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Aug 5

Benchmarking AI Models in Software Engineering: A Review, Search Tool, and Enhancement Protocol

Benchmarks are essential for consistent evaluation and reproducibility. The integration of Artificial Intelligence into Software Engineering (AI4SE) has given rise to numerous benchmarks for tasks such as code generation and bug fixing. However, this surge presents challenges: (1) scattered benchmark knowledge across tasks, (2) difficulty in selecting relevant benchmarks, (3) the absence of a uniform standard for benchmark development, and (4) limitations of existing benchmarks. In this paper, we review 173 studies and identify 204 AI4SE benchmarks. We classify these benchmarks, analyze their limitations, and expose gaps in practices. Based on our review, we created BenchScout, a semantic search tool to find relevant benchmarks, using automated clustering of the contexts from associated studies. We conducted a user study with 22 participants to evaluate BenchScout's usability, effectiveness, and intuitiveness which resulted in average scores of 4.5, 4.0, and 4.1 out of 5. To advance benchmarking standards, we propose BenchFrame, a unified method to enhance benchmark quality. As a case study, we applied BenchFrame to the HumanEval benchmark and addressed its main limitations. This led to HumanEvalNext, featuring (1) corrected errors, (2) improved language conversion, (3) expanded test coverage, and (4) increased difficulty. We then evaluated ten state-of-the-art code language models on HumanEval, HumanEvalPlus, and HumanEvalNext. On HumanEvalNext, models showed a pass@1 score reduction of 31.22% and 19.94% compared to HumanEval and HumanEvalPlus, respectively.

  • 3 authors
·
Mar 7, 2025 2

CADENCE: Closing the Reasoning Gap via Coverage-Adaptive On-Policy Distillation

On-policy knowledge distillation transfers reasoning from large teachers to compact students, but existing approaches suffer three compounding failure modes: (i) cold-start collapse, where a fresh student assigns near-zero mass to teacher-preferred tokens; (ii) state-agnostic divergence scheduling, where time-only forward/reverse-KL interpolation ignores the student's coverage state; and (iii) binary reward sparsity, where pass/fail signals discard information from partially correct traces. We present CADENCE, a unified framework with a targeted fix for each. Its DRIFT mechanism schedules a per-token convex mixture of forward-KL and reverse-KL surrogate objectives on student-sampled trajectories (per-token surrogates, not sequence-level KL gradient estimators). Six components extend it: (A) COVA, a coverage-adaptive β schedule accelerating the forward-to-reverse transition; (B) FTB, a forking-token boost concentrating gradient at high-entropy positions via a globally-normalized entropy reference; (C) CCD, a dense reward adding numerical-proximity partial credit for incorrect-but-close traces; (D) LAP, brevity-preferential correct-rollout reinforcement; (E) EMR, an entropy-matching calibration regularizer; (F) BSD, a bootstrapped self-distillation phase. On GSM8K and MATH-500 (corrected 512-token protocol, 5 seeds, reported std), CADENCE distills a 0.5B student from a 1.5B teacher to 69.8 pm 0.5% GSM8K pass@1 (from 48.7% pretrained; 63.2% of the teacher gap closed) and to 72.1 pm 0.4% with a 3B teacher (76.2% closed), beating the strongest matched-compute label-using baseline (DRIFT+binary reward) by +4.4 pm 0.7 points. All experiments run on a single Apple Mac Studio (M-series, 64GB unified memory), showing principled distillation reaches strong reasoning quality without datacenter-scale hardware.

  • 2 authors
·
Jul 17 2

G-Designer: Architecting Multi-agent Communication Topologies via Graph Neural Networks

Recent advancements in large language model (LLM)-based agents have demonstrated that collective intelligence can significantly surpass the capabilities of individual agents, primarily due to well-crafted inter-agent communication topologies. Despite the diverse and high-performing designs available, practitioners often face confusion when selecting the most effective pipeline for their specific task: Which topology is the best choice for my task, avoiding unnecessary communication token overhead while ensuring high-quality solution? In response to this dilemma, we introduce G-Designer, an adaptive, efficient, and robust solution for multi-agent deployment, which dynamically designs task-aware, customized communication topologies. Specifically, G-Designer models the multi-agent system as a multi-agent network, leveraging a variational graph auto-encoder to encode both the nodes (agents) and a task-specific virtual node, and decodes a task-adaptive and high-performing communication topology. Extensive experiments on six benchmarks showcase that G-Designer is: (1) high-performing, achieving superior results on MMLU with accuracy at 84.50% and on HumanEval with pass@1 at 89.90%; (2) task-adaptive, architecting communication protocols tailored to task difficulty, reducing token consumption by up to 95.33% on HumanEval; and (3) adversarially robust, defending against agent adversarial attacks with merely 0.3% accuracy drop.

  • 9 authors
·
Oct 15, 2024

Finding Duplicates in 1.1M BDD Steps: cukereuse, a Paraphrase-Robust Static Detector for Cucumber and Gherkin

Behaviour-Driven Development (BDD) suites accumulate step-text duplication whose maintenance cost is established in prior work. Existing detection techniques require running the tests (Binamungu et al., 2018-2023) or are confined to a single organisation (Irshad et al., 2020-2022), leaving a gap: a purely static, paraphrase-robust, step-level detector usable on any repository. We fill the gap with cukereuse, an open-source Python CLI combining exact hashing, Levenshtein ratio, and sentence-transformer embeddings in a layered pipeline, released alongside an empirical corpus of 347 public GitHub repositories, 23,667 parsed .feature files, and 1,113,616 Gherkin steps. The step-weighted exact-duplicate rate is 80.2 %; the median-repository rate is 58.6 % (Spearman rho = 0.51 with size). The top hybrid cluster groups 20.7k occurrences across 2.2k files. Against 1,020 pairs manually labelled by the three authors under a released rubric (inter-annotator Fleiss' kappa = 0.84 on a 60-pair overlap), we report precision, recall, and F1 with bootstrap 95 % CIs under two protocols: the primary rubric and a score-free second-pass relabelling. The strongest honest pair-level number is near-exact at F1 = 0.822 on score-free labels; the primary-rubric semantic F1 = 0.906 is inflated by a stratification artefact that pins recall at 1.000. Lexical baselines (SourcererCC-style, NiCad-style) reach primary F1 = 0.761 and 0.799. The paper also presents a CDN-structured critique of Gherkin (Cognitive Dimensions of Notations); eight of fourteen dimensions are rated problematic or unsupported. The tool, corpus, labelled pairs, rubric, and pipeline are released under permissive licences.

  • 3 authors
·
Apr 21 1

Breaking the Protocol: Security Analysis of the Model Context Protocol Specification and Prompt Injection Vulnerabilities in Tool-Integrated LLM Agents

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

  • 2 authors
·
Jan 23

LDP: An Identity-Aware Protocol for Multi-Agent LLM Systems

As multi-agent AI systems grow in complexity, the protocols connecting them constrain their capabilities. Current protocols such as A2A and MCP do not expose model-level properties as first-class primitives, ignoring properties fundamental to effective delegation: model identity, reasoning profile, quality calibration, and cost characteristics. We present the LLM Delegate Protocol (LDP), an AI-native communication protocol introducing five mechanisms: (1) rich delegate identity cards with quality hints and reasoning profiles; (2) progressive payload modes with negotiation and fallback; (3) governed sessions with persistent context; (4) structured provenance tracking confidence and verification status; (5) trust domains enforcing security boundaries at the protocol level. We implement LDP as a plugin for the JamJet agent runtime and evaluate against A2A and random baselines using local Ollama models and LLM-as-judge evaluation. Identity-aware routing achieves ~12x lower latency on easy tasks through delegate specialization, though it does not improve aggregate quality in our small delegate pool; semantic frame payloads reduce token count by 37% (p=0.031) with no observed quality loss; governed sessions eliminate 39% token overhead at 10 rounds; and noisy provenance degrades synthesis quality below the no-provenance baseline, arguing that confidence metadata is harmful without verification. Simulated analyses show architectural advantages in attack detection (96% vs. 6%) and failure recovery (100% vs. 35% completion). This paper contributes a protocol design, reference implementation, and initial evidence that AI-native protocol primitives enable more efficient and governable delegation.

  • 1 authors
·
Mar 8

AIP: Agent Identity Protocol for Verifiable Delegation Across MCP and A2A

AI agents increasingly call tools via the Model Context Protocol (MCP) and delegate to other agents via Agent-to-Agent (A2A), yet neither protocol verifies agent identity. A scan of approximately 2,000 MCP servers found all lacked authentication. In our survey, we did not identify a prior implemented protocol that jointly combines public-key verifiable delegation, holder-side attenuation, expressive chained policy, transport bindings across MCP/A2A/HTTP, and provenance-oriented completion records. We introduce Invocation-Bound Capability Tokens (IBCTs), a primitive that fuses identity, attenuated authorization, and provenance binding into a single append-only token chain. IBCTs operate in two wire formats: compact mode (a signed JWT for single-hop cases) and chained mode (a Biscuit token with Datalog policies for multi-hop delegation). We provide reference implementations in Python and Rust with full cross-language interoperability. Compact mode verification takes 0.049ms (Rust) and 0.189ms (Python), with 0.22ms overhead over no-auth in real MCP-over-HTTP deployment. In a real multi-agent deployment with Gemini 2.5 Flash, AIP adds 2.35ms of overhead (0.086% of total end-to-end latency). Adversarial evaluation across 600 attack attempts shows 100% rejection rate, with two attack categories (delegation depth violation and audit evasion through empty context) uniquely caught by AIP's chained delegation model that neither unsigned nor plain JWT deployments detect.

  • 1 authors
·
Mar 24

A Formal Analysis of SCTP: Attack Synthesis and Patch Verification

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.

  • 5 authors
·
Mar 8, 2024

AEGIS: Assay-Aware Protocol Validation and Runtime Monitoring for Open-Source Liquid Handling Robots

Self-driving laboratories increasingly rely on low-cost liquid handlers such as the Opentrons OT-2, which ship without the pressure-based aspiration monitoring of Hamilton or Tecan systems and are typically run open-loop. Two failure modes go undetected: protocols that are syntactically valid but violate assay-specific invariants (e.g., tip reuse between a PCR template and a no-template control), and physical execution failures (partial dispense, air bubbles, missing tips) at runtime. We present AEGIS, a two-layer guardian for both. Layer 1 pairs a curated machine-readable assay rule database with an LLM that reasons over OT-2 Python code, reaching an adjusted F1 of 0.97 on a 24-protocol benchmark across five assay families and beating rules-only and LLM-only ablations across five backends; a free open-weight model ties the best proprietary one, so no paid API is required. Layer 2 fits a PCA world model to YOLO-cropped four-frame pipette trajectories; under a leakage-free leave-one-plate-out evaluation it reaches average precision 0.89 and operating-point F1 0.71 (AUROC 0.80), a deployment-faithful number that matches the live demonstration, and we characterize the small-pipette (p20) resolution limit (F1 0.47). A live demonstration on a physical OT-2 (five replicates per condition) catches planted no-tip failures deterministically and partial dispense on coloured dyes, with an always-VLM self-vote gate lifting partial-dispense recall to 5/5; transparent water is a principled limit of any front-view-only monitor, which AEGIS surfaces as low-confidence VLM reasoning rather than a wrong verdict. Cascade triage holds VLM cost near 1.63 per plate versus 10.33 for an always-VLM baseline. AEGIS is open source and, to our knowledge, the first system to unify pre-flight assay-aware validation with runtime visual monitoring for an open-source liquid handler.

  • 4 authors
·
Jul 16

On Randomness in Agentic Evals

Agentic systems are evaluated on benchmarks where agents interact with environments to solve tasks. Most papers report a pass@1 score computed from a single run per task, assuming this gives a reliable performance estimate. We test this assumption by collecting 60,000 agentic trajectories on SWE-Bench-Verified, spanning three models and two scaffolds. We find substantial variance: single-run pass@1 estimates vary by 2.2 to 6.0 percentage points depending on which run is selected, with standard deviations exceeding 1.5 percentage points even at temperature 0. This variance has critical implications: reported improvements of 2--3 percentage points may reflect evaluation noise rather than genuine algorithmic progress. Through token-level analysis, we show that trajectories diverge early, often within the first few percent of tokens, and that these small differences cascade into different solution strategies. To enable reliable evaluation of agentic systems, we recommend three concrete practices: (1) estimate pass@1 from multiple independent runs per task, especially when measuring small improvements, (2) use statistical power analysis to determine the number of runs needed to detect expected effect sizes, and (3) consider metrics like pass@k (optimistic bound) and pass^k (pessimistic bound) with k>1 to better characterize the full performance envelope. While these practices increase evaluation cost, they are essential for distinguishing genuine scientific progress from statistical noise.

Collaborative Human-Agent Protocol (CHAP)

Foundation models are moving from response generation into operational roles. They plan across steps, call tools, request human input, coordinate with other agents, and increasingly carry responsibility for work that affects customers, claims, code, contracts, and clinical decisions. Production deployments are no longer one human supervising one model. They are multi-human, multi-agent collaborations that cross teams, time zones, and trust boundaries. The technical surface for this collaboration remains weakly specified. When an agent drafts a response and a human edits it before it ships, the moment of human judgement is the most valuable signal in the system. In current practice it is recorded, if at all, in application code, chat threads, ticket comments, and tribal memory. Two protocol standards address adjacent concerns: MCP standardises agent access to tools and data, and A2A standardises agent-to-agent interoperability. Neither defines the shared workspace in which humans and agents perform accountable work together. This paper presents CHAP, the Collaborative Human-Agent Protocol. Under CHAP, the override that used to vanish into a chat thread becomes a structured event carrying a diff, a rationale, and a content hash. The handoff between shifts becomes a portable envelope rather than a pinned message. The human approval of an agent's draft becomes a non-repudiable signed decision that can be replayed years later. The protocol achieves this through a small Core (workspaces, participants, tasks, artefacts, and an append-only evidence log) together with composable profiles that add review, modes, routing, deliberation, handoff, identity, signatures, and transparency-backed audit as deployments require them. Specification, reference implementation, conformance suite, and worked examples are available at: https://github.com/BrightbeamAI/chap

  • 3 authors
·
Jun 19

AI Control: Improving Safety Despite Intentional Subversion

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.

  • 4 authors
·
Dec 11, 2023

Exploiting Verification-Generation Gap: Test-Time Reinforcement Learning with Confidence-Conditioned Verification

Test-time reinforcement learning has emerged as a promising paradigm for enhancing the complex reasoning abilities of large language models in a completely label-free manner. Despite existing studies focusing on Pass@1 performance, optimizing Pass@k remains under-explored yet critical in label-free settings, which measures generation coverage for sustained exploration. Optimizing Pass@k in label-free setting is highly non-trivial, as directly applying the Pass@k advantage designs effective for RLVR yields unsatisfactory performance. Through in-depth empirical analysis, we discover the root causes hindering performance: pseudo-label estimations for low-confidence samples have a high probability of being incorrect, while candidate answers for high-confidence samples suffer from severe diversity collapse. To overcome these hurdles, we propose TTRL-CoCoV (Test-Time Reinforcement Learning with Confidence-Conditioned Verification), a novel confidence-adaptive framework that expands Pass@k coverage and improves Pass@1 performance. Based on our key insight that verification capability generally leads generation capability, TTRL-CoCoV employs a confidence-conditioned mechanism: for high-confidence samples, it bootstraps verifier and applies an exploration-enhancing reward to prevent diversity collapse; for low-confidence samples, it delegates pseudo-label selection to the verifier to filter incorrect pseudo-labels; and for medium-confidence samples, it bypasses verification entirely. Extensive experiments demonstrate that TTRL-CoCoV outperforms the best competing methods across 6 widely-recognized benchmarks, achieves average absolute gains of +9.8% in Pass@1 and +18.7% in Pass@16 over TTRL, and even achieves absolute Pass@1 improvements of up to +5.0% across multiple reasoning benchmarks when compared against fully supervised RL methods. Our code repository: https://github.com/shanjf666/CoCoV.

  • 8 authors
·
Jun 1

Entanglement Purification in Quantum Networks: Guaranteed Improvement and Optimal Time

While the concept of entanglement purification protocols (EPPs) is straightforward, the integration of EPPs in network architectures requires careful performance evaluations and optimizations that take into account realistic conditions and imperfections, especially probabilistic entanglement generation and quantum memory decoherence. It is important to understand what is guaranteed to be improved from successful EPP with arbitrary non-identical input, which determines whether we want to perform the EPP at all. When successful EPP can offer improvement, the time to perform the EPP should also be optimized to maximize the improvement. In this work, we study the guaranteed improvement and optimal time for the CNOT-based recurrence EPP, previously shown to be optimal in various scenarios. We firstly prove guaranteed improvement for multiple figures of merit, including fidelity and several entanglement measures when compared to practical baselines as functions of input states. However, it is noteworthy that the guaranteed improvement we prove does not imply the universality of the EPP as introduced in arXiv:2407.21760. Then we prove robust, parameter-independent optimal time for typical error models and figures of merit. We further explore memory decoherence described by continuous-time Pauli channels, and demonstrate the phenomenon of optimal time transition when the memory decoherence error pattern changes. Our work deepens the understanding of EPP performance in realistic scenarios and offers insights into optimizing quantum networks that integrate EPPs.

  • 5 authors
·
May 4, 2025

Claw-Eval: Toward Trustworthy Evaluation of Autonomous Agents

Large language models are increasingly deployed as autonomous agents executing multi-step workflows in real-world software environments. However, existing agent benchmarks suffer from three critical limitations: (1) trajectory-opaque grading that checks only final outputs, (2) underspecified safety and robustness evaluation, and (3) narrow modality coverage and interaction paradigms. We introduce Claw-Eval, an end-to-end evaluation suite addressing all three gaps. It comprises 300 human-verified tasks spanning 9 categories across three groups (general service orchestration, multimodal perception and generation, and multi-turn professional dialogue). Every agent action is recorded through three independent evidence channels (execution traces, audit logs, and environment snapshots), enabling trajectory-aware grading over 2,159 fine-grained rubric items. The scoring protocol evaluates Completion, Safety, and Robustness, reporting Average Score, Pass@k, and Pass^k across three trials to distinguish genuine capability from lucky outcomes. Experiments on 14 frontier models reveal that: (1) trajectory-opaque evaluation is systematically unreliable, missing 44% of safety violations and 13% of robustness failures that our hybrid pipeline catches; (2) controlled error injection primarily degrades consistency rather than peak capability, with Pass^3 dropping up to 24% while Pass@3 remains stable; (3) multimodal performance varies sharply, with most models performing poorer on video than on document or image, and no single model dominating across all modalities. Beyond benchmarking, Claw-Eval highlights actionable directions for agent development, shedding light on what it takes to build agents that are not only capable but reliably deployable.

claw-eval Claw-Eval
·
Apr 6 5

DPBench: Structural Determinants of Multi-Agent LLM Coordination Under Simultaneous Resource Contention

We present DPBench, a benchmark for evaluating coordination in multi-agent systems built from large language models. Existing benchmarks measure task-level success under a fixed protocol; the structural conditions under which coordination succeeds or fails at all have not been characterised. DPBench adapts the Dining Philosophers problem into a controlled testbed where the action protocol, the communication structure, and the group size each vary independently. We evaluate six agents: GPT-5.2, Claude Opus 4.5, Grok 4.1, Gemini 2.5 Flash, Llama 4 Maverick, and a uniform-random baseline. Under simultaneous action at N=5 with the default prompt, deadlock ranges from 25.0% (95% Wilson CI [11.2, 46.9]) for GPT-5.2 to 90.0% [74.4, 96.5] for Gemini 2.5 Flash; sequential action is solved by four of the six. Holding the model fixed at Gemini 2.5 Flash, three protocol variables drive deadlock from 90% to within CI of zero: three rounds of pre-commitment communication (0.0% vs. single-round 86.7%), a prompt encoding a classical concurrency primitive (0.0% for resource-ordering and symmetry-breaking, against 100% for the minimal prompt), or doubling the group from N=5 to N=10 (90.0% to 10.0%). Single-round messaging and memory of past timesteps do not change the rate at the sample size we ran. Whether the same model coordinates or deadlocks is determined by the protocol, not by the model's capability.

  • 2 authors
·
Jun 2

CryptoNite: Revealing the Pitfalls of End-to-End Private Inference at Scale

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.

  • 5 authors
·
Nov 3, 2021

Unleashing Scientific Reasoning for Bio-experimental Protocol Generation via Structured Component-based Reward Mechanism

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.

  • 11 authors
·
Oct 17, 2025 2

The Last Word Often Wins: A Format Confound in Chain-of-Thought Corruption Studies

Corruption studies, the primary tool for evaluating chain-of-thought (CoT) faithfulness, identify which chain positions are "computationally important" by measuring accuracy when steps are replaced with errors. We identify a systematic confound: for chains with explicit terminal answer statements, the dominant format in standard benchmarks, corruption studies detect where the answer text appears, not where computation occurs. A within-dataset format ablation provides the key evidence: on standard GSM8K chains ending with "the answer is X," removing only the answer statement, preserving all reasoning, collapses suffix sensitivity ~19x at 3B (N=300, p=0.022). Conflicting-answer experiments quantify the causal mechanism: at 7B, CC accuracy drops to near-zero (<=0.02) across five architecture families; the followed-wrong rate spans 0.63-1.00 at 3B-7B and attenuates at larger scales (0.300 at Phi-4-14B, ~0.01 at 32B). A within-stable 7B replication (9.3x attenuation, N=76, p=7.8e-3; Qwen3-8B N=299, p=0.004) provides converging evidence, and the pattern replicates on MATH (DeepSeek-R1-7B: 10.9x suffix-survival recovery). On chains without answer suffixes the same protocol identifies the prefix as load-bearing (Delta=-0.77, p<10^-12). Generation-time probes confirm a dissociation: the answer is not early-determined during generation (early commitment <5%), yet at consumption time model outputs systematically follow the explicit answer text. The format-determination effect persists through 14B (8.5x ratio, p=0.001) and converges toward zero at 32B. We propose a three-prerequisite protocol (question-only control, format characterization, all-position sweep) as a minimum standard for corruption-based faithfulness studies.

  • 1 authors
·
May 10