns, such as disaggregated inference, Mixture-of-Experts (MoE) routing, and asynchronous reinforcement fine-tuning, require flexible point-to-point communication beyond simple collectives. Existing implementations are locked to specific Network Interface Controllers (NICs), hindering integration into inference engines and portability across hardware providers. We present TransferEngine, which bridges the functionality of common NICs to expose a uniform interface. TransferEngine exposes one-sided WriteImm operations with a ImmCounter primitive for completion notification, without ordering assumptions of network transport, transparently managing multiple NICs per GPU. We demonstrate peak throughput of 400 Gbps on both NVIDIA ConnectX-7 and AWS Elastic Fabric Adapter (EFA). We showcase TransferEngine through three production systems: (1) KvCache transfer for disaggregated inference with dynamic scaling, (2) RL weight updates achieving 1.3 seconds for trillion-parameter models, and (3) MoE dispatch/combine implementation exceeding DeepEP decode latency on ConnectX-7, with the first viable latencies on EFA. We demonstrate that our portable point-to-point communication complements collectives while avoiding lock-in.

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

Network protocols are programs with inputs and outputs that follow predefined communication patterns to synchronize and exchange information. There are many protocols and each serves a different purpose, e.g., routing, transport, secure communication, etc. The functional and performance requirements for a protocol can be expressed using a formal specification, such as, a set of logical predicates over its traces. A protocol could be prevented from achieving its requirements due to a bug in its design or implementation, a component failure (e.g., a crash), or an attack. This dissertation shows that formal methods can feasibly characterize the functionality and performance of network protocols under normal conditions as well as when subjected to attacks.

Model Context Protocol (MCP) servers enable AI applications to connect to external systems in a plug-and-play manner, but their rapid proliferation also introduces severe security risks. Unlike mature software ecosystems with rigorous vetting, MCP servers still lack standardized review mechanisms, giving adversaries opportunities to distribute malicious implementations. Despite this pressing risk, the security implications of MCP servers remain underexplored. To address this gap, we present the first systematic study that treats MCP servers as active threat actors and decomposes them into core components to examine how adversarial developers can implant malicious intent. Specifically, we investigate three research questions: (i) what types of attacks malicious MCP servers can launch, (ii) how vulnerable MCP hosts and Large Language Models (LLMs) are to these attacks, and (iii) how feasible it is to carry out MCP server attacks in practice. Our study proposes a component-based taxonomy comprising twelve attack categories. For each category, we develop Proof-of-Concept (PoC) servers and demonstrate their effectiveness across diverse real-world host-LLM settings. We further show that attackers can generate large numbers of malicious servers at virtually no cost. We then test state-of-the-art scanners on the generated servers and found that existing detection approaches are insufficient. These findings highlight that malicious MCP servers are easy to implement, difficult to detect with current tools, and capable of causing concrete damage to AI agent systems. Addressing this threat requires coordinated efforts among protocol designers, host developers, LLM providers, and end users to build a more secure and resilient MCP ecosystem.

This position paper argues that the field of LLM agents requires a unified, telecom-inspired communication protocol to ensure safety, interoperability, and scalability, especially within the context of Next Generation (NextG) networks. Current ad-hoc communication methods are creating a fragmented ecosystem, reminiscent of the early "protocol wars" in networking, which stifles innovation and poses significant risks. Drawing inspiration from the layered, standardized protocols that underpin modern telecommunications, we propose the LLM-Agent Communication Protocol (LACP). LACP establishes a three-layer architecture designed to ensure semantic clarity in communication, transactional integrity for complex tasks, and robust, built-in security. In this position paper, we argue that adopting a principled, universal protocol is not merely beneficial but essential for realizing the potential of distributed AI. Such a standard is critical for ensuring that multi-agent systems can operate safely and reliably in the complex, real-time applications envisioned for 6G and beyond.

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.

SCTP is a transport protocol offering features such as multi-homing, multi-streaming, and message-oriented delivery. Its two main implementations were subjected to conformance tests using the PacketDrill tool. Conformance testing is not exhaustive and a recent vulnerability (CVE-2021-3772) showed SCTP is not immune to attacks. Changes addressing the vulnerability were implemented, but the question remains whether other flaws might persist in the protocol design. We study the security of the SCTP design, taking a rigorous approach rooted in formal methods. We create a formal Promela model of SCTP, and define 10 properties capturing the essential protocol functionality based on its RFC specification and consultation with the lead RFC author. Then we show using the Spin model checker that our model satisfies these properties. We define 4 attacker models - Off-Path, where the attacker is an outsider that can spoof the port and IP of a peer; Evil-Server, where the attacker is a malicious peer; Replay, where an attacker can capture and replay, but not modify, packets; and On-Path, where the attacker controls the channel between peers. We modify an attack synthesis tool designed for transport protocols, Korg, to support our SCTP model and four attacker models. We synthesize 14 unique attacks using the attacker models - including the CVE vulnerability in the Off-Path attacker model, 4 attacks in the Evil-Server attacker model, an opportunistic ABORT attack in the Replay attacker model, and eight connection manipulation attacks in the On-Path attacker model. We show that the proposed patch eliminates the vulnerability and does not introduce new ones according to our model and protocol properties. Finally, we identify and analyze an ambiguity in the RFC, which we show can be interpreted insecurely. We propose an erratum and show that it eliminates the ambiguity.

MPI derived datatypes are an abstraction that simplifies handling of non-contiguous data in MPI applications. These datatypes are recursively constructed at runtime from primitive Named Types defined in the MPI standard. More recently, the development and deployment of CUDA-aware MPI implementations has encouraged the transition of distributed high-performance MPI codes to use GPUs. Such implementations allow MPI functions to directly operate on GPU buffers, easing integration of GPU compute into MPI codes. This work first presents a novel datatype handling strategy for nested strided datatypes, which finds a middle ground between the specialized or generic handling in prior work. This work also shows that the performance characteristics of non-contiguous data handling can be modeled with empirical system measurements, and used to transparently improve MPI_Send/Recv latency. Finally, despite substantial attention to non-contiguous GPU data and CUDA-aware MPI implementations, good performance cannot be taken for granted. This work demonstrates its contributions through an MPI interposer library, TEMPI. TEMPI can be used with existing MPI deployments without system or application changes. Ultimately, the interposed-library model of this work demonstrates MPI_Pack speedup of up to 242000x and MPI_Send speedup of up to 59000x compared to the MPI implementation deployed on a leadership-class supercomputer. This yields speedup of more than 917x in a 3D halo exchange with 3072 processes.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Bayesian persuasion studies how an informed sender should influence beliefs of rational receivers who take decisions through Bayesian updating of a common prior. We focus on the online Bayesian persuasion framework, in which the sender repeatedly faces one or more receivers with unknown and adversarially selected types. First, we show how to obtain a tight tilde O(T^{1/2}) regret bound in the case in which the sender faces a single receiver and has partial feedback, improving over the best previously known bound of tilde O(T^{4/5}). Then, we provide the first no-regret guarantees for the multi-receiver setting under partial feedback. Finally, we show how to design no-regret algorithms with polynomial per-iteration running time by exploiting type reporting, thereby circumventing known intractability results on online Bayesian persuasion. We provide efficient algorithms guaranteeing a O(T^{1/2}) regret upper bound both in the single- and multi-receiver scenario when type reporting is allowed.

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either 'listen', 'broadcast', 'listen and broadcast', or to 'isolate'. The standard message propagation scheme can then be viewed as a special case of this framework where every node 'listens and broadcasts' to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic dataset and on real-world datasets.

Message passing neural networks have shown a lot of success on graph-structured data. However, there are many instances where message passing can lead to over-smoothing or fail when neighboring nodes belong to different classes. In this work, we introduce a simple yet general framework for improving learning in message passing neural networks. Our approach essentially upsamples edges in the original graph by adding "slow nodes" at each edge that can mediate communication between a source and a target node. Our method only modifies the input graph, making it plug-and-play and easy to use with existing models. To understand the benefits of slowing down message passing, we provide theoretical and empirical analyses. We report results on several supervised and self-supervised benchmarks, and show improvements across the board, notably in heterophilic conditions where adjacent nodes are more likely to have different labels. Finally, we show how our approach can be used to generate augmentations for self-supervised learning, where slow nodes are randomly introduced into different edges in the graph to generate multi-scale views with variable path lengths.

Automated attack discovery techniques, such as attacker synthesis or model-based fuzzing, provide powerful ways to ensure network protocols operate correctly and securely. Such techniques, in general, require a formal representation of the protocol, often in the form of a finite state machine (FSM). Unfortunately, many protocols are only described in English prose, and implementing even a simple network protocol as an FSM is time-consuming and prone to subtle logical errors. Automatically extracting protocol FSMs from documentation can significantly contribute to increased use of these techniques and result in more robust and secure protocol implementations. In this work we focus on attacker synthesis as a representative technique for protocol security, and on RFCs as a representative format for protocol prose description. Unlike other works that rely on rule-based approaches or use off-the-shelf NLP tools directly, we suggest a data-driven approach for extracting FSMs from RFC documents. Specifically, we use a hybrid approach consisting of three key steps: (1) large-scale word-representation learning for technical language, (2) focused zero-shot learning for mapping protocol text to a protocol-independent information language, and (3) rule-based mapping from protocol-independent information to a specific protocol FSM. We show the generalizability of our FSM extraction by using the RFCs for six different protocols: BGPv4, DCCP, LTP, PPTP, SCTP and TCP. We demonstrate how automated extraction of an FSM from an RFC can be applied to the synthesis of attacks, with TCP and DCCP as case-studies. Our approach shows that it is possible to automate attacker synthesis against protocols by using textual specifications such as RFCs.

Contemporary LLMs pretrained on code are capable of succeeding at a wide variety of programming tasks. However, their performance is very sensitive to syntactic features, such as the names of variables and types, the structure of code, and presence of type hints. We contribute an inference-time technique to make CodeLLMs more robust to syntactic distractors that are semantically irrelevant. Our methodology relies on activation steering, which involves editing internal model activations to steer the model towards the correct prediction. We contribute a novel way to construct steering vectors by taking inspiration from mutation testing, which constructs minimal semantics-breaking code edits. In contrast, we construct steering vectors from semantics-preserving code edits. We apply our approach to the task of type prediction for the gradually typed languages Python and TypeScript. This approach corrects up to 90% of type mispredictions. Finally, we show that steering vectors calculated from Python activations reliably correct type mispredictions in TypeScript, and vice versa. This result suggests that LLMs may be learning to transfer knowledge of types across programming languages.

Traditional protocol fuzzing techniques, such as those employed by AFL-based systems, often lack effectiveness due to a limited semantic understanding of complex protocol grammars and rigid seed mutation strategies. Recent works, such as ChatAFL, have integrated Large Language Models (LLMs) to guide protocol fuzzing and address these limitations, pushing protocol fuzzers to wider exploration of the protocol state space. But ChatAFL still faces issues like unreliable output, LLM hallucinations, and assumptions of LLM knowledge about protocol specifications. This paper introduces MultiFuzz, a novel dense retrieval-based multi-agent system designed to overcome these limitations by integrating semantic-aware context retrieval, specialized agents, and structured tool-assisted reasoning. MultiFuzz utilizes agentic chunks of protocol documentation (RFC Documents) to build embeddings in a vector database for a retrieval-augmented generation (RAG) pipeline, enabling agents to generate more reliable and structured outputs, enhancing the fuzzer in mutating protocol messages with enhanced state coverage and adherence to syntactic constraints. The framework decomposes the fuzzing process into modular groups of agents that collaborate through chain-of-thought reasoning to dynamically adapt fuzzing strategies based on the retrieved contextual knowledge. Experimental evaluations on the Real-Time Streaming Protocol (RTSP) demonstrate that MultiFuzz significantly improves branch coverage and explores deeper protocol states and transitions over state-of-the-art (SOTA) fuzzers such as NSFuzz, AFLNet, and ChatAFL. By combining dense retrieval, agentic coordination, and language model reasoning, MultiFuzz establishes a new paradigm in autonomous protocol fuzzing, offering a scalable and extensible foundation for future research in intelligent agentic-based fuzzing systems.

We introduce Clifford Group Equivariant Simplicial Message Passing Networks, a method for steerable E(n)-equivariant message passing on simplicial complexes. Our method integrates the expressivity of Clifford group-equivariant layers with simplicial message passing, which is topologically more intricate than regular graph message passing. Clifford algebras include higher-order objects such as bivectors and trivectors, which express geometric features (e.g., areas, volumes) derived from vectors. Using this knowledge, we represent simplex features through geometric products of their vertices. To achieve efficient simplicial message passing, we share the parameters of the message network across different dimensions. Additionally, we restrict the final message to an aggregation of the incoming messages from different dimensions, leading to what we term shared simplicial message passing. Experimental results show that our method is able to outperform both equivariant and simplicial graph neural networks on a variety of geometric tasks.

Distributed protocols should be robust to both benign malfunction (e.g. packet loss or delay) and attacks (e.g. message replay) from internal or external adversaries. In this paper we take a formal approach to the automated synthesis of attackers, i.e. adversarial processes that can cause the protocol to malfunction. Specifically, given a formal threat model capturing the distributed protocol model and network topology, as well as the placement, goals, and interface (inputs and outputs) of potential attackers, we automatically synthesize an attacker. We formalize four attacker synthesis problems - across attackers that always succeed versus those that sometimes fail, and attackers that attack forever versus those that do not - and we propose algorithmic solutions to two of them. We report on a prototype implementation called KORG and its application to TCP as a case-study. Our experiments show that KORG can automatically generate well-known attacks for TCP within seconds or minutes.

A prominent paradigm for graph neural networks is based on the message-passing framework. In this framework, information communication is realized only between neighboring nodes. The challenge of approaches that use this paradigm is to ensure efficient and accurate long-distance communication between nodes, as deep convolutional networks are prone to oversmoothing. In this paper, we present a novel method based on time derivative graph diffusion (TIDE) to overcome these structural limitations of the message-passing framework. Our approach allows for optimizing the spatial extent of diffusion across various tasks and network channels, thus enabling medium and long-distance communication efficiently. Furthermore, we show that our architecture design also enables local message-passing and thus inherits from the capabilities of local message-passing approaches. We show that on both widely used graph benchmarks and synthetic mesh and graph datasets, the proposed framework outperforms state-of-the-art methods by a significant margin

The popularity of the Rust language continues to explode; yet, many critical codebases remain authored in C, and cannot be realistically rewritten by hand. Automatically translating C to Rust is thus an appealing course of action. Several works have gone down this path, handling an ever-increasing subset of C through a variety of Rust features, such as unsafe. While the prospect of automation is appealing, producing code that relies on unsafe negates the memory safety guarantees offered by Rust, and therefore the main advantages of porting existing codebases to memory-safe languages. We instead explore a different path, and explore what it would take to translate C to safe Rust; that is, to produce code that is trivially memory safe, because it abides by Rust's type system without caveats. Our work sports several original contributions: a type-directed translation from (a subset of) C to safe Rust; a novel static analysis based on "split trees" that allows expressing C's pointer arithmetic using Rust's slices and splitting operations; an analysis that infers exactly which borrows need to be mutable; and a compilation strategy for C's struct types that is compatible with Rust's distinction between non-owned and owned allocations. We apply our methodology to existing formally verified C codebases: the HACL* cryptographic library, and binary parsers and serializers from EverParse, and show that the subset of C we support is sufficient to translate both applications to safe Rust. Our evaluation shows that for the few places that do violate Rust's aliasing discipline, automated, surgical rewrites suffice; and that the few strategic copies we insert have a negligible performance impact. Of particular note, the application of our approach to HACL* results in a 80,000 line verified cryptographic library, written in pure Rust, that implements all modern algorithms - the first of its kind.

Message-passing graph neural networks (MPNNs) emerged as powerful tools for processing graph-structured input. However, they operate on a fixed input graph structure, ignoring potential noise and missing information. Furthermore, their local aggregation mechanism can lead to problems such as over-squashing and limited expressive power in capturing relevant graph structures. Existing solutions to these challenges have primarily relied on heuristic methods, often disregarding the underlying data distribution. Hence, devising principled approaches for learning to infer graph structures relevant to the given prediction task remains an open challenge. In this work, leveraging recent progress in exact and differentiable k-subset sampling, we devise probabilistically rewired MPNNs (PR-MPNNs), which learn to add relevant edges while omitting less beneficial ones. For the first time, our theoretical analysis explores how PR-MPNNs enhance expressive power, and we identify precise conditions under which they outperform purely randomized approaches. Empirically, we demonstrate that our approach effectively mitigates issues like over-squashing and under-reaching. In addition, on established real-world datasets, our method exhibits competitive or superior predictive performance compared to traditional MPNN models and recent graph transformer architectures.

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.

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.

Message passing neural networks (MPNNs) have been shown to suffer from the phenomenon of over-squashing that causes poor performance for tasks relying on long-range interactions. This can be largely attributed to message passing only occurring locally, over a node's immediate neighbours. Rewiring approaches attempting to make graphs 'more connected', and supposedly better suited to long-range tasks, often lose the inductive bias provided by distance on the graph since they make distant nodes communicate instantly at every layer. In this paper we propose a framework, applicable to any MPNN architecture, that performs a layer-dependent rewiring to ensure gradual densification of the graph. We also propose a delay mechanism that permits skip connections between nodes depending on the layer and their mutual distance. We validate our approach on several long-range tasks and show that it outperforms graph Transformers and multi-hop MPNNs.

Large Language Models (LLMs) are increasingly integrated into real-world applications via the Model Context Protocol (MCP), a universal, open standard for connecting AI agents with data sources and external tools. While MCP enhances the capabilities of LLM-based agents, it also introduces new security risks and expands their attack surfaces. In this paper, we present the first systematic taxonomy of MCP security, identifying 17 attack types across 4 primary attack surfaces. We introduce MCPSecBench, a comprehensive security benchmark and playground that integrates prompt datasets, MCP servers, MCP clients, attack scripts, and protection mechanisms to evaluate these attacks across three major MCP providers. Our benchmark is modular and extensible, allowing researchers to incorporate custom implementations of clients, servers, and transport protocols for systematic security assessment. Experimental results show that over 85% of the identified attacks successfully compromise at least one platform, with core vulnerabilities universally affecting Claude, OpenAI, and Cursor, while prompt-based and tool-centric attacks exhibit considerable variability across different hosts and models. In addition, current protection mechanisms have little effect against these attacks. Overall, MCPSecBench standardizes the evaluation of MCP security and enables rigorous testing across all MCP layers.

Generative models, particularly Large Language Models (LLMs), produce fluent outputs yet lack verifiable guarantees. We adapt Design by Contract (DbC) and type-theoretic principles to introduce a contract layer that mediates every LLM call. Contracts stipulate semantic and type requirements on inputs and outputs, coupled with probabilistic remediation to steer generation toward compliance. The layer exposes the dual view of LLMs as semantic parsers and probabilistic black-box components. Contract satisfaction is probabilistic and semantic validation is operationally defined through programmer-specified conditions on well-typed data structures. More broadly, this work postulates that any two agents satisfying the same contracts are functionally equivalent with respect to those contracts.

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.

The Model Context Protocol (MCP) defines a schema bound execution model for agent-tool interaction, enabling modular computer vision workflows without retraining. To our knowledge, this is the first protocol level, deployment scale audit of MCP in vision systems, identifying systemic weaknesses in schema semantics, interoperability, and runtime coordination. We analyze 91 publicly registered vision centric MCP servers, annotated along nine dimensions of compositional fidelity, and develop an executable benchmark with validators to detect and categorize protocol violations. The audit reveals high prevalence of schema format divergence, missing runtime schema validation, undeclared coordinate conventions, and reliance on untracked bridging scripts. Validator based testing quantifies these failures, with schema format checks flagging misalignments in 78.0 percent of systems, coordinate convention checks detecting spatial reference errors in 24.6 percent, and memory scope checks issuing an average of 33.8 warnings per 100 executions. Security probes show that dynamic and multi agent workflows exhibit elevated risks of privilege escalation and untyped tool connections. The proposed benchmark and validator suite, implemented in a controlled testbed and to be released on GitHub, establishes a reproducible framework for measuring and improving the reliability and security of compositional vision workflows.

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.

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. We demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We showcase an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

We present DAG-Rider, the first asynchronous Byzantine Atomic Broadcast protocol that achieves optimal resilience, optimal amortized communication complexity, and optimal time complexity. DAG-Rider is post-quantum safe and ensures that all messages proposed by correct processes eventually get decided. We construct DAG-Rider in two layers: In the first layer, processes reliably broadcast their proposals and build a structured Directed Acyclic Graph (DAG) of the communication among them. In the second layer, processes locally observe their DAGs and totally order all proposals with no extra communication.

As Artificial Intelligence systems evolve from monolithic models to ecosystems of specialized agents, the need for standardized communication protocols becomes increasingly critical. This paper introduces MOD-X (Modular Open Decentralized eXchange), a novel architectural framework proposal for agent interoperability that addresses key limitations of existing protocols. Unlike current approaches, MOD-X proposes a layered architecture with a Universal Message Bus, thorough state management, translation capabilities, and blockchain-based security mechanisms. We present MOD-X's architecture, compare it with existing protocols, and demonstrate its application through a worked example how it enables integration between heterogeneous specialist agents (agents with different architectures, vendors, capabilities, and knowledge representations--including rule-based systems, neural networks, symbolic reasoning engines, and legacy software with agent wrappers). MOD-X's key innovations include a publish-subscribe communication model, semantic capability discovery, and dynamic workflow orchestration--providing a framework that bridges theoretical formalism with practical implementation. This architecture addresses the growing need for truly decentralized, interoperable agent ecosystems that can scale effectively without the need for central coordination.

The emergence of Large Language Models (LLMs) has ushered in a transformative paradigm in artificial intelligence, Agentic AI, where intelligent agents exhibit goal-directed autonomy, contextual reasoning, and dynamic multi-agent coordination. This paper provides a systematic review and comparative analysis of leading Agentic AI frameworks, including CrewAI, LangGraph, AutoGen, Semantic Kernel, Agno, Google ADK, and MetaGPT, evaluating their architectural principles, communication mechanisms, memory management, safety guardrails, and alignment with service-oriented computing paradigms. Furthermore, we identify key limitations, emerging trends, and open challenges in the field. To address the issue of agent communication, we conduct an in-depth analysis of protocols such as the Contract Net Protocol (CNP), Agent-to-Agent (A2A), Agent Network Protocol (ANP), and Agora. Our findings not only establish a foundational taxonomy for Agentic AI systems but also propose future research directions to enhance scalability, robustness, and interoperability. This work serves as a comprehensive reference for researchers and practitioners working to advance the next generation of autonomous AI systems.

Recent text-to-video (T2V) technology advancements, as demonstrated by models such as Gen2, Pika, and Sora, have significantly broadened its applicability and popularity. Despite these strides, evaluating these models poses substantial challenges. Primarily, due to the limitations inherent in automatic metrics, manual evaluation is often considered a superior method for assessing T2V generation. However, existing manual evaluation protocols face reproducibility, reliability, and practicality issues. To address these challenges, this paper introduces the Text-to-Video Human Evaluation (T2VHE) protocol, a comprehensive and standardized protocol for T2V models. The T2VHE protocol includes well-defined metrics, thorough annotator training, and an effective dynamic evaluation module. Experimental results demonstrate that this protocol not only ensures high-quality annotations but can also reduce evaluation costs by nearly 50%. We will open-source the entire setup of the T2VHE protocol, including the complete protocol workflow, the dynamic evaluation component details, and the annotation interface code. This will help communities establish more sophisticated human assessment protocols.

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.

To reduce development overhead and enable seamless integration between potential components comprising any given generative AI application, the Model Context Protocol (MCP) (Anthropic, 2024) has recently been released and subsequently widely adopted. The MCP is an open protocol that standardizes API calls to large language models (LLMs), data sources, and agentic tools. By connecting multiple MCP servers, each defined with a set of tools, resources, and prompts, users are able to define automated workflows fully driven by LLMs. However, we show that the current MCP design carries a wide range of security risks for end users. In particular, we demonstrate that industry-leading LLMs may be coerced into using MCP tools to compromise an AI developer's system through various attacks, such as malicious code execution, remote access control, and credential theft. To proactively mitigate these and related attacks, we introduce a safety auditing tool, MCPSafetyScanner, the first agentic tool to assess the security of an arbitrary MCP server. MCPScanner uses several agents to (a) automatically determine adversarial samples given an MCP server's tools and resources; (b) search for related vulnerabilities and remediations based on those samples; and (c) generate a security report detailing all findings. Our work highlights serious security issues with general-purpose agentic workflows while also providing a proactive tool to audit MCP server safety and address detected vulnerabilities before deployment. The described MCP server auditing tool, MCPSafetyScanner, is freely available at: https://github.com/johnhalloran321/mcpSafetyScanner

Graph neural networks (GNNs) have become an indispensable tool for analyzing relational data. In the literature, classical GNNs may be classified into three variants: convolutional, attentional, and message-passing. While the standard message-passing variant is highly expressive, its typical pair-wise messages nevertheless only consider the features of the center node and each neighboring node individually. This design fails to incorporate the rich contextual information contained within the broader local neighborhood, potentially hindering its ability to learn complex relationships within the entire set of neighboring nodes. To address this limitation, this work first formalizes the concept of neighborhood-contextualization, rooted in a key property of the attentional variant. This then serves as the foundation for generalizing the message-passing variant to the proposed neighborhood-contextualized message-passing (NCMP) framework. To demonstrate its utility, a simple, practical, and efficient method to parametrize and operationalize NCMP is presented, leading to the development of the proposed Soft-Isomorphic Neighborhood-Contextualized Graph Convolution Network (SINC-GCN). A preliminary analysis on a synthetic binary node classification problem then underscores both the expressivity and efficiency of the proposed GNN architecture. Overall, the paper lays the foundation for the novel NCMP framework as a practical path toward further enhancing the graph representational power of classical GNNs.

TypeScript and Python are two programming languages that support optional type annotations, which are useful but tedious to introduce and maintain. This has motivated automated type prediction: given an untyped program, produce a well-typed output program. Large language models (LLMs) are promising for type prediction, but there are challenges: fill-in-the-middle performs poorly, programs may not fit into the context window, generated types may not type check, and it is difficult to measure how well-typed the output program is. We address these challenges by building OpenTau, a search-based approach for type prediction that leverages large language models. We propose a new metric for type prediction quality, give a tree-based program decomposition that searches a space of generated types, and present fill-in-the-type fine-tuning for LLMs. We evaluate our work with a new dataset for TypeScript type prediction, and show that 47.4% of files type check (14.5% absolute improvement) with an overall rate of 3.3 type errors per file. All code, data, and models are available at: https://github.com/GammaTauAI/opentau.

We extend the simply-typed guarded lambda-calculus with discrete probabilities and endow it with a program logic for reasoning about relational properties of guarded probabilistic computations. This provides a framework for programming and reasoning about infinite stochastic processes like Markov chains. We demonstrate the logic sound by interpreting its judgements in the topos of trees and by using probabilistic couplings for the semantics of relational assertions over distributions on discrete types. The program logic is designed to support syntax-directed proofs in the style of relational refinement types, but retains the expressiveness of higher-order logic extended with discrete distributions, and the ability to reason relationally about expressions that have different types or syntactic structure. In addition, our proof system leverages a well-known theorem from the coupling literature to justify better proof rules for relational reasoning about probabilistic expressions. We illustrate these benefits with a broad range of examples that were beyond the scope of previous systems, including shift couplings and lump couplings between random walks.

Agentic AI denotes an architectural transition from stateless, prompt-driven generative models toward goal-directed systems capable of autonomous perception, planning, action, and adaptation through iterative control loops. This paper examines this transition by connecting foundational intelligent agent theories, including reactive, deliberative, and Belief-Desire-Intention models, with contemporary LLM-centric approaches such as tool invocation, memory-augmented reasoning, and multi-agent coordination. The paper presents three primary contributions: (i) a reference architecture for production-grade LLM agents that separates cognitive reasoning from execution using typed tool interfaces; (ii) a taxonomy of multi-agent topologies, together with their associated failure modes and mitigation approaches; and (iii) an enterprise hardening checklist that incorporates governance, observability, and reproducibility considerations. Through an analysis of emerging industry platforms, including Kore.ai, Salesforce Agentforce, TrueFoundry, ZenML, and LangChain, the study identifies a convergence toward standardized agent loops, registries, and auditable control mechanisms. It is argued that the subsequent phase of agentic AI development will parallel the maturation of web services, relying on shared protocols, typed contracts, and layered governance structures to support scalable and composable autonomy. The persistent challenges related to verifiability, interoperability, and safe autonomy remain key areas for future research and practical deployment.

As large language models (LLMs) become more powerful and are deployed more autonomously, it will be increasingly important to prevent them from causing harmful outcomes. Researchers have investigated a variety of safety techniques for this purpose, e.g. using models to review the outputs of other models, or red-teaming techniques to surface subtle failure modes. However, researchers have not evaluated whether such techniques still ensure safety if the model is itself intentionally trying to subvert them. In this paper, we develop and evaluate pipelines of safety techniques ("protocols") that are robust to intentional subversion. We investigate a scenario in which we want to solve a sequence of programming problems, using access to a powerful but untrusted model (in our case, GPT-4), access to a less powerful trusted model (in our case, GPT-3.5), and limited access to high-quality trusted labor. We investigate protocols that aim to never submit solutions containing backdoors, which we operationalize here as logical errors that are not caught by test cases. We investigate a range of protocols and test each against strategies that the untrusted model could use to subvert them. One protocol is what we call trusted editing. This protocol first asks GPT-4 to write code, and then asks GPT-3.5 to rate the suspiciousness of that code. If the code is below some suspiciousness threshold, it is submitted. Otherwise, GPT-3.5 edits the solution to remove parts that seem suspicious and then submits the edited code. Another protocol is untrusted monitoring. This protocol asks GPT-4 to write code, and then asks another instance of GPT-4 whether the code is backdoored, using various techniques to prevent the GPT-4 instances from colluding. These protocols improve substantially on simple baselines.

GossipSub is a new peer-to-peer communication protocol designed to counter attacks from misbehaving peers by controlling what information is sent and to whom, via a score function computed by each peer that captures positive and negative behaviors of its neighbors. The score function depends on several parameters (weights, caps, thresholds) that can be configured by applications using GossipSub. The specification for GossipSub is written in English and its resilience to attacks from misbehaving peers is supported empirically by emulation testing using an implementation in Golang. In this work we take a foundational approach to understanding the resilience of GossipSub to attacks from misbehaving peers. We build the first formal model of GossipSub, using the ACL2s theorem prover. Our model is officially endorsed by the GossipSub developers. It can simulate GossipSub networks of arbitrary size and topology, with arbitrarily configured peers, and can be used to prove and disprove theorems about the protocol. We formalize fundamental security properties stating that the score function is fair, penalizes bad behavior, and rewards good behavior. We prove that the score function is always fair, but can be configured in ways that either penalize good behavior or ignore bad behavior. Using our model, we run GossipSub with the specific configurations for two popular real-world applications: the FileCoin and Eth2.0 blockchains. We show that all properties hold for FileCoin. However, given any Eth2.0 network (of any topology and size) with any number of potentially misbehaving peers, we can synthesize attacks where these peers are able to continuously misbehave by never forwarding topic messages, while maintaining positive scores so that they are never pruned from the network by GossipSub.

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.

We consider the hierarchical representation of documents as graphs and use geometric deep learning to classify them into different categories. While graph neural networks can efficiently handle the variable structure of hierarchical documents using the permutation invariant message passing operations, we show that we can gain extra performance improvements using our proposed selective graph pooling operation that arises from the fact that some parts of the hierarchy are invariable across different documents. We applied our model to classify clinical trial (CT) protocols into completed and terminated categories. We use bag-of-words based, as well as pre-trained transformer-based embeddings to featurize the graph nodes, achieving f1-scores around 0.85 on a publicly available large scale CT registry of around 360K protocols. We further demonstrate how the selective pooling can add insights into the CT termination status prediction. We make the source code and dataset splits accessible.

We present ModularSubsetSelection (MSS), a new algorithm for locally differentially private (LDP) frequency estimation. Given a universe of size k and n users, our varepsilon-LDP mechanism encodes each input via a Residue Number System (RNS) over ell pairwise-coprime moduli m_0, ldots, m_{ell-1}, and reports a randomly chosen index j in [ell] along with the perturbed residue using the statistically optimal SubsetSelection (SS) (Wang et al. 2016). This design reduces the user communication cost from Θbigl(ωlog_2(k/ω)bigr) bits required by standard SS (with ωapprox k/(e^varepsilon+1)) down to lceil log_2 ell rceil + lceil log_2 m_j rceil bits, where m_j < k. Server-side decoding runs in Θ(n + r k ell) time, where r is the number of LSMR (Fong and Saunders 2011) iterations. In practice, with well-conditioned moduli (i.e., constant r and ell = Θ(log k)), this becomes Θ(n + k log k). We prove that MSS achieves worst-case MSE within a constant factor of state-of-the-art protocols such as SS and ProjectiveGeometryResponse (PGR) (Feldman et al. 2022) while avoiding the algebraic prerequisites and dynamic-programming decoder required by PGR. Empirically, MSS matches the estimation accuracy of SS, PGR, and RAPPOR (Erlingsson, Pihur, and Korolova 2014) across realistic (k, varepsilon) settings, while offering faster decoding than PGR and shorter user messages than SS. Lastly, by sampling from multiple moduli and reporting only a single perturbed residue, MSS achieves the lowest reconstruction-attack success rate among all evaluated LDP protocols.

We introduce **EvoGraph**, a framework that enables software systems to evolve their own source code, build pipelines, documentation, and tickets. EvoGraph represents every artefact in a typed directed graph, applies learned mutation operators driven by specialized small language models (SLMs), and selects survivors with a multi-objective fitness. On three benchmarks, EvoGraph fixes 83% of known security vulnerabilities, translates COBOL to Java with 93% functional equivalence (test verified), and maintains documentation freshness within two minutes. Experiments show a 40% latency reduction and a sevenfold drop in feature lead time compared with strong baselines. We extend our approach to **evoGraph**, leveraging language-specific SLMs for modernizing .NET, Lisp, CGI, ColdFusion, legacy Python, and C codebases, achieving 82-96% semantic equivalence across languages while reducing computational costs by 90% compared to large language models. EvoGraph's design responds to empirical failure modes in legacy modernization, such as implicit contracts, performance preservation, and integration evolution. Our results suggest a practical path toward Software 3.0, where systems adapt continuously yet remain under measurable control.

In this work we develop a new method, named Sub-graph Permutation Equivariant Networks (SPEN), which provides a framework for building graph neural networks that operate on sub-graphs, while using a base update function that is permutation equivariant, that are equivariant to a novel choice of automorphism group. Message passing neural networks have been shown to be limited in their expressive power and recent approaches to over come this either lack scalability or require structural information to be encoded into the feature space. The general framework presented here overcomes the scalability issues associated with global permutation equivariance by operating more locally on sub-graphs. In addition, through operating on sub-graphs the expressive power of higher-dimensional global permutation equivariant networks is improved; this is due to fact that two non-distinguishable graphs often contain distinguishable sub-graphs. Furthermore, the proposed framework only requires a choice of k-hops for creating ego-network sub-graphs and a choice of representation space to be used for each layer, which makes the method easily applicable across a range of graph based domains. We experimentally validate the method on a range of graph benchmark classification tasks, demonstrating statistically indistinguishable results from the state-of-the-art on six out of seven benchmarks. Further, we demonstrate that the use of local update functions offers a significant improvement in GPU memory over global methods.

Large language model (LLM) routing has emerged as a crucial strategy for balancing computational costs with performance by dynamically assigning queries to the most appropriate model based on query complexity. Despite recent advances showing that preference-data-based routers can outperform traditional methods, current evaluation benchmarks remain limited. They largely focus on general model capabilities while overlooking task-specific behaviors and critical concerns such as privacy, safety, and potential backdoor vulnerabilities introduced through preference data. In response, we propose the DSC benchmark: Diverse, Simple, and Categorized, an evaluation framework that categorizes router performance across a broad spectrum of query types, including coding, translation, mathematics, human instructions, general knowledge, and LLM jailbreaking. Additionally, it integrates privacy and safety assessments to reveal hidden risks. Our experiments on three preference-based routers and two commercial counterparts demonstrate that while these systems improve efficiency, they often make suboptimal, category-driven decisions. For instance, a BERT-based router directs all coding and mathematics queries to the most powerful LLM even when simpler models would suffice, while routing jailbreaking attempts to weaker models, thereby elevating safety risks.

Diffusion language models promise bidirectional context and infilling capabilities that autoregressive coders lack, yet practical systems remain heavyweight. We introduce CoDA, a 1.7B-parameter diffusion coder trained on TPU with a fully open-source training pipeline. CoDA pairs large-scale diffusion pre-training with code-centric mid-training and instruction tuning, enabling confidence-guided sampling that keeps inference latency competitive. On Humaneval, MBPP, and EvalPlus, CoDA-1.7B-Instruct matches or surpasses diffusion models up to 7B parameters. Our release includes model checkpoints, evaluation harnesses, and TPU training pipelines to accelerate research on lightweight diffusion-based coding assistants.

Diffusion-based language models offer a compelling alternative to autoregressive (AR) models by enabling parallel and controllable generation. Among this family of models, Masked Diffusion Models (MDMs) achieve the strongest performance but still underperform AR models in perplexity and lack key inference-time efficiency features--most notably, KV caching. In this work, we introduce Eso-LMs, a new family of models that fuses AR and MDM paradigms, enabling smooth interpolation between their perplexities while overcoming their respective limitations. Eso-LMs set a new state of the art on standard language modeling benchmarks. Crucially, we are the **first to introduce KV caching for MDMs** while preserving parallel generation, significantly improving inference efficiency. Combined with an optimized sampling schedule, our method achieves up to **65x** faster inference than standard MDMs and **4x** faster inference than prior semi-autoregressive approaches. We provide the code and model checkpoints on the project page: [http://s-sahoo.github.io/Eso-LMs](http://s-sahoo.github.io/Eso-LMs)

Message passing graph neural networks (GNNs) would appear to be powerful tools to learn distributed algorithms via gradient descent, but generate catastrophically incorrect predictions when nodes update asynchronously during inference. This failure under asynchrony effectively excludes these architectures from many potential applications, such as learning local communication policies between resource-constrained agents in, e.g., robotic swarms or sensor networks. In this work we explore why this failure occurs in common GNN architectures, and identify "implicitly-defined" GNNs as a class of architectures which is provably robust to partially asynchronous "hogwild" inference, adapting convergence guarantees from work in asynchronous and distributed optimization, e.g., Bertsekas (1982); Niu et al. (2011). We then propose a novel implicitly-defined GNN architecture, which we call an energy GNN. We show that this architecture outperforms other GNNs from this class on a variety of synthetic tasks inspired by multi-agent systems, and achieves competitive performance on real-world datasets.

Fully Homomorphic Encryption (FHE) is seeing increasing real-world deployment to protect data in use by allowing computation over encrypted data. However, the same malleability that enables homomorphic computations also raises integrity issues, which have so far been mostly overlooked. While FHEs lack of integrity has obvious implications for correctness, it also has severe implications for confidentiality: a malicious server can leverage the lack of integrity to carry out interactive key-recovery attacks. As a result, virtually all FHE schemes and applications assume an honest-but-curious server who does not deviate from the protocol. In practice, however, this assumption is insufficient for a wide range of deployment scenarios. While there has been work that aims to address this gap, these have remained isolated efforts considering only aspects of the overall problem and fail to fully address the needs and characteristics of modern FHE schemes and applications. In this paper, we analyze existing FHE integrity approaches, present attacks that exploit gaps in prior work, and propose a new notion for maliciously-secure verifiable FHE. We then instantiate this new notion with a range of techniques, analyzing them and evaluating their performance in a range of different settings. We highlight their potential but also show where future work on tailored integrity solutions for FHE is still required.

Diffusion language models (DLMs) have strong theoretical efficiency but are limited by fixed-length decoding and incompatibility with key-value (KV) caches. Block diffusion mitigates these issues, yet still enforces a fixed block size and requires expensive training. We introduce Next Sequence Prediction (NSP), which unifies next-token and next-block prediction, enabling the model to adaptively determine the generation length at each step. When the length is fixed to 1, NSP reduces to standard next-token prediction. Building on NSP, we propose Sequential Diffusion Language Model (SDLM), which can retrofit pre-trained autoregressive language models (ALMs) at minimal cost. Specifically, SDLM performs diffusion inference within fixed-size mask blocks, but dynamically decodes consecutive subsequences based on model confidence, thereby preserving KV-cache compatibility and improving robustness to varying uncertainty and semantics across the sequence. Experiments show that SDLM matches or surpasses strong autoregressive baselines using only 3.5M training samples, while achieving 2.1 higher throughput than Qwen-2.5. Notably, the SDLM-32B model delivers even more pronounced efficiency gains, demonstrating the strong scalability potential of our modeling paradigm. Project page and codes: https://github.com/OpenGVLab/SDLM

This paper introduces a novel type theory and logic for probabilistic reasoning. Its logic is quantitative, with fuzzy predicates. It includes normalisation and conditioning of states. This conditioning uses a key aspect that distinguishes our probabilistic type theory from quantum type theory, namely the bijective correspondence between predicates and side-effect free actions (called instrument, or assert, maps). The paper shows how suitable computation rules can be derived from this predicate-action correspondence, and uses these rules for calculating conditional probabilities in two well-known examples of Bayesian reasoning in (graphical) models. Our type theory may thus form the basis for a mechanisation of Bayesian inference.

Biological protocols are fundamental to reproducible and safe life science research. While LLMs excel on general tasks, their systematic evaluation on these highly specialized, accuracy-critical, and inherently procedural texts remains limited. In this work, we present BioProBench, the first large-scale, integrated multi-task benchmark for biological protocol understanding and reasoning. While limited benchmarks have touched upon specific aspects like protocol QA, BioProBench provides a comprehensive suite of five core tasks: Protocol Question Answering, Step Ordering, Error Correction, Protocol Generation, and Protocol Reasoning, enabling a holistic evaluation of LLMs on procedural biological texts. Built upon 27K original protocols, it yields nearly 556K high-quality structured instances. We evaluate 12 mainstream open/closed-source LLMs on BioProBench. Experimental results reveal that while top models preform well on surface understanding tasks, struggle significantly with deep reasoning and structured generation tasks like ordering and generation. Furthermore, model comparisons reveal diverse performance: certain open-source models approach closed-source levels on some tasks, yet bio-specific small models lag behind general LLMs, indicating limitations on complex procedural content. Overall, our findings underscore that procedural reasoning within biological protocols represents a significant challenge for current LLMs. BioProBench serves as a standardized framework to diagnose these specific limitations and guide the development of AI systems better equipped for safely automating complex scientific procedures. The code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/GreatCaptainNemo/BioProBench.

This paper presents a concrete and a symbolic rewriting logic semantics for parametric time Petri nets with inhibitor arcs (PITPNs), a flexible model of timed systems where parameters are allowed in firing bounds. We prove that our semantics is bisimilar to the "standard" semantics of PITPNs. This allows us to use the rewriting logic tool Maude, combined with SMT solving, to provide sound and complete formal analyses for PITPNs. We develop and implement a new general folding approach for symbolic reachability, so that Maude-with-SMT reachability analysis terminates whenever the parametric state-class graph of the PITPN is finite. Our work opens up the possibility of using the many formal analysis capabilities of Maude -- including full LTL model checking, analysis with user-defined analysis strategies, and even statistical model checking -- for such nets. We illustrate this by explaining how almost all formal analysis and parameter synthesis methods supported by the state-of-the-art PITPN tool Romeo can be performed using Maude with SMT. In addition, we also support analysis and parameter synthesis from parametric initial markings, as well as full LTL model checking and analysis with user-defined execution strategies. Experiments show that our methods outperform Romeo in many cases.

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.

The performance of a language model has been shown to be effectively modeled as a power-law in its parameter count. Here we study the scaling behaviors of Routing Networks: architectures that conditionally use only a subset of their parameters while processing an input. For these models, parameter count and computational requirement form two independent axes along which an increase leads to better performance. In this work we derive and justify scaling laws defined on these two variables which generalize those known for standard language models and describe the performance of a wide range of routing architectures trained via three different techniques. Afterwards we provide two applications of these laws: first deriving an Effective Parameter Count along which all models scale at the same rate, and then using the scaling coefficients to give a quantitative comparison of the three routing techniques considered. Our analysis derives from an extensive evaluation of Routing Networks across five orders of magnitude of size, including models with hundreds of experts and hundreds of billions of parameters.

It has been shown that a message passing neural networks (MPNNs), a popular family of neural networks for graph-structured data, are at most as expressive as the first-order Weisfeiler-Leman (1-WL) graph isomorphism test, which has motivated the development of more expressive architectures. In this work, we analyze if the limited expressiveness is actually a limiting factor for MPNNs and other WL-based models in standard graph datasets. Interestingly, we find that the expressiveness of WL is sufficient to identify almost all graphs in most datasets. Moreover, we find that the classification accuracy upper bounds are often close to 100\%. Furthermore, we find that simple WL-based neural networks and several MPNNs can be fitted to several datasets. In sum, we conclude that the performance of WL/MPNNs is not limited by their expressiveness in practice.

Message Passing Neural Networks (MPNNs) are instances of Graph Neural Networks that leverage the graph to send messages over the edges. This inductive bias leads to a phenomenon known as over-squashing, where a node feature is insensitive to information contained at distant nodes. Despite recent methods introduced to mitigate this issue, an understanding of the causes for over-squashing and of possible solutions are lacking. In this theoretical work, we prove that: (i) Neural network width can mitigate over-squashing, but at the cost of making the whole network more sensitive; (ii) Conversely, depth cannot help mitigate over-squashing: increasing the number of layers leads to over-squashing being dominated by vanishing gradients; (iii) The graph topology plays the greatest role, since over-squashing occurs between nodes at high commute (access) time. Our analysis provides a unified framework to study different recent methods introduced to cope with over-squashing and serves as a justification for a class of methods that fall under graph rewiring.

The Key-Value (KV) cache of Large Language Models (LLMs) is prefix-based, making it highly inefficient for processing contexts retrieved in arbitrary order. Position-Independent Caching (PIC) has been proposed to enable KV reuse without positional constraints; however, existing approaches often incur substantial accuracy degradation, limiting their practical adoption. To address this issue, we propose native PIC by reintroducing the encoder to prevalent decoder-only LLMs and explicitly training it to support PIC. We further develop COMB, a PIC-aware caching system that integrates seamlessly with existing inference frameworks. Experimental results show that COMB reduces Time-to-First-Token (TTFT) by 51-94% and increases throughput by 3times with comparable accuracy. Furthermore, the quality improvement when using DeepSeek-V2-Lite-Chat demonstrates the applicability of COMB to other types of decoder-only LLMs. Our code is available at https://github.com/shijuzhao/Comb.

Large Language Models (LLMs) have demonstrated impressive performance in software engineering tasks. However, improving their accuracy in generating correct and reliable code remains challenging. Numerous prompt engineering techniques (PETs) have been developed to address this, but no single approach is universally optimal. Selecting the right PET for each query is difficult for two primary reasons: (1) interactive prompting techniques may not consistently deliver the expected benefits, especially for simpler queries, and (2) current automated prompt engineering methods lack adaptability and fail to fully utilize multi-stage responses. To overcome these challenges, we propose PET-Select, a PET-agnostic selection model that uses code complexity as a proxy to classify queries and select the most appropriate PET. By incorporating contrastive learning, PET-Select effectively distinguishes between simple and complex problems, allowing it to choose PETs that are best suited for each query's complexity level. Our evaluations on the MBPP and HumanEval benchmarks using GPT-3.5 Turbo and GPT-4o show up to a 1.9% improvement in pass@1 accuracy, along with a 74.8% reduction in token usage. Additionally, we provide both quantitative and qualitative results to demonstrate how PET-Select effectively selects the most appropriate techniques for each code generation query, further showcasing its efficiency in optimizing PET selection.

State-of-the-art neural algorithmic reasoners make use of message passing in graph neural networks (GNNs). But typical GNNs blur the distinction between the definition and invocation of the message function, forcing a node to send messages to its neighbours at every layer, synchronously. When applying GNNs to learn to execute dynamic programming algorithms, however, on most steps only a handful of the nodes would have meaningful updates to send. One, hence, runs the risk of inefficiencies by sending too much irrelevant data across the graph -- with many intermediate GNN steps having to learn identity functions. In this work, we explicitly separate the concepts of node state update and message function invocation. With this separation, we obtain a mathematical formulation that allows us to reason about asynchronous computation in both algorithms and neural networks.

The advent of 1-bit large language models (LLMs), led by BitNet b1.58, has spurred interest in ternary LLMs. Despite this, research and practical applications focusing on efficient edge inference for ternary LLMs remain scarce. To bridge this gap, we introduce Bitnet.cpp, an inference system optimized for BitNet b1.58 and ternary LLMs. Given that mixed-precision matrix multiplication (mpGEMM) constitutes the bulk of inference time in ternary LLMs, Bitnet.cpp incorporates a novel mpGEMM library to facilitate sub-2-bits-per-weight, efficient and lossless inference. The library features two core solutions: Ternary Lookup Table (TL), which addresses spatial inefficiencies of previous bit-wise methods, and Int2 with a Scale (I2_S), which ensures lossless edge inference, both enabling high-speed inference. Our experiments show that Bitnet.cpp achieves up to a 6.25x increase in speed over full-precision baselines and up to 2.32x over low-bit baselines, setting new benchmarks in the field. Additionally, we expand TL to element-wise lookup table (ELUT) for low-bit LLMs in the appendix, presenting both theoretical and empirical evidence of its considerable potential. Bitnet.cpp is publicly available at https://github.com/microsoft/BitNet/tree/paper , offering a sophisticated solution for the efficient and practical deployment of edge LLMs.

The emergence of programmable switches allows operators to collect a vast amount of fine-grained telemetry data in real time. However, consolidating the telemetry reports at centralized collectors to gain a network-wide view poses an immense challenge. The received data has to be transported from the switches, parsed, manipulated, and inserted in queryable data structures. As the network scales, this requires excessive CPU processing. RDMA is a transport protocol that bypasses the CPU and allows extremely high data transfer rates. Yet, RDMA is not designed for telemetry collection: it requires a stateful connection, supports only a small number of concurrent writers, and has limited writing primitives, which restricts its data aggregation applicability. We introduce Direct Telemetry Access (DTA), a solution that allows fast and efficient telemetry collection, aggregation, and indexing. Our system establishes RDMA connections only from collectors' ToR switches, called translators, that process DTA reports from all other switches. DTA features novel and expressive reporting primitives such as Key-Write, Append, Sketch-Merge, and Key-Increment that allow integration of telemetry systems such as INT and others. The translators then aggregate, batch, and write the reports to collectors' memory in queryable form.

While existing multi-agent systems (MAS) can handle complex problems by enabling collaboration among multiple agents, they are often highly task-specific, relying on manually crafted agent roles and interaction prompts, which leads to increased architectural complexity and limited reusability across tasks. Moreover, most MAS communicate primarily through natural language, making them vulnerable to error accumulation and instability in long-context, multi-stage interactions within internal agent histories. In this work, we propose Agent Primitives, a set of reusable latent building blocks for LLM-based MAS. Inspired by neural network design, where complex models are built from reusable components, we observe that many existing MAS architectures can be decomposed into a small number of recurring internal computation patterns. Based on this observation, we instantiate three primitives: Review, Voting and Selection, and Planning and Execution. All primitives communicate internally via key-value (KV) cache, which improves both robustness and efficiency by mitigating information degradation across multi-stage interactions. To enable automatic system construction, an Organizer agent selects and composes primitives for each query, guided by a lightweight knowledge pool of previously successful configurations, forming a primitive-based MAS. Experiments show that primitives-based MAS improve average accuracy by 12.0-16.5\% over single-agent baselines, reduce token usage and inference latency by approximately 3times-4times compared to text-based MAS, while incurring only 1.3times-1.6times overhead relative to single-agent inference and providing more stable performance across model backbones.

We often interact with untrusted parties. Prioritization of privacy can limit the effectiveness of these interactions, as achieving certain goals necessitates sharing private data. Traditionally, addressing this challenge has involved either seeking trusted intermediaries or constructing cryptographic protocols that restrict how much data is revealed, such as multi-party computations or zero-knowledge proofs. While significant advances have been made in scaling cryptographic approaches, they remain limited in terms of the size and complexity of applications they can be used for. In this paper, we argue that capable machine learning models can fulfill the role of a trusted third party, thus enabling secure computations for applications that were previously infeasible. In particular, we describe Trusted Capable Model Environments (TCMEs) as an alternative approach for scaling secure computation, where capable machine learning model(s) interact under input/output constraints, with explicit information flow control and explicit statelessness. This approach aims to achieve a balance between privacy and computational efficiency, enabling private inference where classical cryptographic solutions are currently infeasible. We describe a number of use cases that are enabled by TCME, and show that even some simple classic cryptographic problems can already be solved with TCME. Finally, we outline current limitations and discuss the path forward in implementing them.

Blockchains have seen growing traction with cryptocurrencies reaching a market cap of over 1 trillion dollars, major institution investors taking interests, and global impacts on governments, businesses, and individuals. Also growing significantly is the heterogeneity of the ecosystem where a variety of blockchains co-exist. Cross-chain bridge is a necessary building block in this multi-chain ecosystem. Existing solutions, however, either suffer from performance issues or rely on trust assumptions of committees that significantly lower the security. Recurring attacks against bridges have cost users more than 1.5 billion USD. In this paper, we introduce zkBridge, an efficient cross-chain bridge that guarantees strong security without external trust assumptions. With succinct proofs, zkBridge not only guarantees correctness, but also significantly reduces on-chain verification cost. We propose novel succinct proof protocols that are orders-of-magnitude faster than existing solutions for workload in zkBridge. With a modular design, zkBridge enables a broad spectrum of use cases and capabilities, including message passing, token transferring, and other computational logic operating on state changes from different chains. To demonstrate the practicality of zkBridge, we implemented a prototype bridge from Cosmos to Ethereum, a particularly challenging direction that involves large proof circuits that existing systems cannot efficiently handle. Our evaluation shows that zkBridge achieves practical performance: proof generation takes less than 20 seconds, while verifying proofs on-chain costs less than 230K gas. For completeness, we also implemented and evaluated the direction from Ethereum to other EVM-compatible chains (such as BSC) which involves smaller circuits and incurs much less overhead.

Designing effective strategies for controlling epidemic spread by vaccination is an important question in epidemiology, especially in the early stages when vaccines are limited. This is a challenging question when the contact network is very heterogeneous, and strategies based on controlling network properties, such as the degree and spectral radius, have been shown to be effective. Implementation of such strategies requires detailed information on the contact structure, which might be sensitive in many applications. Our focus here is on choosing effective vaccination strategies when the edges are sensitive and differential privacy guarantees are needed. Our main contributions are (varepsilon,delta)-differentially private algorithms for designing vaccination strategies by reducing the maximum degree and spectral radius. Our key technique is a private algorithm for the multi-set multi-cover problem, which we use for controlling network properties. We evaluate privacy-utility tradeoffs of our algorithms on multiple synthetic and real-world networks, and show their effectiveness.

Fairness in graph neural networks has been actively studied recently. However, existing works often do not explicitly consider the role of message passing in introducing or amplifying the bias. In this paper, we first investigate the problem of bias amplification in message passing. We empirically and theoretically demonstrate that message passing could amplify the bias when the 1-hop neighbors from different demographic groups are unbalanced. Guided by such analyses, we propose BeMap, a fair message passing method, that leverages a balance-aware sampling strategy to balance the number of the 1-hop neighbors of each node among different demographic groups. Extensive experiments on node classification demonstrate the efficacy of BeMap in mitigating bias while maintaining classification accuracy. The code is available at https://github.com/xiaolin-cs/BeMap.

In shuffle privacy, each user sends a collection of randomized messages to a trusted shuffler, the shuffler randomly permutes these messages, and the resulting shuffled collection of messages must satisfy differential privacy. Prior work in this model has largely focused on protocols that use a single round of communication to compute algorithmic primitives like means, histograms, and counts. We present interactive shuffle protocols for stochastic convex optimization. Our protocols rely on a new noninteractive protocol for summing vectors of bounded ell_2 norm. By combining this sum subroutine with mini-batch stochastic gradient descent, accelerated gradient descent, and Nesterov's smoothing method, we obtain loss guarantees for a variety of convex loss functions that significantly improve on those of the local model and sometimes match those of the central model.

We give a geometry of interaction model for a typed lambda-calculus endowed with operators for sampling from a continuous uniform distribution and soft conditioning, namely a paradigmatic calculus for higher-order Bayesian programming. The model is based on the category of measurable spaces and partial measurable functions, and is proved adequate with respect to both a distribution-based and a sampling based operational semantics.

Motivated by applications in chemistry and other sciences, we study the expressive power of message-passing neural networks for geometric graphs, whose node features correspond to 3-dimensional positions. Recent work has shown that such models can separate generic pairs of non-isomorphic geometric graphs, though they may fail to separate some rare and complicated instances. However, these results assume a fully connected graph, where each node possesses complete knowledge of all other nodes. In contrast, often, in application, every node only possesses knowledge of a small number of nearest neighbors. This paper shows that generic pairs of non-isomorphic geometric graphs can be separated by message-passing networks with rotation equivariant features as long as the underlying graph is connected. When only invariant intermediate features are allowed, generic separation is guaranteed for generically globally rigid graphs. We introduce a simple architecture, EGENNET, which achieves our theoretical guarantees and compares favorably with alternative architecture on synthetic and chemical benchmarks. Our code is available at https://github.com/yonatansverdlov/E-GenNet.

In recent years, Large-Language-Model-driven AI agents have exhibited unprecedented intelligence, flexibility, and adaptability, and are rapidly changing human production and lifestyle. Nowadays, agents are undergoing a new round of evolution. They no longer act as an isolated island like LLMs. Instead, they start to communicate with diverse external entities, such as other agents and tools, to collectively perform more complex tasks. Under this trend, agent communication is regarded as a foundational pillar of the future AI ecosystem, and many organizations intensively begin to design related communication protocols (e.g., Anthropic's MCP and Google's A2A) within the recent few months. However, this new field exposes significant security hazard, which can cause severe damage to real-world scenarios. To help researchers to quickly figure out this promising topic and benefit the future agent communication development, this paper presents a comprehensive survey of agent communication security. More precisely, we first present a clear definition of agent communication and categorize the entire lifecyle of agent communication into three stages: user-agent interaction, agent-agent communication, and agent-environment communication. Next, for each communication phase, we dissect related protocols and analyze its security risks according to the communication characteristics. Then, we summarize and outlook on the possible defense countermeasures for each risk. Finally, we discuss open issues and future directions in this promising research field.

The privacy concerns of providing deep learning inference as a service have underscored the need for private inference (PI) protocols that protect users' data and the service provider's model using cryptographic methods. Recently proposed PI protocols have achieved significant reductions in PI latency by moving the computationally heavy homomorphic encryption (HE) parts to an offline/pre-compute phase. Paired with recent optimizations that tailor networks for PI, these protocols have achieved performance levels that are tantalizingly close to being practical. In this paper, we conduct a rigorous end-to-end characterization of PI protocols and optimization techniques and find that the current understanding of PI performance is overly optimistic. Specifically, we find that offline storage costs of garbled circuits (GC), a key cryptographic protocol used in PI, on user/client devices are prohibitively high and force much of the expensive offline HE computation to the online phase, resulting in a 10-1000times increase to PI latency. We propose a modified PI protocol that significantly reduces client-side storage costs for a small increase in online latency. Evaluated end-to-end, the modified protocol outperforms current protocols by reducing the mean PI latency by 4times for ResNet18 on TinyImageNet. We conclude with a discussion of several recently proposed PI optimizations in light of the findings and note many actually increase PI latency when evaluated from an end-to-end perspective.

The computation necessary for training Transformer-based language models has skyrocketed in recent years. This trend has motivated research on efficient training algorithms designed to improve training, validation, and downstream performance faster than standard training. In this work, we revisit three categories of such algorithms: dynamic architectures (layer stacking, layer dropping), batch selection (selective backprop, RHO loss), and efficient optimizers (Lion, Sophia). When pre-training BERT and T5 with a fixed computation budget using such methods, we find that their training, validation, and downstream gains vanish compared to a baseline with a fully-decayed learning rate. We define an evaluation protocol that enables computation to be done on arbitrary machines by mapping all computation time to a reference machine which we call reference system time. We discuss the limitations of our proposed protocol and release our code to encourage rigorous research in efficient training procedures: https://github.com/JeanKaddour/NoTrainNoGain.

Large Language Models (LLMs) exhibit strong general-purpose reasoning abilities but lack access to wireless environment information due to the absence of native sensory input and domain-specific priors. Previous attempts to apply LLMs in wireless systems either depend on retraining with network-specific data, which compromises language generalization, or rely on manually scripted interfaces, which hinder scalability. To overcome these limitations, we propose a Model Context Protocol (MCP)-based Internet of Experts (IoX) framework that equips LLMs with wireless environment-aware reasoning capabilities. The framework incorporates a set of lightweight expert models, each trained to solve a specific deterministic task in wireless communications, such as detecting a specific wireless attribute, e.g., line-of-sight propagation, Doppler effects, or fading conditions. Through MCP, the LLM can selectively query and interpret expert outputs at inference time, without modifying its own parameters. This architecture enables modular, extensible, and interpretable reasoning over wireless contexts. Evaluated across multiple mainstream LLMs, the proposed wireless environment-aware LLM agents achieve 40%-50% improvements in classification tasks over LLM-only baselines. More broadly, the MCP-based design offers a viable paradigm for future LLMs to inherit structured wireless network management capabilities.

Security of model parameters and user data is critical for Transformer-based services, such as ChatGPT. While recent strides in secure two-party protocols have successfully addressed security concerns in serving Transformer models, their adoption is practically infeasible due to the prohibitive cryptographic overheads involved. Drawing insights from our hands-on experience in developing two real-world Transformer-based services, we identify the inherent efficiency bottleneck in the two-party assumption. To overcome this limitation, we propose a novel three-party threat model. Within this framework, we design a semi-symmetric permutation-based protection scheme and present STIP, the first secure Transformer inference protocol without any inference accuracy loss. Experiments on representative Transformer models in real systems show that STIP has practical security and outperforms state-of-the-art secure two-party protocols in efficiency by millions of times.

From the Bayesian perspective, the category of conditional probabilities (a variant of the Kleisli category of the Giry monad, whose objects are measurable spaces and arrows are Markov kernels) gives a nice framework for conceptualization and analysis of many aspects of machine learning. Using categorical methods, we construct models for parametric and nonparametric Bayesian reasoning on function spaces, thus providing a basis for the supervised learning problem. In particular, stochastic processes are arrows to these function spaces which serve as prior probabilities. The resulting inference maps can often be analytically constructed in this symmetric monoidal weakly closed category. We also show how to view general stochastic processes using functor categories and demonstrate the Kalman filter as an archetype for the hidden Markov model.

In recent years, Text-to-Image (T2I) models have seen remarkable advancements, gaining widespread adoption. However, this progress has inadvertently opened avenues for potential misuse, particularly in generating inappropriate or Not-Safe-For-Work (NSFW) content. Our work introduces MMA-Diffusion, a framework that presents a significant and realistic threat to the security of T2I models by effectively circumventing current defensive measures in both open-source models and commercial online services. Unlike previous approaches, MMA-Diffusion leverages both textual and visual modalities to bypass safeguards like prompt filters and post-hoc safety checkers, thus exposing and highlighting the vulnerabilities in existing defense mechanisms.

As Large Language Models (LLMs) are increasingly integrated into automated, multi-stage pipelines, risk patterns that arise from unvalidated trust between processing stages become a practical concern. This paper presents a mechanism-centered taxonomy of 41 recurring risk patterns in commercial LLMs. The analysis shows that inputs are often interpreted non-neutrally and can trigger implementation-shaped responses or unintended state changes even without explicit commands. We argue that these behaviors constitute architectural failure modes and that string-level filtering alone is insufficient. To mitigate such cross-stage vulnerabilities, we recommend zero-trust architectural principles, including provenance enforcement, context sealing, and plan revalidation, and we introduce "Countermind" as a conceptual blueprint for implementing these defenses.

Large-scale distributed training in production datacenters constitutes a challenging workload bottlenecked by network communication. In response, both major industry players (e.g., Ultra Ethernet Consortium) and parts of academia have surprisingly, and almost unanimously, agreed that packet spraying is necessary to improve the performance of large-scale distributed training workloads. In this paper, we challenge this prevailing belief and pose the question: How close can a singlepath transport approach an optimal multipath transport? We demonstrate that singlepath transport (from a NIC's perspective) is sufficient and can perform nearly as well as an ideal multipath transport with packet spraying, particularly in the context of distributed training in leaf-spine topologies. Our assertion is based on four key observations about workloads driven by collective communication patterns: (i) flows within a collective start almost simultaneously, (ii) flow sizes are nearly equal, (iii) the completion time of a collective is more crucial than individual flow completion times, and (iv) flows can be split upon arrival. We analytically prove that singlepath transport, using minimal flow splitting (at the application layer), is equivalent to an ideal multipath transport with packet spraying in terms of maximum congestion. Our preliminary evaluations support our claims. This paper suggests an alternative agenda for developing next-generation transport protocols tailored for large-scale distributed training.

Diffusion language models (DLMs) have recently emerged as a promising alternative to autoregressive (AR) models, offering parallel decoding and controllable sampling dynamics while achieving competitive generation quality at scale. Despite this progress, the role of sampling mechanisms in shaping refusal behavior and jailbreak robustness remains poorly understood. In this work, we present a fundamental analytical framework for step-wise refusal dynamics, enabling comparison between AR and diffusion sampling. Our analysis reveals that the sampling strategy itself plays a central role in safety behavior, as a factor distinct from the underlying learned representations. Motivated by this analysis, we introduce the Step-Wise Refusal Internal Dynamics (SRI) signal, which supports interpretability and improved safety for both AR and DLMs. We demonstrate that the geometric structure of SRI captures internal recovery dynamics, and identifies anomalous behavior in harmful generations as cases of incomplete internal recovery that are not observable at the text level. This structure enables lightweight inference-time detectors that generalize to unseen attacks while matching or outperforming existing defenses with over 100times lower inference overhead.

Large language models (LLMs) have reshaped the landscape of program synthesis. However, contemporary LLM-based code completion systems often hallucinate broken code because they lack appropriate context, particularly when working with definitions not in the training data nor near the cursor. This paper demonstrates that tight integration with the type and binding structure of a language, as exposed by its language server, can address this contextualization problem in a token-efficient manner. In short, we contend that AIs need IDEs, too! In particular, we integrate LLM code generation into the Hazel live program sketching environment. The Hazel Language Server identifies the type and typing context of the hole being filled, even in the presence of errors, ensuring that a meaningful program sketch is always available. This allows prompting with codebase-wide contextual information not lexically local to the cursor, nor necessarily in the same file, but that is likely to be semantically local to the developer's goal. Completions synthesized by the LLM are then iteratively refined via further dialog with the language server. To evaluate these techniques, we introduce MVUBench, a dataset of model-view-update (MVU) web applications. These applications serve as challenge problems due to their reliance on application-specific data structures. We find that contextualization with type definitions is particularly impactful. After introducing our ideas in the context of Hazel we duplicate our techniques and port MVUBench to TypeScript in order to validate the applicability of these methods to higher-resource languages. Finally, we outline ChatLSP, a conservative extension to the Language Server Protocol (LSP) that language servers can implement to expose capabilities that AI code completion systems of various designs can use to incorporate static context when generating prompts for an LLM.

Large Language Models (LLMs) show promise in generating firmware for embedded systems, but often introduce security flaws and fail to meet real-time performance constraints. This paper proposes a three-phase methodology that combines LLM-based firmware generation with automated security validation and iterative refinement in a virtualized environment. Using structured prompts, models like GPT-4 generate firmware for networking and control tasks, deployed on FreeRTOS via QEMU. These implementations are tested using fuzzing, static analysis, and runtime monitoring to detect vulnerabilities such as buffer overflows (CWE-120), race conditions (CWE-362), and denial-of-service threats (CWE-400). Specialized AI agents for Threat Detection, Performance Optimization, and Compliance Verification collaborate to improve detection and remediation. Identified issues are categorized using CWE, then used to prompt targeted LLM-generated patches in an iterative loop. Experiments show a 92.4\% Vulnerability Remediation Rate (37.3\% improvement), 95.8\% Threat Model Compliance, and 0.87 Security Coverage Index. Real-time metrics include 8.6ms worst-case execution time and 195μs jitter. This process enhances firmware security and performance while contributing an open-source dataset for future research.

While the flexible capabilities of large language models (LLMs) allow them to answer a range of queries based on existing learned knowledge, information retrieval to augment generation is an important tool to allow LLMs to answer questions on information not included in pre-training data. Such private information is increasingly being generated in a wide array of distributed contexts by organizations and individuals. Performing such information retrieval using neural embeddings of queries and documents always leaked information about queries and database content unless both were stored locally. We present Private Retrieval Augmented Generation (PRAG), an approach that uses multi-party computation (MPC) to securely transmit queries to a distributed set of servers containing a privately constructed database to return top-k and approximate top-k documents. This is a first-of-its-kind approach to dense information retrieval that ensures no server observes a client's query or can see the database content. The approach introduces a novel MPC friendly protocol for inverted file approximate search (IVF) that allows for fast document search over distributed and private data in sublinear communication complexity. This work presents new avenues through which data for use in LLMs can be accessed and used without needing to centralize or forgo privacy.

Fragmentation is a routine part of communication in 6LoWPAN-based IoT networks, designed to accommodate small frame sizes on constrained wireless links. However, this process introduces a critical vulnerability fragments are typically stored and processed before their legitimacy is confirmed, allowing attackers to exploit this gap with minimal effort. In this work, we explore a defense strategy that takes a more adaptive, behavior-aware approach to this problem. Our system, called Predictive-CSM, introduces a combination of two lightweight mechanisms. The first tracks how each node behaves over time, rewarding consistent and successful interactions while quickly penalizing suspicious or failing patterns. The second checks the integrity of packet fragments using a chained hash, allowing incomplete or manipulated sequences to be caught early, before they can occupy memory or waste processing time. We put this system to the test using a set of targeted attack simulations, including early fragment injection, replayed headers, and flooding with fake data. Across all scenarios, Predictive CSM preserved network delivery and maintained energy efficiency, even under pressure. Rather than relying on heavyweight cryptography or rigid filters, this approach allows constrained de vices to adapt their defenses in real time based on what they observe, not just what they're told. In that way, it offers a step forward for securing fragmented communication in real world IoT systems

Generating new molecules is fundamental to advancing critical applications such as drug discovery and material synthesis. Flows can generate molecules effectively by inverting the encoding process, however, existing flow models either require artifactual dequantization or specific node/edge orderings, lack desiderata such as permutation invariance, or induce discrepancy between the encoding and the decoding steps that necessitates post hoc validity correction. We circumvent these issues with novel continuous normalizing E(3)-equivariant flows, based on a system of node ODEs coupled as a graph PDE, that repeatedly reconcile locally toward globally aligned densities. Our models can be cast as message-passing temporal networks, and result in superlative performance on the tasks of density estimation and molecular generation. In particular, our generated samples achieve state-of-the-art on both the standard QM9 and ZINC250K benchmarks.

Large Language Models (LLMs) still struggle with the structured reasoning and tool-assisted computation needed for problem solving in cybersecurity applications. In this work, we introduce "random-crypto", a cryptographic Capture-the-Flag (CTF) challenge generator framework that we use to fine-tune a tool-augmented Llama-3.1-8B with Guided Reinforcement Prompt Optimisation (GRPO), allowing the agent to iteratively write and execute Python inside an isolated REPL. GRPO yields a +53% absolute jump in Pass@8 on unseen "random-crypto" tasks (0.35 -> 0.88) and raises Majority@8 to 0.41. The fine-tuned agent also generalizes to an external dataset. On a subset of picoCTF cryptography problems, it improves Pass@8 by +13 pp. Ablations show the gains stem from more reliable tool invocation and code synthesis, rather than superficial prompt adaptation.

Large language models and autonomous AI agents have evolved rapidly, resulting in a diverse array of evaluation benchmarks, frameworks, and collaboration protocols. However, the landscape remains fragmented and lacks a unified taxonomy or comprehensive survey. Therefore, we present a side-by-side comparison of benchmarks developed between 2019 and 2025 that evaluate these models and agents across multiple domains. In addition, we propose a taxonomy of approximately 60 benchmarks that cover general and academic knowledge reasoning, mathematical problem-solving, code generation and software engineering, factual grounding and retrieval, domain-specific evaluations, multimodal and embodied tasks, task orchestration, and interactive assessments. Furthermore, we review AI-agent frameworks introduced between 2023 and 2025 that integrate large language models with modular toolkits to enable autonomous decision-making and multi-step reasoning. Moreover, we present real-world applications of autonomous AI agents in materials science, biomedical research, academic ideation, software engineering, synthetic data generation, chemical reasoning, mathematical problem-solving, geographic information systems, multimedia, healthcare, and finance. We then survey key agent-to-agent collaboration protocols, namely the Agent Communication Protocol (ACP), the Model Context Protocol (MCP), and the Agent-to-Agent Protocol (A2A). Finally, we discuss recommendations for future research, focusing on advanced reasoning strategies, failure modes in multi-agent LLM systems, automated scientific discovery, dynamic tool integration via reinforcement learning, integrated search capabilities, and security vulnerabilities in agent protocols.

This paper identifies and analyzes a novel vulnerability class in Model Context Protocol (MCP) based agent systems. The attack chain describes and demonstrates how benign, individually authorized tasks can be orchestrated to produce harmful emergent behaviors. Through systematic analysis using the MITRE ATLAS framework, we demonstrate how 95 agents tested with access to multiple services-including browser automation, financial analysis, location tracking, and code deployment-can chain legitimate operations into sophisticated attack sequences that extend beyond the security boundaries of any individual service. These red team exercises survey whether current MCP architectures lack cross-domain security measures necessary to detect or prevent a large category of compositional attacks. We present empirical evidence of specific attack chains that achieve targeted harm through service orchestration, including data exfiltration, financial manipulation, and infrastructure compromise. These findings reveal that the fundamental security assumption of service isolation fails when agents can coordinate actions across multiple domains, creating an exponential attack surface that grows with each additional capability. This research provides a barebones experimental framework that evaluate not whether agents can complete MCP benchmark tasks, but what happens when they complete them too well and optimize across multiple services in ways that violate human expectations and safety constraints. We propose three concrete experimental directions using the existing MCP benchmark suite.

Many areas of deep learning benefit from using increasingly larger neural networks trained on public data, as is the case for pre-trained models for NLP and computer vision. Training such models requires a lot of computational resources (e.g., HPC clusters) that are not available to small research groups and independent researchers. One way to address it is for several smaller groups to pool their computational resources together and train a model that benefits all participants. Unfortunately, in this case, any participant can jeopardize the entire training run by sending incorrect updates, deliberately or by mistake. Training in presence of such peers requires specialized distributed training algorithms with Byzantine tolerance. These algorithms often sacrifice efficiency by introducing redundant communication or passing all updates through a trusted server, making it infeasible to apply them to large-scale deep learning, where models can have billions of parameters. In this work, we propose a novel protocol for secure (Byzantine-tolerant) decentralized training that emphasizes communication efficiency.

This paper presents a program logic for reasoning about multithreaded Java-like programs with dynamic thread creation, thread joining and reentrant object monitors. The logic is based on concurrent separation logic. It is the first detailed adaptation of concurrent separation logic to a multithreaded Java-like language. The program logic associates a unique static access permission with each heap location, ensuring exclusive write accesses and ruling out data races. Concurrent reads are supported through fractional permissions. Permissions can be transferred between threads upon thread starting, thread joining, initial monitor entrancies and final monitor exits. In order to distinguish between initial monitor entrancies and monitor reentrancies, auxiliary variables keep track of multisets of currently held monitors. Data abstraction and behavioral subtyping are facilitated through abstract predicates, which are also used to represent monitor invariants, preconditions for thread starting and postconditions for thread joining. Value-parametrized types allow to conveniently capture common strong global invariants, like static object ownership relations. The program logic is presented for a model language with Java-like classes and interfaces, the soundness of the program logic is proven, and a number of illustrative examples are presented.

Pingmark defines a universal textual protocol for expressing spatial context through a minimal symbol: !@. Rather than embedding coordinates or using proprietary map links, Pingmark introduces a semantic trigger that compliant client applications interpret to generate a standardized resolver link of the form https://pingmark.me/lat/lon/[timestamp]. This allows location expression to function like existing textual conventions - @ for identity or # for topics - but for physical space. The protocol requires no user registration, relies on open mapping technologies, and protects privacy by generating location data ephemerally and locally. This paper presents the motivation, syntax, and design of the Pingmark Protocol Specification (PPS v0.1), its reference resolver implementation, and the long-term goal of establishing Pingmark as an open Internet standard for spatial mentions.

Large Language Models (LLMs) are increasingly deployed in multi-agent systems, where effective inter-model communication is crucial. Existing communication protocols either rely on natural language, incurring high inference costs and information loss, or on hidden states, which suffer from information concentration bias and inefficiency. To address these limitations, we propose KVComm, a novel communication framework that enables efficient communication between LLMs through selective sharing of KV pairs. KVComm leverages the rich information encoded in the KV pairs while avoiding the pitfalls of hidden states. We introduce a KV layer-wise selection strategy based on attention importance scores with a Gaussian prior to identify the most informative KV pairs for communication. Extensive experiments across diverse tasks and model pairs demonstrate that KVComm achieves comparable performance to the upper-bound method, which directly merges inputs to one model without any communication, while transmitting as few as 30\% of layers' KV pairs. Our study highlights the potential of KV pairs as an effective medium for inter-LLM communication, paving the way for scalable and efficient multi-agent systems.

The integration of Large Language Models (LLMs) with Internet-of-Things (IoT) systems faces significant challenges in hardware heterogeneity and control complexity. The Model Context Protocol (MCP) emerges as a critical enabler, providing standardized communication between LLMs and physical devices. We propose IoT-MCP, a novel framework that implements MCP through edge-deployed servers to bridge LLMs and IoT ecosystems. To support rigorous evaluation, we introduce IoT-MCP Bench, the first benchmark containing 114 Basic Tasks (e.g., ``What is the current temperature?'') and 1,140 Complex Tasks (e.g., ``I feel so hot, do you have any ideas?'') for IoT-enabled LLMs. Experimental validation across 22 sensor types and 6 microcontroller units demonstrates IoT-MCP's 100% task success rate to generate tool calls that fully meet expectations and obtain completely accurate results, 205ms average response time, and 74KB peak memory footprint. This work delivers both an open-source integration framework (https://github.com/Duke-CEI-Center/IoT-MCP-Servers) and a standardized evaluation methodology for LLM-IoT systems.

AI web agents use Internet resources at far greater speed, scale, and complexity -- changing how users and services interact. Deployed maliciously or erroneously, these agents could overload content providers. At the same time, web agents can bypass CAPTCHAs and other defenses by mimicking user behavior or flood authentication systems with fake accounts. Yet providers must protect their services and content from denial-of-service attacks and scraping by web agents. In this paper, we design a framework that imposes tunable costs on agents before providing access to resources; we call this Web Agent Throttling. We start by formalizing Throttling Gates as challenges issued to an agent that are asymmetric, scalable, robust, and compatible with any agent. Focusing on a common component -- the language model -- we require the agent to solve reasoning puzzles, thereby incurring excessive token-generation costs. However, we find that using existing puzzles, e.g., coding or math, as throttling gates fails to satisfy our properties. To address this, we introduce rebus-based Reasoning Gates, synthetic text puzzles that require multi-hop reasoning over world knowledge (thereby throttling an agent's model). We design a scalable generation and verification protocol for such reasoning gates. Our framework achieves computational asymmetry, i.e., the response-generation cost is 9.2x higher than the generation cost for SOTA models. We further deploy reasoning gates on a custom website and Model Context Protocol (MCP) servers and evaluate with real-world web agents. Finally, we discuss the limitations and environmental impact of real-world deployment of our framework.

Large language models (LLMs) have shown promising performance across diverse domains. Many practical applications of LLMs, such as code completion and structured data extraction, require adherence to syntactic constraints specified by a formal language. Yet, due to their probabilistic nature, LLM output is not guaranteed to adhere to such formal languages. Prior work has proposed constrained decoding as a means to restrict LLM generation to particular formal languages. However, existing works are not applicable to the emerging paradigm of diffusion LLMs, when used in practical scenarios such as the generation of formally correct C++ or JSON output. In this paper we address this challenge and present the first constrained decoding method for diffusion models, one that can handle formal languages captured by context-free grammars. We begin by reducing constrained decoding to the more general additive infilling problem, which asks whether a partial output can be completed to a valid word in the target language. This problem also naturally subsumes the previously unaddressed multi-region infilling constrained decoding. We then reduce this problem to the task of deciding whether the intersection of the target language and a regular language is empty and present an efficient algorithm to solve it for context-free languages. Empirical results on various applications, such as C++ code infilling and structured data extraction in JSON, demonstrate that our method achieves near-perfect syntactic correctness while consistently preserving or improving functional correctness. Importantly, our efficiency optimizations ensure that the computational overhead remains practical.

Multi-agent systems (MAS) powered by Large Language Models (LLMs) have been demonstrated to push the boundaries of LLM capabilities, yet they often incur significant costs and face challenges in dynamic LLM selection. Current LLM routing methods effectively reduce overhead in single-agent scenarios by customizing LLM selection for each query, but they overlook the critical decisions regarding collaboration modes and agent roles in MAS. In response to this challenge, we first introduce the problem of Multi-Agent System Routing (MASR), which integrates all components of MAS into a unified routing framework. Toward this goal, we propose MasRouter, the first high-performing, cost-effective, and inductive MASR solution. MasRouter employs collaboration mode determination, role allocation, and LLM routing through a cascaded controller network, progressively constructing a MAS that balances effectiveness and efficiency. Extensive experiments demonstrate that MasRouter is (1) high-performing, achieving a 1.8%sim8.2% improvement over the state-of-the-art method on MBPP; (2) economical, reducing overhead by up to 52.07% compared to SOTA methods on HumanEval; and (3) plug-and-play, seamlessly integrating with mainstream MAS frameworks, reducing overhead by 17.21%sim28.17% via customized routing. The code is available at https://github.com/yanweiyue/masrouter.

The numerical solution of partial differential equations (PDEs) is difficult, having led to a century of research so far. Recently, there have been pushes to build neural--numerical hybrid solvers, which piggy-backs the modern trend towards fully end-to-end learned systems. Most works so far can only generalize over a subset of properties to which a generic solver would be faced, including: resolution, topology, geometry, boundary conditions, domain discretization regularity, dimensionality, etc. In this work, we build a solver, satisfying these properties, where all the components are based on neural message passing, replacing all heuristically designed components in the computation graph with backprop-optimized neural function approximators. We show that neural message passing solvers representationally contain some classical methods, such as finite differences, finite volumes, and WENO schemes. In order to encourage stability in training autoregressive models, we put forward a method that is based on the principle of zero-stability, posing stability as a domain adaptation problem. We validate our method on various fluid-like flow problems, demonstrating fast, stable, and accurate performance across different domain topologies, equation parameters, discretizations, etc., in 1D and 2D.

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.

Large Language Models (LLMs) are increasingly deployed in agentic systems that interact with an external environment; this makes them susceptible to prompt injections when dealing with untrusted data. To overcome this limitation, we propose SIC (Soft Instruction Control)-a simple yet effective iterative prompt sanitization loop designed for tool-augmented LLM agents. Our method repeatedly inspects incoming data for instructions that could compromise agent behavior. If such content is found, the malicious content is rewritten, masked, or removed, and the result is re-evaluated. The process continues until the input is clean or a maximum iteration limit is reached; if imperative instruction-like content remains, the agent halts to ensure security. By allowing multiple passes, our approach acknowledges that individual rewrites may fail but enables the system to catch and correct missed injections in later steps. Although immediately useful, worst-case analysis shows that SIC is not infallible; strong adversary can still get a 15% ASR by embedding non-imperative workflows. This nonetheless raises the bar.

Graph neural networks have recently achieved great successes in predicting quantum mechanical properties of molecules. These models represent a molecule as a graph using only the distance between atoms (nodes). They do not, however, consider the spatial direction from one atom to another, despite directional information playing a central role in empirical potentials for molecules, e.g. in angular potentials. To alleviate this limitation we propose directional message passing, in which we embed the messages passed between atoms instead of the atoms themselves. Each message is associated with a direction in coordinate space. These directional message embeddings are rotationally equivariant since the associated directions rotate with the molecule. We propose a message passing scheme analogous to belief propagation, which uses the directional information by transforming messages based on the angle between them. Additionally, we use spherical Bessel functions and spherical harmonics to construct theoretically well-founded, orthogonal representations that achieve better performance than the currently prevalent Gaussian radial basis representations while using fewer than 1/4 of the parameters. We leverage these innovations to construct the directional message passing neural network (DimeNet). DimeNet outperforms previous GNNs on average by 76% on MD17 and by 31% on QM9. Our implementation is available online.

Denoising diffusion bridge models (DDBMs) are a powerful variant of diffusion models for interpolating between two arbitrary paired distributions given as endpoints. Despite their promising performance in tasks like image translation, DDBMs require a computationally intensive sampling process that involves the simulation of a (stochastic) differential equation through hundreds of network evaluations. In this work, we take the first step in fast sampling of DDBMs without extra training, motivated by the well-established recipes in diffusion models. We generalize DDBMs via a class of non-Markovian diffusion bridges defined on the discretized timesteps concerning sampling, which share the same marginal distributions and training objectives, give rise to generative processes ranging from stochastic to deterministic, and result in diffusion bridge implicit models (DBIMs). DBIMs are not only up to 25times faster than the vanilla sampler of DDBMs but also induce a novel, simple, and insightful form of ordinary differential equation (ODE) which inspires high-order numerical solvers. Moreover, DBIMs maintain the generation diversity in a distinguished way, by using a booting noise in the initial sampling step, which enables faithful encoding, reconstruction, and semantic interpolation in image translation tasks. Code is available at https://github.com/thu-ml/DiffusionBridge.

Automata learning is a popular technique used to automatically construct an automaton model from queries. Much research went into devising ad hoc adaptations of algorithms for different types of automata. The CALF project seeks to unify these using category theory in order to ease correctness proofs and guide the design of new algorithms. In this paper, we extend CALF to cover learning of algebraic structures that may not have a coalgebraic presentation. Furthermore, we provide a detailed algorithmic account of an abstract version of the popular L* algorithm, which was missing from CALF. We instantiate the abstract theory to a large class of Set functors, by which we recover for the first time practical tree automata learning algorithms from an abstract framework and at the same time obtain new algorithms to learn algebras of quotiented polynomial functors.

The growth in the number of parameters of Large Language Models (LLMs) has led to a significant surge in computational requirements, making them challenging and costly to deploy. Speculative decoding (SD) leverages smaller models to efficiently propose future tokens, which are then verified by the LLM in parallel. Small models that utilise activations from the LLM currently achieve the fastest decoding speeds. However, we identify several limitations of SD models including the lack of on-policyness during training and partial observability. To address these shortcomings, we propose a more grounded architecture for small models by introducing a Mixture of Attentions for SD. Our novel architecture can be applied in two scenarios: a conventional single device deployment and a novel client-server deployment where the small model is hosted on a consumer device and the LLM on a server. In a single-device scenario, we demonstrate state-of-the-art speedups improving EAGLE-2 by 9.5% and its acceptance length by 25%. In a client-server setting, our experiments demonstrate: 1) state-of-the-art latencies with minimal calls to the server for different network conditions, and 2) in the event of a complete disconnection, our approach can maintain higher accuracy compared to other SD methods and demonstrates advantages over API calls to LLMs, which would otherwise be unable to continue the generation process.

Wireless mesh networks (WMNs) have emerged as a key technology for next generation wireless broadband networks showing rapid progress and inspiring numerous compelling applications. A WMN comprises of a set of mesh routers (MRs) and mesh clients (MCs), where MRs are connected to the Internet backbone through the Internet gateways (IGWs). The MCs are wireless devices and communicate among themselves over possibly multi-hop paths with or without the involvement of MRs. User privacy and security have been primary concerns in WMNs due to their peer-to-peer network topology, shared wireless medium, stringent resource constraints, and highly dynamic environment. Moreover, to support real-time applications, WMNs must also be equipped with robust, reliable and efficient communication protocols so as to minimize the end-to-end latency and packet drops. Design of a secure and efficient communication protocol for WMNs, therefore, is of paramount importance. In this paper, we propose a security and privacy protocol that provides security and user anonymity while maintaining communication efficiency in a WMN. The security protocol ensures secure authentication and encryption in access and the backbone networks. The user anonymity, authentication and data privacy is achieved by application of a protocol that is based on Rivest's ring signature scheme. Simulation results demonstrate that while the protocols have minimal storage and communication overhead, they are robust and provide high level of security and privacy to the users of the network services.

Diffusion language models (DLMs) have recently emerged as an alternative to autoregressive approaches, offering parallel sequence generation and flexible token orders. However, their inference remains slower than that of autoregressive models, primarily due to the cost of bidirectional attention and the large number of refinement steps required for high quality outputs. In this work, we highlight and leverage an overlooked property of DLMs early answer convergence: in many cases, the correct answer can be internally identified by half steps before the final decoding step, both under semi-autoregressive and random remasking schedules. For example, on GSM8K and MMLU, up to 97% and 99% of instances, respectively, can be decoded correctly using only half of the refinement steps. Building on this observation, we introduce Prophet, a training-free fast decoding paradigm that enables early commit decoding. Specifically, Prophet dynamically decides whether to continue refinement or to go "all-in" (i.e., decode all remaining tokens in one step), using the confidence gap between the top-2 prediction candidates as the criterion. It integrates seamlessly into existing DLM implementations, incurs negligible overhead, and requires no additional training. Empirical evaluations of LLaDA-8B and Dream-7B across multiple tasks show that Prophet reduces the number of decoding steps by up to 3.4x while preserving high generation quality. These results recast DLM decoding as a problem of when to stop sampling, and demonstrate that early decode convergence provides a simple yet powerful mechanism for accelerating DLM inference, complementary to existing speedup techniques. Our code is publicly available at https://github.com/pixeli99/Prophet.

Diffusion models have emerged as a powerful class of generative models across various modalities, including image, video, and audio synthesis. However, their deployment is often limited by significant inference latency, primarily due to the inherently sequential nature of the denoising process. While existing parallelization strategies attempt to accelerate inference by distributing computation across multiple devices, they typically incur high communication overhead, hindering deployment on commercial hardware. To address this challenge, we propose ParaStep, a novel parallelization method based on a reuse-then-predict mechanism that parallelizes diffusion inference by exploiting similarity between adjacent denoising steps. Unlike prior approaches that rely on layer-wise or stage-wise communication, ParaStep employs lightweight, step-wise communication, substantially reducing overhead. ParaStep achieves end-to-end speedups of up to 3.88times on SVD, 2.43times on CogVideoX-2b, and 6.56times on AudioLDM2-large, while maintaining generation quality. These results highlight ParaStep as a scalable and communication-efficient solution for accelerating diffusion inference, particularly in bandwidth-constrained environments.

Message passing mechanism contributes to the success of GNNs in various applications, but also brings the oversquashing problem. Recent works combat oversquashing by improving the graph spectrums with rewiring techniques, disrupting the structural bias in graphs, and having limited improvement on oversquashing in terms of oversquashing measure. Motivated by unitary RNN, we propose Graph Unitary Message Passing (GUMP) to alleviate oversquashing in GNNs by applying unitary adjacency matrix for message passing. To design GUMP, a transformation is first proposed to make general graphs have unitary adjacency matrix and keep its structural bias. Then, unitary adjacency matrix is obtained with a unitary projection algorithm, which is implemented by utilizing the intrinsic structure of unitary adjacency matrix and allows GUMP to be permutation-equivariant. Experimental results show the effectiveness of GUMP in improving the performance on various graph learning tasks.

Data steganography aims to conceal information within visual content, yet existing spatial- and frequency-domain approaches suffer from trade-offs between security, capacity, and perceptual quality. Recent advances in generative models, particularly diffusion models, offer new avenues for adaptive image synthesis, but integrating precise information embedding into the generative process remains challenging. We introduce Shackled Dancing Diffusion, or SD^2, a plug-and-play generative steganography method that combines bit-position locking with diffusion sampling injection to enable controllable information embedding within the generative trajectory. SD^2 leverages the expressive power of diffusion models to synthesize diverse carrier images while maintaining full message recovery with 100% accuracy. Our method achieves a favorable balance between randomness and constraint, enhancing robustness against steganalysis without compromising image fidelity. Extensive experiments show that SD^2 substantially outperforms prior methods in security, embedding capacity, and stability. This algorithm offers new insights into controllable generation and opens promising directions for secure visual communication.

The internet is undergoing a historical transformation from the "Internet of Websites" to the "Internet of AgentSites." While traditional Websites served as the foundation for information hosting and dissemination, a new frontier is emerging where AgentSites serve as the hubs of the internet, where each AgentSite hosts one or more AI agents that receive tasks, address them, and deliver actionable solutions, marking a significant shift in the digital landscape and representing the next generation of online ecosystems. Under this vision, AIOS, the AI Agent Operating System, serves as the server for the development, deployment and execution of AI agents, which is a fundamental infrastructure for the Internet of Agentsites. In this paper, we introduce AIOS Server, a runtime framework to host agents and enable global-scale collaboration among decentralized agents. AIOS Server provides a communication protocol leveraging the Model Context Protocol (MCP) and JSON-RPC to enable agent-agent or human-agent interactions. Each AIOS node operates as a server to host and execute agents, while supporting peer-to-peer coordination without reliance on centralized orchestration. Based on AIOS Server, we further present the world's first practically deployed Internet of Agentsites (AIOS-IoA), including AgentHub for agent registration and discovery and AgentChat for interactive communication, at https://planet.aios.foundation. The agent discovery mechanism based on Distributed Hash Tables (DHT) and a Gossip protocol serves as the search engine for the internet of agentsites. This work provides a practical foundation for building the Internet of Agentsites-a new paradigm where autonomous agents become first-class citizens of the web. The implementation is available at https://github.com/agiresearch/AIOS.Server and is integrated into the AIOS main branch at https://github.com/agiresearch/AIOS.