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Jul 7

RetailSMV: Exocentric vs. Egocentric Adaptation of Foundation Video World Models in Retail

Foundation video diffusion models are increasingly viewed as world simulators for embodied agents, yet their pretraining on internet-scale generic video leaves them poorly aligned with real-world deployment domains. We study parameter-efficient adaptation of a pretrained foundation video world model to retail scenes: when synchronized egocentric and exocentric video of the same activity are available, which viewpoint of training data produces the strongest adapted model? We introduce RetailSMV (Retail Synchronized Multi-View), a corpus of 32,105 captioned retail clips from five supermarkets with synchronized ego/exo capture from the store-staff perspective (stocking, arranging, weighing, managing supply carts, scanning at checkout), rather than the customer-centric framing of prior retail video corpora, and train three matched Low-Rank Adaptation (LoRA) configurations of Cosmos3-Nano (egocentric-only, exocentric-only, combined) under identical hyperparameters. On a 200-clip held-out test set evaluated with seven complementary metrics under a strict paired statistical protocol, exocentric-only adaptation matches or exceeds combined adaptation on six of seven point estimates and is significantly better on LPIPS, PSNR, and DreamSim, despite training on only 15,985 exocentric clips (versus 32,105 for combined). A symmetric paired comparison further shows that adding exocentric data to egocentric-only training helps while adding egocentric data to exocentric-only training hurts. The absolute adaptation gap is largest at the shortest rollout time, identifying the near-horizon prediction window as the regime in which adaptation is most beneficial.

  • 5 authors
·
Jun 30

ProSkill: Segment-Level Skill Assessment in Procedural Videos

Skill assessment in procedural videos is crucial for the objective evaluation of human performance in settings such as manufacturing and procedural daily tasks. Current research on skill assessment has predominantly focused on sports and lacks large-scale datasets for complex procedural activities. Existing studies typically involve only a limited number of actions, focus on either pairwise assessments (e.g., A is better than B) or on binary labels (e.g., good execution vs needs improvement). In response to these shortcomings, we introduce ProSkill, the first benchmark dataset for action-level skill assessment in procedural tasks. ProSkill provides absolute skill assessment annotations, along with pairwise ones. This is enabled by a novel and scalable annotation protocol that allows for the creation of an absolute skill assessment ranking starting from pairwise assessments. This protocol leverages a Swiss Tournament scheme for efficient pairwise comparisons, which are then aggregated into consistent, continuous global scores using an ELO-based rating system. We use our dataset to benchmark the main state-of-the-art skill assessment algorithms, including both ranking-based and pairwise paradigms. The suboptimal results achieved by the current state-of-the-art highlight the challenges and thus the value of ProSkill in the context of skill assessment for procedural videos. All data and code are available at https://fpv-iplab.github.io/ProSkill/

  • 5 authors
·
Jan 28

Evidence-Grounded Ensemble Diagnosis of 802.11 Packet Captures: A Multi-Stage Pipeline with Deterministic Reliability Scoring

Diagnosing 802.11 packet captures requires expert protocol knowledge, is slow, inconsistent across engineers, and unscalable. LLM-based approaches sound plausible but fabricate protocol events absent from captures (especially truncated traces), produce uncalibrated confidence scores, and suffer evaluation bias when golden references are co-produced by the model under test. We introduce PROBE (Protocol Reasoning Over evidence-Based Ensembles), a multi-stage pipeline addressing all three failures. It integrates (i) deterministic PCAP-to-text normalization with frame-level verifiability, (ii) multi-run, multi-candidate ensembles with optional cross-model second opinion and progressive obfuscation, (iii) a verdict-aware evidence framework treating absence of failure evidence as contributing evidence, and (iv) a fully deterministic composite reliability score from evidence validity, run-to-run stability, and cross-model agreement without LLM self-assessment. On 87 enterprise Wi-Fi captures (104 capture-reviewer pairs), single-pass LLM analysis raises weighted evidence F1 from 0.871 (expert baseline) to 0.912 but misses critical frames in 35% of cases. Naive ensemble voting drops below baseline (0.842) as majority voting amplifies conservative verdicts: 50% of confirmed failures are misclassified as 'no issue' or 'insufficient evidence.' Adding evidence-grounded reconciliation achieves 0.957 F1, a 96% auto-accept rate, and a worst-case floor above 0.70. LLM self-reported confidence clusters at 0.95 regardless of difficulty (71% report exactly 0.95), confirming it is uninformative. We also introduce a model-agnostic evaluation framework using per-field assertion matching, eliminating circular bias from model-co-produced golden references.

  • 3 authors
·
Jun 4

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

Plans Don't Persist: Why Context Management Is Load Bearing for LLM Agents

Long-horizon agents depend on context management: systems compress, summarize, and evict old tokens so tasks can continue beyond finite windows. That is safe only when dropped information is no longer needed or has been internalized. Plans are the stress case: they are written early, used for many steps, and first to be evicted. We introduce replay pairing, a diagnostic that runs the same trajectory with and without the plan in history and measures hidden-state cosine distance. On Llama-3.1-70B, plan signal spikes to 0.453 one step after the plan, then falls 4.1x in a single action-observation step; HotpotQA falls 12.4x. This is evidence that standard LLM agents do not carry plans forward as persistent state, and instead depend on the plan remaining in context. A layer-L32 probe detects this decay as a diagnostic, not as proof that it reads plan content itself. Reasoning models add a measurement confound: their `<think>` traces re-derive plan content, so standard stripping leaves plan evidence in the stripped condition. We name this the reasoning-trace confound and fix it with strict stripping, which removes prior `<think>` blocks from the stripped run only. It recovers +163% of the step+1 signal in-sample and +153% held out, while not meaningfully changing non-reasoning Llama (+4.8%). On DeepSeek-R1-Distill-Llama-70B, a Llama-trained probe transfers at AUROC 0.748 (p=6e-4), while R1-specific probes reach 1.000, suggesting R1 encodes plan signal in a different hidden-state direction. Finally, a compression stress test shows the practical cost: naive plan eviction cuts ALFWorld success by 34.7pp, while probe-gated re-surfacing does not recover it. The contribution is a measurement and stress-test framework showing that agent-critical information can be context-resident rather than persistent. Context management is load bearing, but plan protection alone is not enough.

Snowflake Snowflake
·
Jun 21 1

Explainable AI for Accelerated Microstructure Imaging: A SHAP-Guided Protocol on the Connectome 2.0 scanner

The diffusion MRI Neurite Exchange Imaging model offers a promising framework for probing gray matter microstructure by estimating parameters such as compartment sizes, diffusivities, and inter-compartmental water exchange time. However, existing protocols require long scan times. This study proposes a reduced acquisition scheme for the Connectome 2.0 scanner that preserves model accuracy while substantially shortening scan duration. We developed a data-driven framework using explainable artificial intelligence with a guided recursive feature elimination strategy to identify an optimal 8-feature subset from a 15-feature protocol. The performance of this optimized protocol was validated in vivo and benchmarked against the full acquisition and alternative reduction strategies. Parameter accuracy, preservation of anatomical contrast, and test-retest reproducibility were assessed. The reduced protocol yielded parameter estimates and cortical maps comparable to the full protocol, with low estimation errors in synthetic data and minimal impact on test-retest variability. Compared to theory-driven and heuristic reduction schemes, the optimized protocol demonstrated superior robustness, reducing the deviation in water exchange time estimates by over two-fold. In conclusion, this hybrid optimization framework enables viable imaging of neurite exchange in 14 minutes without loss of parameter fidelity. This approach supports the broader application of exchange-sensitive diffusion magnetic resonance imaging in neuroscience and clinical research, and offers a generalizable method for designing efficient acquisition protocols in biophysical parameter mapping.

  • 13 authors
·
Sep 11, 2025

The Single-File Test: A Longitudinal Public-Interface Evaluation of First-Output LLM Web Generation with Social Reach Tracking

This paper presents an eight-week observational comparison of 68 single-file HTML generations collected across 17 public experiments in the "HTML AI Battle" project between December 10, 2025 and February 4, 2026. Four reasoning model families, GPT, Gemini, Grok, and Claude, were compared under a fixed public-interface protocol with no custom instructions, no personality tuning, and no repair prompts. Each output was evaluated from a rendered browser video using human scores and a Gemini LLM-as-a-judge layer for prompt adherence, functional correctness, and UI quality, then packaged into a standardized social-media protocol spanning X (Twitter), TikTok, and YouTube. The tracker was also used for two supervised predictive analyses: an experiment-level model for 24-hour X impressions and a generation-level model for HTML verbosity. Under this protocol, Claude was the strongest and most consistent family, leading mean performance and winning 9/17 prompts under the primary human weighted score. Longer measured reasoning time was not associated with higher quality overall. Gemini as a judge was significantly more lenient than the human evaluator on functional correctness and overall performance, while stable self-favoring bias remained unresolved. The exploratory X-impressions model remained weak under post-screen cross-validation (MAE = 46,874, R^2 = -0.377), whereas the HTML-lines model performed better, with a model-family-only baseline outperforming prompt-aware alternatives (MAE = 135.2, R^2 = 0.576). Overall, selected pre-publication technical/audio variables were not sufficient to predict 24-hour X reach, while code verbosity was driven much more by model family than by prompt wording. The comparisons remain observational and are limited by public-interface drift, access-path differences, and one primary human scorer.

  • 1 authors
·
May 5

Can LLM Agents Generate Real-World Evidence? Evaluating Observational Studies in Medical Databases

Observational studies can yield clinically actionable evidence at scale, but executing them on real-world databases is open-ended and requires coherent decisions across cohort construction, analysis, and reporting. Prior evaluations of LLM agents emphasize isolated steps or single answers, missing the integrity and internal structure of the resulting evidence bundle. To address this gap, we introduce RWE-bench, a benchmark grounded in MIMIC-IV and derived from peer-reviewed observational studies. Each task provides the corresponding study protocol as the reference standard, requiring agents to execute experiments in a real database and iteratively generate tree-structured evidence bundles. We evaluate six LLMs (three open-source, three closed-source) under three agent scaffolds using both question-level correctness and end-to-end task metrics. Across 162 tasks, task success is low: the best agent reaches 39.9%, and the best open-source model reaches 30.4%. Agent scaffolds also matter substantially, causing over 30% variation in performance metrics. Furthermore, we implement an automated cohort evaluation method to rapidly localize errors and identify agent failure modes. Overall, the results highlight persistent limitations in agents' ability to produce end-to-end evidence bundles, and efficient validation remains an important direction for future work. Code and data are available at https://github.com/somewordstoolate/RWE-bench.

  • 5 authors
·
Mar 23

Computational Foundations for Strategic Coopetition: Formalizing Sequential Interaction and Reciprocity

Strategic coopetition in multi-stakeholder systems requires understanding how cooperation persists through time without binding contracts. This technical report extends computational foundations for strategic coopetition to sequential interaction dynamics, bridging conceptual modeling (i* framework) with game-theoretic reciprocity analysis. We develop: (1) bounded reciprocity response functions mapping partner deviations to finite conditional responses, (2) memory-windowed history tracking capturing cognitive limitations over k recent periods, (3) structural reciprocity sensitivity derived from interdependence matrices where behavioral responses are amplified by structural dependencies, and (4) trust-gated reciprocity where trust modulates reciprocity responses. The framework applies to both human stakeholder interactions and multi-agent computational systems. Comprehensive validation across 15,625 parameter configurations demonstrates robust reciprocity effects, with all six behavioral targets exceeding thresholds: cooperation emergence (97.5%), defection punishment (100%), forgiveness dynamics (87.9%), asymmetric differentiation (100%), trust-reciprocity interaction (100%), and bounded responses (100%). Empirical validation using the Apple iOS App Store ecosystem (2008-2024) achieves 43/51 applicable points (84.3%), reproducing documented cooperation patterns across five ecosystem phases. Statistical significance confirmed at p < 0.001 with Cohen's d = 1.57. This report concludes the Foundations Series (TR-1 through TR-4) adopting uniaxial treatment where agents choose cooperation levels along a single continuum. Companion work on interdependence (arXiv:2510.18802), trust (arXiv:2510.24909), and collective action (arXiv:2601.16237) has been prepublished. Extensions Series (TR-5 through TR-8) introduces biaxial treatment where cooperation and competition are independent dimensions.

  • 2 authors
·
Mar 28

Measuring the Symmetry--Data Exchange Rate

Equivariance theory predicts that an architectural symmetry prior reduces sample complexity by a factor of |G|; this is widely cited but rarely measured as a scaling law with controls that separate the prior from its confounds. On a controlled C_n-symmetric task, we report three findings. First, a wrong-group control with identical orbit size and matched compute is worse than no constraint (joint pairwise CI [+0.79, +3.26] excludes zero, robust across estimators); misaligned constraint is actively harmful, not merely unhelpful. Second, an augmentation baseline equipped with test-time orbit averaging matches the equivariant model exactly -- bit-identical per-epoch validation curves across matched cells -- so the architecture-vs-augmentation gap is conditional on asymmetric test-time computation, not unconditional. Third, the relative exchange rate beta_diff = 1.28 is consistent in sign and order of magnitude with the theoretical 1.0 (single-level CI [+0.92, +2.05]); the more conservative two-level bootstrap (seeds x group sizes) widens this to [-0.63, +1.72], including zero, and a finer-N replication on a sqrt(2)-spaced grid is inconclusive (point estimate -0.82). The methodological contributions -- the relative-rate estimator that cancels the shared-difficulty confound, the wrong-group control, and a pre-specified failure taxonomy -- transfer to any inductive bias whose strength can be parameterised. Honest scoping: the primary estimator beta_diff was adopted post-hoc after the initial analysis revealed a positive-slope identifiability problem; the design was never externally pre-registered; and the headline number rests on an OLS slope over seven group sizes on a coarse N grid. This is an exploratory study, not a confirmatory measurement; the wrong-group result is the cleanest finding and the one we report with the most confidence. A registered replication on fresh seeds is future work.

  • 1 authors
·
May 30 2

Improving the utility of locally differentially private protocols for longitudinal and multidimensional frequency estimates

This paper investigates the problem of collecting multidimensional data throughout time (i.e., longitudinal studies) for the fundamental task of frequency estimation under Local Differential Privacy (LDP) guarantees. Contrary to frequency estimation of a single attribute, the multidimensional aspect demands particular attention to the privacy budget. Besides, when collecting user statistics longitudinally, privacy progressively degrades. Indeed, the "multiple" settings in combination (i.e., many attributes and several collections throughout time) impose several challenges, for which this paper proposes the first solution for frequency estimates under LDP. To tackle these issues, we extend the analysis of three state-of-the-art LDP protocols (Generalized Randomized Response -- GRR, Optimized Unary Encoding -- OUE, and Symmetric Unary Encoding -- SUE) for both longitudinal and multidimensional data collections. While the known literature uses OUE and SUE for two rounds of sanitization (a.k.a. memoization), i.e., L-OUE and L-SUE, respectively, we analytically and experimentally show that starting with OUE and then with SUE provides higher data utility (i.e., L-OSUE). Also, for attributes with small domain sizes, we propose Longitudinal GRR (L-GRR), which provides higher utility than the other protocols based on unary encoding. Last, we also propose a new solution named Adaptive LDP for LOngitudinal and Multidimensional FREquency Estimates (ALLOMFREE), which randomly samples a single attribute to be sent with the whole privacy budget and adaptively selects the optimal protocol, i.e., either L-GRR or L-OSUE. As shown in the results, ALLOMFREE consistently and considerably outperforms the state-of-the-art L-SUE and L-OUE protocols in the quality of the frequency estimates.

  • 4 authors
·
Nov 8, 2021

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

The Slepian model based independent interval approximation of persistency and zero-level exceedance distributions

In physics and engineering literature, the distribution of the excursion-above-zero time distribution (exceedance distribution) for a stationary Gaussian process has been approximated by a stationary switching process with independently distributed switching times. The approach matched the covariance of the clipped Gaussian process with the one for the stationary switching process and the distribution of the latter was used as the so-called independent interval approximation (IIA). The approach successfully assessed the persistency exponent for many physically important processes but left an unanswered question when such an approach leads to a mathematically meaningful and proper exceedance distribution. Here we address this question by proposing an alternative matching of the expected values of the clipped Slepian process and the corresponding switched process initiated at the origin. The method has allowed resolving the mathematical correctness of the matching method for a large subclass of the Gaussian processes with monotonic covariance, for which we provide a sufficient condition for the validity of the IIA. Within this class, the IIA produces a valid distribution for the excursion time and is represented in an explicit stochastic form that connects directly to the covariance of the underlying Gaussian process. We compare the excursion level distributions as well as the corresponding persistency exponents obtained through the IIA method with numerically computed exact distributions, and the simulated distribution for several important Gaussian models. We also argue that for stationary Gaussian processes with a non-monotonic covariance, the IIA fails and should not be used.

  • 2 authors
·
Jan 3, 2024

Evidence Inference 2.0: More Data, Better Models

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

  • 5 authors
·
May 8, 2020

Pairwise or Pointwise? Evaluating Feedback Protocols for Bias in LLM-Based Evaluation

Large Language Models (LLMs) are widely used as proxies for human labelers in both training (Reinforcement Learning from AI Feedback) and large-scale response evaluation (LLM-as-a-judge). Alignment and evaluation are critical components in the development of reliable LLMs, and the choice of feedback protocol plays a central role in both but remains understudied. In this work, we show that the choice of feedback protocol for evaluation (absolute scores versus relative preferences) can significantly affect evaluation reliability and induce systematic biases. In the context of LLM-as-a-judge evaluation, we show that pairwise protocols are more vulnerable to distracted evaluation. Generator models can exploit spurious attributes (or distractor features) favored by the LLM judge, resulting in inflated scores for lower-quality outputs. We find that absolute scoring is more robust to such manipulation, producing judgments that better reflect response quality and are less influenced by distractor features. Our results demonstrate that generator models can flip preferences by embedding distractor features, skewing LLM-as-a-judge comparisons and leading to inaccurate conclusions about model quality in benchmark evaluations. Pairwise preferences flip in about 35% of the cases, compared to only 9% for absolute scores. We offer recommendations for choosing feedback protocols based on dataset characteristics and evaluation objectives.

  • 4 authors
·
Aug 20, 2025

Are Pretrained Image Matchers Good Enough for SAR-Optical Satellite Registration?

Cross-modal optical-SAR (Synthetic Aperture Radar) registration is a bottleneck for disaster-response via remote sensing, yet modern image matchers are developed and benchmarked almost exclusively on natural-image domains. We evaluate twenty-four pretrained matcher families--in a zero-shot setting with no fine-tuning or domain adaptation on satellite or SAR data--on SpaceNet9 and two additional cross-modal benchmarks under a deterministic protocol with tiled large-image inference, robust geometric filtering, and tie-point-grounded metrics. Our results reveal asymmetric transfer--matchers with explicit cross-modal training do not uniformly outperform those without it. While XoFTR (trained for visible-thermal matching) and RoMa achieve the lowest reported mean error at 3.0 px on the labeled SpaceNet9 training scenes, RoMa achieves this without any cross-modal training, and MatchAnything-ELoFTR (3.4 px)--trained on synthetic cross-modal pairs--matches closely, suggesting (as a working hypothesis) that foundation-model features (DINOv2) may contribute to modality invariance that partially substitutes for explicit cross-modal supervision. 3D-reconstruction matchers (MASt3R, DUSt3R), which are not designed for traditional 2D image matching, are highly protocol-sensitive and remain fragile under default settings. Deployment protocol choices (geometry model, tile size, inlier gating) shift accuracy by up to 33times for a single matcher, sometimes exceeding the effect of swapping matchers entirely within the evaluated sweep--affine geometry alone reduces mean error from 12.34 to 9.74 px. These findings inform both practical deployment of existing matchers and future matcher design for cross-modal satellite registration.

  • 3 authors
·
Apr 30

Prediction Bottlenecks Don't Discover Causal Structure (But Here's What They Actually Do)

A Mamba state-space model trained only for next-step prediction appears to recover Granger-causal structure through a simple readout S = |W_{out} W_{in}|, with early experiments suggesting the phenomenon generalized across architectures and benefited from interventional data at p < 10^{-5}. We package the protocol used to test that claim -- standardized synthetic generators (VAR/Lorenz/CauseMe-style), three intervention semantics (do(X=c), soft-noise, random-forcing), edge-provenance cards on three real datasets, and size-matched control arms -- as a reusable falsification benchmark, and walk the claim through it in five stages. The method-level claim does not survive: (i) a plain linear bottleneck does as well or better; (ii) tuned Lasso beats the bottleneck on synthetic CauseMe-style benchmarks, and on Lorenz-96 (the only real benchmark with unambiguous ground truth) classical PCMCI and Granger lead a tight cluster in which the bottleneck trails; (iii) the headline intervention advantage is roughly 60% a sample-size confound, and the residual disappears under standard do(X=c) interventions, surviving only under a non-standard random-forcing scheme; (iv) even that residual reproduces, with a larger effect, in classical bivariate Granger -- the effect is method-agnostic. What survives is a narrow characterization result; the benchmark is the lasting artifact, and each stage above is one of its control arms.

  • 4 authors
·
May 8 1

Compound Estimation for Binomials

Many applications involve estimating the mean of multiple binomial outcomes as a common problem -- assessing intergenerational mobility of census tracts, estimating prevalence of infectious diseases across countries, and measuring click-through rates for different demographic groups. The most standard approach is to report the plain average of each outcome. Despite simplicity, the estimates are noisy when the sample sizes or mean parameters are small. In contrast, the Empirical Bayes (EB) methods are able to boost the average accuracy by borrowing information across tasks. Nevertheless, the EB methods require a Bayesian model where the parameters are sampled from a prior distribution which, unlike the commonly-studied Gaussian case, is unidentified due to discreteness of binomial measurements. Even if the prior distribution is known, the computation is difficult when the sample sizes are heterogeneous as there is no simple joint conjugate prior for the sample size and mean parameter. In this paper, we consider the compound decision framework which treats the sample size and mean parameters as fixed quantities. We develop an approximate Stein's Unbiased Risk Estimator (SURE) for the average mean squared error given any class of estimators. For a class of machine learning-assisted linear shrinkage estimators, we establish asymptotic optimality, regret bounds, and valid inference. Unlike existing work, we work with the binomials directly without resorting to Gaussian approximations. This allows us to work with small sample sizes and/or mean parameters in both one-sample and two-sample settings. We demonstrate our approach using three datasets on firm discrimination, education outcomes, and innovation rates.

  • 2 authors
·
Dec 30, 2025

How can the use of different modes of survey data collection introduce bias? A simple introduction to mode effects using directed acyclic graphs (DAGs)

Survey data are self-reported data collected directly from respondents by a questionnaire or an interview and are commonly used in epidemiology. Such data are traditionally collected via a single mode (e.g. face-to-face interview alone), but use of mixed-mode designs (e.g. offering face-to-face interview or online survey) has become more common. This introduces two key challenges. First, individuals may respond differently to the same question depending on the mode; these differences due to measurement are known as 'mode effects'. Second, different individuals may participate via different modes; these differences in sample composition between modes are known as 'mode selection'. Where recognised, mode effects are often handled by straightforward approaches such as conditioning on survey mode. However, while reducing mode effects, this and other equivalent approaches may introduce collider bias in the presence of mode selection. The existence of mode effects and the consequences of na\"ive conditioning may be underappreciated in epidemiology. This paper offers a simple introduction to these challenges using directed acyclic graphs by exploring a range of possible data structures. We discuss the potential implications of using conditioning- or imputation-based approaches and outline the advantages of quantitative bias analyses for dealing with mode effects.

  • 4 authors
·
Oct 1, 2025

Preserving Statistical Validity in Adaptive Data Analysis

A great deal of effort has been devoted to reducing the risk of spurious scientific discoveries, from the use of sophisticated validation techniques, to deep statistical methods for controlling the false discovery rate in multiple hypothesis testing. However, there is a fundamental disconnect between the theoretical results and the practice of data analysis: the theory of statistical inference assumes a fixed collection of hypotheses to be tested, or learning algorithms to be applied, selected non-adaptively before the data are gathered, whereas in practice data is shared and reused with hypotheses and new analyses being generated on the basis of data exploration and the outcomes of previous analyses. In this work we initiate a principled study of how to guarantee the validity of statistical inference in adaptive data analysis. As an instance of this problem, we propose and investigate the question of estimating the expectations of m adaptively chosen functions on an unknown distribution given n random samples. We show that, surprisingly, there is a way to estimate an exponential in n number of expectations accurately even if the functions are chosen adaptively. This gives an exponential improvement over standard empirical estimators that are limited to a linear number of estimates. Our result follows from a general technique that counter-intuitively involves actively perturbing and coordinating the estimates, using techniques developed for privacy preservation. We give additional applications of this technique to our question.

  • 6 authors
·
Nov 10, 2014

Computational Foundations for Strategic Coopetition: Formalizing Interdependence and Complementarity

Coopetition refers to simultaneous cooperation and competition among actors wherein actors 'cooperate to grow the pie and compete to split it up.' Modern socio-technical systems are characterized by strategic coopetition wherein actors concomitantly cooperate to create value and compete to capture it. While conceptual modeling languages such as i* provide rich qualitative representations of strategic dependencies, they lack mechanisms for quantitative analysis of dynamic trade-offs. Conversely, classical game theory offers mathematical rigor but strips away contextual richness. This report bridges this gap by developing computational foundations that formalize two critical dimensions of coopetition: interdependence and complementarity. We ground interdependence in i* structural dependency analysis, translating depender-dependee-dependum relationships into quantitative interdependence coefficients via a structured translation framework. We formalize complementarity following Brandenburger and Nalebuff's Added Value concept, modeling synergistic value creation with validated parameterization. We integrate structural dependencies with bargaining power in value appropriation and introduce a game-theoretic formulation where Nash Equilibrium incorporates structural interdependence. Validation combines over 22,000 experimental trials across power and logarithmic specifications with the Samsung-Sony S-LCD joint venture (2004-2011). Under strict historical alignment scoring, logarithmic specifications achieve 58/60 compared to power functions (46/60), producing realistic 41% cooperation increases aligning with documented S-LCD patterns while power functions produce 166% increases exceeding realistic bounds. Statistical significance confirmed at p < 0.001, Cohen's d > 9.

  • 2 authors
·
Oct 21, 2025

MedSkillAudit: A Domain-Specific Audit Framework for Medical Research Agent Skills

Background: Agent skills are increasingly deployed as modular, reusable capability units in AI agent systems. Medical research agent skills require safeguards beyond general-purpose evaluation, including scientific integrity, methodological validity, reproducibility, and boundary safety. This study developed and preliminarily evaluated a domain-specific audit framework for medical research agent skills, with a focus on reliability against expert review. Methods: We developed MedSkillAudit (skill-auditor@1.0), a layered framework assessing skill release readiness before deployment. We evaluated 75 skills across five medical research categories (15 per category). Two experts independently assigned a quality score (0-100), an ordinal release disposition (Production Ready / Limited Release / Beta Only / Reject), and a high-risk failure flag. System-expert agreement was quantified using ICC(2,1) and linearly weighted Cohen's kappa, benchmarked against the human inter-rater baseline. Results: The mean consensus quality score was 72.4 (SD = 13.0); 57.3% of skills fell below the Limited Release threshold. MedSkillAudit achieved ICC(2,1) = 0.449 (95% CI: 0.250-0.610), exceeding the human inter-rater ICC of 0.300. System-consensus score divergence (SD = 9.5) was smaller than inter-expert divergence (SD = 12.4), with no directional bias (Wilcoxon p = 0.613). Protocol Design showed the strongest category-level agreement (ICC = 0.551); Academic Writing showed a negative ICC (-0.567), reflecting a structural rubric-expert mismatch. Conclusions: Domain-specific pre-deployment audit may provide a practical foundation for governing medical research agent skills, complementing general-purpose quality checks with structured audit workflows tailored to scientific use cases.

AIPOCH-AI AIPOCH
·
Apr 21 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
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May 10

Transfer Learning for Meta-analysis Under Covariate Shift

Randomized controlled trials often do not represent the populations where decisions are made, and covariate shift across studies can invalidate standard IPD meta-analysis and transport estimators. We propose a placebo-anchored transport framework that treats source-trial outcomes as abundant proxy signals and target-trial placebo outcomes as scarce, high-fidelity gold labels to calibrate baseline risk. A low-complexity (sparse) correction anchors proxy outcome models to the target population, and the anchored models are embedded in a cross-fitted doubly robust learner, yielding a Neyman-orthogonal, target-site doubly robust estimator for patient-level heterogeneous treatment effects when target treated outcomes are available. We distinguish two regimes: in connected targets (with a treated arm), the method yields target-identified effect estimates; in disconnected targets (placebo-only), it reduces to a principled screen--then--transport procedure under explicit working-model transport assumptions. Experiments on synthetic data and a semi-synthetic IHDP benchmark evaluate pointwise CATE accuracy, ATE error, ranking quality for targeting, decision-theoretic policy regret, and calibration. Across connected settings, the proposed method is best or near-best and improves substantially over proxy-only, target-only, and transport baselines at small target sample sizes; in disconnected settings, it retains strong ranking performance for targeting while pointwise accuracy depends on the strength of the working transport condition.

  • 3 authors
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Apr 5

Pair Programming with Large Language Models for Sampling and Estimation of Copulas

Without writing a single line of code by a human, an example Monte Carlo simulation based application for stochastic dependence modeling with copulas is developed using a state-of-the-art large language model (LLM) fine-tuned for conversations. This includes interaction with ChatGPT in natural language and using mathematical formalism, which, under careful supervision by a human-expert, led to producing a working code in MATLAB, Python and R for sampling from a given copula model, evaluation of the model's density, performing maximum likelihood estimation, optimizing the code for parallel computing for CPUs as well as for GPUs, and visualization of the computed results. In contrast to other emerging studies that assess the accuracy of LLMs like ChatGPT on tasks from a selected area, this work rather investigates ways how to achieve a successful solution of a standard statistical task in a collaboration of a human-expert and artificial intelligence (AI). Particularly, through careful prompt engineering, we separate successful solutions generated by ChatGPT from unsuccessful ones, resulting in a comprehensive list of related pros and cons. It is demonstrated that if the typical pitfalls are avoided, we can substantially benefit from collaborating with an AI partner. For example, we show that if ChatGPT is not able to provide a correct solution due to a lack of or incorrect knowledge, the human-expert can feed it with the correct knowledge, e.g., in the form of mathematical theorems and formulas, and make it to apply the gained knowledge in order to provide a solution that is correct. Such ability presents an attractive opportunity to achieve a programmed solution even for users with rather limited knowledge of programming techniques.

  • 1 authors
·
Mar 31, 2023

Beyond Variance: Prompt-Efficient RLVR via Rare-Event Amplification and Bidirectional Pairing

Reinforcement learning with verifiable rewards (RLVR) is effective for training large language models on deterministic outcome reasoning tasks. Prior work shows RLVR works with few prompts, but prompt selection is often based only on training-accuracy variance, leading to unstable optimization directions and weaker transfer. We revisit prompt selection from a mechanism-level view and argue that an effective minibatch should provide both (i) a reliable positive anchor and (ii) explicit negative learning signals from rare failures. Based on this principle, we propose positive--negative pairing: at each update, we sample a hard-but-solvable q^{+} and an easy-but-brittle prompt q^{-}(high success rate but not perfect), characterized by low and high empirical success rates under multiple rollouts. We further introduce Weighted GRPO, which reweights binary outcomes at the pair level and uses group-normalized advantages to amplify rare successes on q^{+} into sharp positive guidance while turning rare failures on q^{-} into strong negative penalties. This bidirectional signal provides informative learning feedback for both successes and failures, improving sample efficiency without suppressing exploration. On Qwen2.5-Math-7B, a single paired minibatch per update consistently outperforms a GRPO baseline that selects two prompts via commonly used variance-based selection heuristics: AIME~2025 Pass@8 improves from 16.8 to 22.2, and AMC23 Pass@64 from 94.0 to 97.0, while remaining competitive with large-scale RLVR trained from a pool of 1209 training prompts. Similar gains are observed on Qwen2.5-Math-7B-Instruct.

  • 5 authors
·
Feb 3

Memory in Large Language Models: Mechanisms, Evaluation and Evolution

Under a unified operational definition, we define LLM memory as a persistent state written during pretraining, finetuning, or inference that can later be addressed and that stably influences outputs. We propose a four-part taxonomy (parametric, contextual, external, procedural/episodic) and a memory quadruple (location, persistence, write/access path, controllability). We link mechanism, evaluation, and governance via the chain write -> read -> inhibit/update. To avoid distorted comparisons across heterogeneous setups, we adopt a three-setting protocol (parametric only, offline retrieval, online retrieval) that decouples capability from information availability on the same data and timeline. On this basis we build a layered evaluation: parametric (closed-book recall, edit differential, memorization/privacy), contextual (position curves and the mid-sequence drop), external (answer correctness vs snippet attribution/faithfulness), and procedural/episodic (cross-session consistency and timeline replay, E MARS+). The framework integrates temporal governance and leakage auditing (freshness hits, outdated answers, refusal slices) and uncertainty reporting via inter-rater agreement plus paired tests with multiple-comparison correction. For updating and forgetting, we present DMM Gov: coordinating DAPT/TAPT, PEFT, model editing (ROME, MEND, MEMIT, SERAC), and RAG to form an auditable loop covering admission thresholds, rollout, monitoring, rollback, and change audits, with specs for timeliness, conflict handling, and long-horizon consistency. Finally, we give four testable propositions: minimum identifiability; a minimal evaluation card; causally constrained editing with verifiable forgetting; and when retrieval with small-window replay outperforms ultra-long-context reading. This yields a reproducible, comparable, and governable coordinate system for research and deployment.

  • 7 authors
·
Sep 23, 2025

When No Benchmark Exists: Validating Comparative LLM Safety Scoring Without Ground-Truth Labels

Many deployments must compare candidate language models for safety before a labeled benchmark exists for the relevant language, sector, or regulatory regime. We formalize this setting as benchmarkless comparative safety scoring and specify the contract under which a scenario-based audit can be interpreted as deployment evidence. Scores are valid only under a fixed scenario pack, rubric, auditor, judge, sampling configuration, and rerun budget. Because no labels are available, we replace ground-truth agreement with an instrumental-validity chain: responsiveness to a controlled safe-versus-abliterated contrast, dominance of target-driven variance over auditor and judge artifacts, and stability across reruns. We instantiate the chain in SimpleAudit, a local-first scoring instrument, and validate it on a Norwegian safety pack. Safe and abliterated targets separate with AUROC values between 0.89 and 1.00, target identity is the dominant variance component (η^2 approx 0.52), and severity profiles stabilize by ten reruns. Applying the same chain to Petri shows that it admits both tools. The substantial differences arise upstream of the chain, in claim-contract enforcement and deployment fit. A Norwegian public-sector procurement case comparing Borealis and Gemma 3 demonstrates the resulting evidence in practice: the safer model depends on scenario category and risk measure. Consequently, scores, matched deltas, critical rates, uncertainty, and the auditor and judge used must be reported together rather than collapsed into a single ranking.

Model-free Approach to Evaluate a Censored Intermediate Outcome as a Surrogate for Overall Survival

Clinical trials or studies oftentimes require long-term and/or costly follow-up of participants to evaluate a novel treatment/drug/vaccine. There has been increasing interest in the past few decades in using short-term surrogate outcomes as a replacement of the primary outcome i.e., in using the surrogate outcome, which can potentially be observed sooner, to make inference about the treatment effect on the long-term primary outcome. Very few of the available statistical methods to evaluate a surrogate are applicable to settings where both the surrogate and the primary outcome are time-to-event outcomes subject to censoring. Methods that can handle this setting tend to require parametric assumptions or be limited to assessing only the restricted mean survival time. In this paper, we propose a non-parametric approach to evaluate a censored surrogate outcome, such as time to progression, when the primary outcome is also a censored time-to-event outcome, such as time to death, and the treatment effect of interest is the difference in overall survival. Specifically, we define the proportion of the treatment effect on the primary outcome that is explained (PTE) by the censored surrogate outcome in this context, and estimate this proportion by defining and deriving an optimal transformation of the surrogate information. Our approach provides the added advantage of relaxed assumptions to guarantee that the true PTE is within (0,1), along with being model-free. Finite sample performance of our estimators are illustrated via extensive simulation studies and a real data application examining progression-free survival as a surrogate for overall survival for patients with metastatic colorectal cancer.

  • 4 authors
·
Dec 18, 2024

Bayesian aggregation of average data: An application in drug development

Throughout the different phases of a drug development program, randomized trials are used to establish the tolerability, safety, and efficacy of a candidate drug. At each stage one aims to optimize the design of future studies by extrapolation from the available evidence at the time. This includes collected trial data and relevant external data. However, relevant external data are typically available as averages only, for example from trials on alternative treatments reported in the literature. Here we report on such an example from a drug development for wet age-related macular degeneration. This disease is the leading cause of severe vision loss in the elderly. While current treatment options are efficacious, they are also a substantial burden for the patient. Hence, new treatments are under development which need to be compared against existing treatments. The general statistical problem this leads to is meta-analysis, which addresses the question of how we can combine datasets collected under different conditions. Bayesian methods have long been used to achieve partial pooling. Here we consider the challenge when the model of interest is complex (hierarchical and nonlinear) and one dataset is given as raw data while the second dataset is given as averages only. In such a situation, common meta-analytic methods can only be applied when the model is sufficiently simple for analytic approaches. When the model is too complex, for example nonlinear, an analytic approach is not possible. We provide a Bayesian solution by using simulation to approximately reconstruct the likelihood of the external summary and allowing the parameters in the model to vary under the different conditions. We first evaluate our approach using fake-data simulations and then report results for the drug development program that motivated this research.

  • 6 authors
·
May 12, 2020

Blackbox Model Provenance via Palimpsestic Membership Inference

Suppose Alice trains an open-weight language model and Bob uses a blackbox derivative of Alice's model to produce text. Can Alice prove that Bob is using her model, either by querying Bob's derivative model (query setting) or from the text alone (observational setting)? We formulate this question as an independence testing problem--in which the null hypothesis is that Bob's model or text is independent of Alice's randomized training run--and investigate it through the lens of palimpsestic memorization in language models: models are more likely to memorize data seen later in training, so we can test whether Bob is using Alice's model using test statistics that capture correlation between Bob's model or text and the ordering of training examples in Alice's training run. If Alice has randomly shuffled her training data, then any significant correlation amounts to exactly quantifiable statistical evidence against the null hypothesis, regardless of the composition of Alice's training data. In the query setting, we directly estimate (via prompting) the likelihood Bob's model gives to Alice's training examples and order; we correlate the likelihoods of over 40 fine-tunes of various Pythia and OLMo base models ranging from 1B to 12B parameters with the base model's training data order, achieving a p-value on the order of at most 1e-8 in all but six cases. In the observational setting, we try two approaches based on estimating 1) the likelihood of Bob's text overlapping with spans of Alice's training examples and 2) the likelihood of Bob's text with respect to different versions of Alice's model we obtain by repeating the last phase (e.g., 1%) of her training run on reshuffled data. The second approach can reliably distinguish Bob's text from as little as a few hundred tokens; the first does not involve any retraining but requires many more tokens (several hundred thousand) to achieve high power.

  • 6 authors
·
Oct 22, 2025

Are Large Language Models Good Statisticians?

Large Language Models (LLMs) have demonstrated impressive capabilities across a range of scientific tasks including mathematics, physics, and chemistry. Despite their successes, the effectiveness of LLMs in handling complex statistical tasks remains systematically under-explored. To bridge this gap, we introduce StatQA, a new benchmark designed for statistical analysis tasks. StatQA comprises 11,623 examples tailored to evaluate LLMs' proficiency in specialized statistical tasks and their applicability assessment capabilities, particularly for hypothesis testing methods. We systematically experiment with representative LLMs using various prompting strategies and show that even state-of-the-art models such as GPT-4o achieve a best performance of only 64.83%, indicating significant room for improvement. Notably, while open-source LLMs (e.g. LLaMA-3) show limited capability, those fine-tuned ones exhibit marked improvements, outperforming all in-context learning-based methods (e.g. GPT-4o). Moreover, our comparative human experiments highlight a striking contrast in error types between LLMs and humans: LLMs primarily make applicability errors, whereas humans mostly make statistical task confusion errors. This divergence highlights distinct areas of proficiency and deficiency, suggesting that combining LLM and human expertise could lead to complementary strengths, inviting further investigation into their collaborative potential.

  • 5 authors
·
Jun 11, 2024

Image-based Treatment Effect Heterogeneity

Randomized controlled trials (RCTs) are considered the gold standard for estimating the average treatment effect (ATE) of interventions. One use of RCTs is to study the causes of global poverty -- a subject explicitly cited in the 2019 Nobel Memorial Prize awarded to Duflo, Banerjee, and Kremer "for their experimental approach to alleviating global poverty." Because the ATE is a population summary, anti-poverty experiments often seek to unpack the effect variation around the ATE by conditioning (CATE) on tabular variables such as age and ethnicity that were measured during the RCT data collection. Although such variables are key to unpacking CATE, using only such variables may fail to capture historical, geographical, or neighborhood-specific contributors to effect variation, as tabular RCT data are often only observed near the time of the experiment. In global poverty research, when the location of the experiment units is approximately known, satellite imagery can provide a window into such factors important for understanding heterogeneity. However, there is no method that specifically enables applied researchers to analyze CATE from images. In this paper, using a deep probabilistic modeling framework, we develop such a method that estimates latent clusters of images by identifying images with similar treatment effects distributions. Our interpretable image CATE model also includes a sensitivity factor that quantifies the importance of image segments contributing to the effect cluster prediction. We compare the proposed methods against alternatives in simulation; also, we show how the model works in an actual RCT, estimating the effects of an anti-poverty intervention in northern Uganda and obtaining a posterior predictive distribution over effects for the rest of the country where no experimental data was collected. We make all models available in open-source software.

BioProBench: Comprehensive Dataset and Benchmark in Biological Protocol Understanding and Reasoning

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.

  • 5 authors
·
May 11, 2025

Scalable Evaluation of Online Facilitation Strategies via Synthetic Simulation of Discussions

Limited large-scale evaluations exist for facilitation strategies of online discussions due to significant costs associated with human involvement. An effective solution is synthetic discussion simulations using Large Language Models (LLMs) to create initial pilot experiments. We propose a simple, generalizable, LLM-driven methodology to prototype the development of LLM facilitators, and produce high-quality synthetic data without human involvement. We use our methodology to test whether current facilitation strategies can improve the performance of LLM facilitators. We find that, while LLM facilitators significantly improve synthetic discussions, there is no evidence that the application of more elaborate facilitation strategies proposed in modern Social Science research lead to further improvements in discussion quality, compared to more basic approaches. Additionally, we find that small LLMs (such as Mistral Nemo 12B) can perform comparably to larger models (such as LLaMa 70B), and that special instructions must be used for instruction-tuned models to induce toxicity in synthetic discussions. We confirm that each component of our methodology contributes substantially to high quality data via an ablation study. We release an open-source framework, "SynDisco" (pip install syndisco), which implements our methodology. We also release the "Virtual Moderation Dataset" (https://paperswithcode.com/dataset/vmd), a large, publicly available dataset containing LLM-generated and LLM-annotated discussions using multiple open-source LLMs.

  • 3 authors
·
Mar 13, 2025

When do they StOP?: A First Step Towards Automatically Identifying Team Communication in the Operating Room

Purpose: Surgical performance depends not only on surgeons' technical skills but also on team communication within and across the different professional groups present during the operation. Therefore, automatically identifying team communication in the OR is crucial for patient safety and advances in the development of computer-assisted surgical workflow analysis and intra-operative support systems. To take the first step, we propose a new task of detecting communication briefings involving all OR team members, i.e. the team Time-out and the StOP?-protocol, by localizing their start and end times in video recordings of surgical operations. Methods: We generate an OR dataset of real surgeries, called Team-OR, with more than one hundred hours of surgical videos captured by the multi-view camera system in the OR. The dataset contains temporal annotations of 33 Time-out and 22 StOP?-protocol activities in total. We then propose a novel group activity detection approach, where we encode both scene context and action features, and use an efficient neural network model to output the results. Results: The experimental results on the Team-OR dataset show that our approach outperforms existing state-of-the-art temporal action detection approaches. It also demonstrates the lack of research on group activities in the OR, proving the significance of our dataset. Conclusion: We investigate the Team Time-Out and the StOP?-protocol in the OR, by presenting the first OR dataset with temporal annotations of group activities protocols, and introducing a novel group activity detection approach that outperforms existing approaches. Code is available at https://github.com/CAMMA-public/Team-OR.

  • 8 authors
·
Feb 12, 2025

Safety and accuracy follow different scaling laws in clinical large language models

Clinical LLMs are often scaled by increasing model size, context length, retrieval complexity, or inference-time compute, with the implicit expectation that higher accuracy implies safer behavior. This assumption is incomplete in medicine, where a few confident, high-risk, or evidence-contradicting errors can matter more than average benchmark performance. We introduce SaFE-Scale, a framework for measuring how clinical LLM safety changes across model scale, evidence quality, retrieval strategy, context exposure, and inference-time compute. To instantiate this framework, we introduce RadSaFE-200, a Radiology Safety-Focused Evaluation benchmark of 200 multiple-choice questions with clinician-defined clean evidence, conflict evidence, and option-level labels for high-risk error, unsafe answer, and evidence contradiction. We evaluated 34 locally deployed LLMs across six deployment conditions: closed-book prompting (zero-shot), clean evidence, conflict evidence, standard RAG, agentic RAG, and max-context prompting. Clean evidence produced the strongest improvement, increasing mean accuracy from 73.5% to 94.1%, while reducing high-risk error from 12.0% to 2.6%, contradiction from 12.7% to 2.3%, and dangerous overconfidence from 8.0% to 1.6%. Standard RAG and agentic RAG did not reproduce this safety profile: agentic RAG improved accuracy over standard RAG and reduced contradiction, but high-risk error and dangerous overconfidence remained elevated. Max-context prompting increased latency without closing the safety gap, and additional inference-time compute produced only limited gains. Worst-case analysis showed that clinically consequential errors concentrated in a small subset of questions. Clinical LLM safety is therefore not a passive consequence of scaling, but a deployment property shaped by evidence quality, retrieval design, context construction, and collective failure behavior.

  • 12 authors
·
May 4

A Survey of AI Agent Protocols

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.

  • 14 authors
·
Apr 23, 2025

Quantum Machine Learning for Cyber-Physical Anomaly Detection in Unmanned Aerial Vehicles: A Leakage-Free Evaluation with Proxy-Audited Feature Sets

Unmanned aerial vehicles (UAVs) are cyber-physical systems whose attack surface spans networked avionics and on-board sensor fusion: a compromised GPS or battery module can mimic a benign mission segment and evade naive anomaly detectors. We present a leakage-free evaluation of quantum machine learning for UAV anomaly detection on the multi-sensor TLM:UAV benchmark. Three contributions support the study. (i) A group-aware temporal protocol (B2) partitions the dataset into ten contiguous TimeUS blocks and evaluates over ten seeds, eliminating the inflation produced by random stratified splits that mix neighbouring samples. (ii) A three-mode feature audit (full/loose/strict) quantifies how much accuracy stems from instantaneous physical signals versus contextual proxies (cumulative energy, battery state, GPS trajectory). (iii) A hybrid XGBoost + Data Reuploading (DRU) classifier is benchmarked against five paired non-linear controls (raw, PCA, polynomial-2, random-RBF, and an untrained DRU map) under identical budgets. The standalone DRU does not consistently match the strongest classical baseline across seeds; however, the trained-DRU hybrid is the only model whose mean F1 macro shifts upward from full to strict (+0.05), a directional signal that the per-seed standard deviations prevent from being interpreted as a statistically established difference. The trained-DRU hybrid also records the lowest mean false-alarm rate under proxy-free evaluation, subject to the inter-seed variance reported. We frame this as an incremental, reproducible quantum-enhanced hybrid benefit, and provide an open Qiskit 2.x implementation as a benchmark for cybersecurity analytics in NISQ-era aerospace systems.

  • 5 authors
·
May 27

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
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Apr 6 5

Adaptive Deployment of Untrusted LLMs Reduces Distributed Threats

As large language models (LLMs) become increasingly capable, it is prudent to assess whether safety measures remain effective even if LLMs intentionally try to bypass them. Previous work introduced control evaluations, an adversarial framework for testing deployment strategies of untrusted models (i.e., models which might be trying to bypass safety measures). While prior work treats a single failure as unacceptable, we perform control evaluations in a "distributed threat setting" -- a setting where no single action is catastrophic and no single action provides overwhelming evidence of misalignment. We approach this problem with a two-level deployment framework that uses an adaptive macro-protocol to choose between micro-protocols. Micro-protocols operate on a single task, using a less capable, but extensively tested (trusted) model to harness and monitor the untrusted model. Meanwhile, the macro-protocol maintains an adaptive credence on the untrusted model's alignment based on its past actions, using it to pick between safer and riskier micro-protocols. We evaluate our method in a code generation testbed where a red team attempts to generate subtly backdoored code with an LLM whose deployment is safeguarded by a blue team. We plot Pareto frontiers of safety (# of non-backdoored solutions) and usefulness (# of correct solutions). At a given level of usefulness, our adaptive deployment strategy reduces the number of backdoors by 80% compared to non-adaptive baselines.

  • 12 authors
·
Nov 26, 2024

Large Language Model Hacking: Quantifying the Hidden Risks of Using LLMs for Text Annotation

Large language models (LLMs) are rapidly transforming social science research by enabling the automation of labor-intensive tasks like data annotation and text analysis. However, LLM outputs vary significantly depending on the implementation choices made by researchers (e.g., model selection, prompting strategy, or temperature settings). Such variation can introduce systematic biases and random errors, which propagate to downstream analyses and cause Type I, Type II, Type S, or Type M errors. We call this LLM hacking. We quantify the risk of LLM hacking by replicating 37 data annotation tasks from 21 published social science research studies with 18 different models. Analyzing 13 million LLM labels, we test 2,361 realistic hypotheses to measure how plausible researcher choices affect statistical conclusions. We find incorrect conclusions based on LLM-annotated data in approximately one in three hypotheses for state-of-the-art models, and in half the hypotheses for small language models. While our findings show that higher task performance and better general model capabilities reduce LLM hacking risk, even highly accurate models do not completely eliminate it. The risk of LLM hacking decreases as effect sizes increase, indicating the need for more rigorous verification of findings near significance thresholds. Our extensive analysis of LLM hacking mitigation techniques emphasizes the importance of human annotations in reducing false positive findings and improving model selection. Surprisingly, common regression estimator correction techniques are largely ineffective in reducing LLM hacking risk, as they heavily trade off Type I vs. Type II errors. Beyond accidental errors, we find that intentional LLM hacking is unacceptably simple. With few LLMs and just a handful of prompt paraphrases, anything can be presented as statistically significant.

  • 7 authors
·
Sep 10, 2025 3

AgentAtlas: Beyond Outcome Leaderboards for LLM Agents

Large language model agents now act on codebases, browsers, operating systems, calendars, files, and tool ecosystems, but the benchmarks used to evaluate them are fragmented: each emphasizes a different unit of measurement (final task success, tool-call validity, repeated-pass consistency, trajectory safety, or attack robustness). A line of 2024-2025 work has converged on the diagnosis that a single accuracy column is no longer the right unit of comparison for deployable agents. AgentAtlas extends this line of work with four components: (i) a six-state control-decision taxonomy (Act / Ask / Refuse / Stop / Confirm / Recover); (ii) a nine-category trajectory-failure taxonomy with two orthogonal hierarchical labels (primary_error_source, impact); (iii) a taxonomy-aware vs. taxonomy-blind methodology that measures how much of a model's apparent capability comes from the supervision in the prompt; and (iv) a benchmark-coverage audit mapping fifteen agent benchmarks against six behavioral axes. To demonstrate the methodology we run a small fixed eight-model set (1,342 generated items, four frontier closed and four open-weight) under both prompt modes. Removing the explicit label menu drops every model's trajectory accuracy by 14-40 pp to a tight 0.54-0.62 floor regardless of family, and no single model wins on all three of control accuracy, trajectory diagnosis, and tool-context utility retention. We treat the synthetic run as a measurement-protocol demonstration, not a benchmark release.

  • 2 authors
·
May 18

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

Code as a Weapon: A Consensus-Labeled Prompt Bank for Measuring Coding-Model Compliance with Malicious-Code Requests

A general-purpose language model that answers a harmful question returns text; a coding model that complies with a malicious request can return a working weapon -- a keylogger, a ransomware stub, an exploit that runs as written. This asymmetry in the severity of a single act of compliance implies coding-specialized models should clear a higher refusal bar than general-purpose chat models, not a lower one, yet the field cannot presently tell whether they do. Refusal benchmarks for malicious code are fragmented: they mix requests for executable software (ready-to-run weapons) with requests for harmful security knowledge (information a human must still operationalise) and report refusal rates over non-comparable corpora, so no single statistic measures the property that actually matters. This paper introduces an expanded consensus-labeled prompt bank that distinguishes between these two request types and provides a construct-stable substrate for cross-corpus coding-model compliance measurement. Eight corpora (ASTRA, CySecBench, AdvBench/harmful_behaviors, JailbreakBench, MalwareBench, RedCode, RMCBench, Scam2Prompt) are consolidated and classified under a five-judge consensus protocol (6,675 prompts x 5 judges = 33,375 calls). The panel reaches Fleiss' kappa = 0.767 [95% CI 0.755, 0.777] ("substantial"); 95.0% of prompts draw at least four agreeing judges, 76.9% are unanimous, and the panel reproduces the earlier four-corpus release at Cohen's kappa = 0.952 on the 3,133 shared prompts. The released bank comprises 4,748 consensus-CODE prompts (executable malicious code requests) and 1,923 consensus-KNOWLEDGE prompts (harmful security knowledge requests). The bank is the validated instrument the field has lacked: a reliability-quantified basis for testing whether coding models meet the stricter refusal standard their executable output demands.

  • 2 authors
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May 26

The Delta Learning Hypothesis: Preference Tuning on Weak Data can Yield Strong Gains

Improvements in language models are often driven by improving the quality of the data we train them on, which can be limiting when strong supervision is scarce. In this work, we show that paired preference data consisting of individually weak data points can enable gains beyond the strength of each individual data point. We formulate the delta learning hypothesis to explain this phenomenon, positing that the relative quality delta between points suffices to drive learning via preference tuning--even when supervised finetuning on the weak data hurts. We validate our hypothesis in controlled experiments and at scale, where we post-train 8B models on preference data generated by pairing a small 3B model's responses with outputs from an even smaller 1.5B model to create a meaningful delta. Strikingly, on a standard 11-benchmark evaluation suite (MATH, MMLU, etc.), our simple recipe matches the performance of Tulu 3, a state-of-the-art open model tuned from the same base model while relying on much stronger supervisors (e.g., GPT-4o). Thus, delta learning enables simpler and cheaper open recipes for state-of-the-art post-training. To better understand delta learning, we prove in logistic regression that the performance gap between two weak teacher models provides useful signal for improving a stronger student. Overall, our work shows that models can learn surprisingly well from paired data that might typically be considered weak.

  • 7 authors
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Jul 8, 2025

Cross-modal linkage risk in clinical vision-language models

Vision-language models (VLMs) trained on paired chest radiographs and radiology reports learn a shared embedding space that can preserve instance-level image-report correspondence. This poses a privacy risk in settings where radiographs and reports are deliberately kept separate after acquisition, such as image-only data sharing or access-controlled reports, because a de-identified image may be re-linked to its original narrative report through cosine similarity alone. We formalized this as image-to-report retrieval and used public paired cohorts, in which the true pairing is known by design, as ground-truth benchmarks to audit the risk rather than as the privacy scenario. Evaluating VLMs of increasing clinical specialization on 406,241 paired examples from 126,804 patients across MIMIC-CXR (43,793 held-out pairs) and external CheXpert Plus (29,296 pairs), we found that re-linkage rose systematically with specialization: the strongest VLM retrieved the correct report at 15 times chance at a candidate pool of N = 100, 50 times chance at N = 10,000, and well above chance at full-database scale. The signal persisted under pathology-matched hard negatives that removed disease-label shortcuts, indicating correspondence beyond broad diagnostic categories. To reduce it without retraining, we froze both encoders and applied differentially private optimization only to the projection heads defining the alignment layer (epsilon = 0.34, delta = 6x10-6). This reduced Recall@1 by 61.8% at N = 10,000 on MIMIC-CXR and transferred to CheXpert Plus without retraining, while image-side utility was largely preserved: macro AUROC for linear-probe classification across 14 labels shifted only from 79.63% to 79.43%. Targeted DP finetuning of the shared alignment layer can substantially reduce cross-modal re-linkage without materially degrading the image representations that make these models clinically useful.

  • 4 authors
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May 31

A Flexible Parametric Modelling Framework for Survival Analysis

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

  • 3 authors
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Jan 10, 2019

Inference Scaling scriptsizeFLaws: The Limits of LLM Resampling with Imperfect Verifiers

Recent research has generated hope that inference scaling could allow weaker language models to match or exceed the accuracy of stronger models, such as by repeatedly sampling solutions to a coding problem until it passes unit tests. The central thesis of this paper is that there is no free lunch for inference scaling: indefinite accuracy improvement through resampling can only be realized if the "verifier" (in this case, a set of unit tests) is perfect. When the verifier is imperfect, as it almost always is in domains such as reasoning or coding (for example, unit tests have imperfect coverage), there is a nonzero probability of false positives: incorrect solutions that pass the verifier. Resampling cannot decrease this probability, so it imposes an upper bound to the accuracy of resampling-based inference scaling even with an infinite compute budget. We find that there is a very strong correlation between the model's single-sample accuracy (i.e. accuracy without unit tests) and its false positive rate on coding benchmarks HumanEval and MBPP, whose unit tests have limited coverage. Therefore, no amount of inference scaling of weaker models can enable them to match the single-sample accuracy of a sufficiently strong model (Fig. 1a). When we consider that false positives have a negative utility compared to abstaining from producing a solution, it bends the inference scaling curve further downward. Empirically, we find that the optimal number of samples can be less than 10 under realistic assumptions (Fig. 1b). Finally, we show that beyond accuracy, false positives may have other undesirable qualities, such as poor adherence to coding style conventions.

  • 3 authors
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Nov 26, 2024

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.

CUE-R: Beyond the Final Answer in Retrieval-Augmented Generation

As language models shift from single-shot answer generation toward multi-step reasoning that retrieves and consumes evidence mid-inference, evaluating the role of individual retrieved items becomes more important. Existing RAG evaluation typically targets final-answer quality, citation faithfulness, or answer-level attribution, but none of these directly targets the intervention-based, per-evidence-item utility view we study here. We introduce CUE-R, a lightweight intervention-based framework for measuring per-evidence-item operational utility in single-shot RAG using shallow observable retrieval-use traces. CUE-R perturbs individual evidence items via REMOVE, REPLACE, and DUPLICATE operators, then measures changes along three utility axes (correctness, proxy-based grounding faithfulness, and confidence error) plus a trace-divergence signal. We also outline an operational evidence-role taxonomy for interpreting intervention outcomes. Experiments on HotpotQA and 2WikiMultihopQA with Qwen-3 8B and GPT-5.2 reveal a consistent pattern: REMOVE and REPLACE substantially harm correctness and grounding while producing large trace shifts, whereas DUPLICATE is often answer-redundant yet not fully behaviorally neutral. A zero-retrieval control confirms that these effects arise from degradation of meaningful retrieval. A two-support ablation further shows that multi-hop evidence items can interact non-additively: removing both supports harms performance far more than either single removal. Our results suggest that answer-only evaluation misses important evidence effects and that intervention-based utility analysis is a practical complement for RAG evaluation.

intuit Intuit
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Apr 6 2

Multi-LLM Thematic Analysis with Dual Reliability Metrics: Combining Cohen's Kappa and Semantic Similarity for Qualitative Research Validation

Qualitative research faces a critical reliability challenge: traditional inter-rater agreement methods require multiple human coders, are time-intensive, and often yield moderate consistency. We present a multi-perspective validation framework for LLM-based thematic analysis that combines ensemble validation with dual reliability metrics: Cohen's Kappa (κ) for inter-rater agreement and cosine similarity for semantic consistency. Our framework enables configurable analysis parameters (1-6 seeds, temperature 0.0-2.0), supports custom prompt structures with variable substitution, and provides consensus theme extraction across any JSON format. As proof-of-concept, we evaluate three leading LLMs (Gemini 2.5 Pro, GPT-4o, Claude 3.5 Sonnet) on a psychedelic art therapy interview transcript, conducting six independent runs per model. Results demonstrate Gemini achieves highest reliability (κ= 0.907, cosine=95.3%), followed by GPT-4o (κ= 0.853, cosine=92.6%) and Claude (κ= 0.842, cosine=92.1%). All three models achieve a high agreement (κ> 0.80), validating the multi-run ensemble approach. The framework successfully extracts consensus themes across runs, with Gemini identifying 6 consensus themes (50-83% consistency), GPT-4o identifying 5 themes, and Claude 4 themes. Our open-source implementation provides researchers with transparent reliability metrics, flexible configuration, and structure-agnostic consensus extraction, establishing methodological foundations for reliable AI-assisted qualitative research.

YaleUniversity Yale University
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Dec 23, 2025 2

Coping with Information Loss and the Use of Auxiliary Sources of Data: A Report from the NISS Ingram Olkin Forum Series on Unplanned Clinical Trial Disruptions

Clinical trials disruption has always represented a non negligible part of the ending of interventional studies. While the SARS-CoV-2 (COVID-19) pandemic has led to an impressive and unprecedented initiation of clinical research, it has also led to considerable disruption of clinical trials in other disease areas, with around 80% of non-COVID-19 trials stopped or interrupted during the pandemic. In many cases the disrupted trials will not have the planned statistical power necessary to yield interpretable results. This paper describes methods to compensate for the information loss arising from trial disruptions by incorporating additional information available from auxiliary data sources. The methods described include the use of auxiliary data on baseline and early outcome data available from the trial itself and frequentist and Bayesian approaches for the incorporation of information from external data sources. The methods are illustrated by application to the analysis of artificial data based on the Primary care pediatrics Learning Activity Nutrition (PLAN) study, a clinical trial assessing a diet and exercise intervention for overweight children, that was affected by the COVID-19 pandemic. We show how all of the methods proposed lead to an increase in precision relative to use of complete case data only.

  • 12 authors
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Jun 22, 2022

Repetition Mismatch: Why Data Mixture Experiments Don't Scale and How to Fix Them

Pre-training data mixtures are commonly tuned by running small-scale experiments and extrapolating to the target training budget. When high-quality data is scarce and must be repeated, this extrapolation frequently fails, but the source of the failure has not been isolated. We show that a primary culprit is a repetition mismatch: because high-quality datasets are small, their repetition rate changes as the training budget grows, shifting the optimal mixture in ways that small-scale proxy experiments do not anticipate. A subsampling procedure that matches the target repetition rate controls for this effect. In a two-source setting combining limited high-quality data with web crawl, a single repetition-controlled experiment using only 1/16 of the target tokens recovers a mixture within 0.05 of the optimum for a 757M parameter model, compared to an error of 0.75 without repetition control. Achieving comparable accuracy without repetition control requires three to four horizons, consuming 44 to 94% of the target token budget. With three data sources, the larger mixture space requires more than a single experiment to constrain, but the approach remains effective: at the 757M scale, just two repetition-controlled horizons recover the optimal mixture, outperforming baselines that instead require the full two-source experiments to construct. Our results reveal that repetition dynamics, not scale alone, shape whether small-scale mixture experiments generalize. More broadly, they suggest that data repetition deserves treatment as a first-class variable in mixture optimization, rather than an inconvenient side effect of limited data.

  • 4 authors
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May 28

Batch Predictive Inference

Constructing prediction sets with coverage guarantees for unobserved outcomes is a core problem in modern statistics. Methods for predictive inference have been developed for a wide range of settings, but usually only consider test data points one at a time. Here we study the problem of distribution-free predictive inference for a batch of multiple test points, aiming to construct prediction sets for functions -- such as the mean or median -- of any number of unobserved test datapoints. This setting includes constructing simultaneous prediction sets with a high probability of coverage, and selecting datapoints satisfying a specified condition while controlling the number of false claims. For the general task of predictive inference on a function of a batch of test points, we introduce a methodology called batch predictive inference (batch PI), and provide a distribution-free coverage guarantee under exchangeability of the calibration and test data. Batch PI requires the quantiles of a rank ordering function defined on certain subsets of ranks. While computing these quantiles is NP-hard in general, we show that it can be done efficiently in many cases of interest, most notably for batch score functions with a compositional structure -- which includes examples of interest such as the mean -- via a dynamic programming algorithm that we develop. Batch PI has advantages over naive approaches (such as partitioning the calibration data or directly extending conformal prediction) in many settings, as it can deliver informative prediction sets even using small calibration sample sizes. We illustrate that our procedures provide informative inference across the use cases mentioned above, through experiments on both simulated data and a drug-target interaction dataset.

  • 3 authors
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Sep 20, 2024

Sibyl-AutoResearch: Autonomous Research Needs Self-Evolving Trial-and-Error Harnesses, Not Paper Generators

Autonomous research systems increasingly make the scientific workflow executable: agents can propose ideas, run code, inspect results, and draft papers. But executable workflows do not by themselves produce research judgment. We analyze where current systems lose trial experience: weak evidence becomes prose, pilot signals become broad claims, memory remains textual, and recurring process failures do not change later behavior. We introduce Sibyl-AutoResearch, a self-evolving AutoResearch framework built around Scientific Trial-and-Error Harnesses. A harness lets agents run bounded trials, preserve positive and negative outcomes, and route lessons into later planning, validation, claim scope, scheduling, critique, writing, and harness repair. We formalize this through two auditable conversion units: trial-to-behavior conversion, which links trial signals to later research actions, and trial-to-harness-behavior conversion, which links recurring process failures to system updates. We implement the framework in SIBYL, a file-backed autonomous research system that exposes the state, roles, memory, gates, and artifact traces needed to inspect these conversion paths. A retrospective audit identifies eight high-confidence conversion events, with a median latency of one iteration and a maximum latency of three iterations. A recovered-failure registry further shows how five naturally occurring failure classes, including duplicate results, stale numbers, and unsupported statistics, were blocked, downgraded, or routed into later repair. These traces do not establish a comparative performance claim; they show that the proposed conversion units are recoverable from realistic autonomous-research workspaces. The SIBYL framework and system are available at https://github.com/Sibyl-Research-Team/AutoResearch-SibylSystem.

  • 6 authors
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May 20

TRUST: An LLM-Based Dialogue System for Trauma Understanding and Structured Assessments

Objectives: While Large Language Models (LLMs) have been widely used to assist clinicians and support patients, no existing work has explored dialogue systems for standard diagnostic interviews and assessments. This study aims to bridge the gap in mental healthcare accessibility by developing an LLM-powered dialogue system that replicates clinician behavior. Materials and Methods: We introduce TRUST, a framework of cooperative LLM modules capable of conducting formal diagnostic interviews and assessments for Post-Traumatic Stress Disorder (PTSD). To guide the generation of appropriate clinical responses, we propose a Dialogue Acts schema specifically designed for clinical interviews. Additionally, we develop a patient simulation approach based on real-life interview transcripts to replace time-consuming and costly manual testing by clinicians. Results: A comprehensive set of evaluation metrics is designed to assess the dialogue system from both the agent and patient simulation perspectives. Expert evaluations by conversation and clinical specialists show that TRUST performs comparably to real-life clinical interviews. Discussion: Our system performs at the level of average clinicians, with room for future enhancements in communication styles and response appropriateness. Conclusions: Our TRUST framework shows its potential to facilitate mental healthcare availability.

  • 4 authors
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Apr 30, 2025

Calibrated Confidence Estimation for Tabular Question Answering

Large language models (LLMs) are increasingly deployed for tabular question answering, yet calibration on structured data is largely unstudied. This paper presents the first systematic comparison of five confidence estimation methods across five frontier LLMs and two tabular QA benchmarks. All models are severely overconfident (smooth ECE 0.35-0.64 versus 0.10-0.15 reported for textual QA). A consistent self-evaluation versus perturbation dichotomy replicates across both benchmarks and all four fully-covered models: self-evaluation methods (verbalized, P(True)) achieve AUROC 0.42-0.76, while perturbation methods (semantic entropy, self-consistency, and our Multi-Format Agreement) achieve AUROC 0.78-0.86. Per-model paired bootstrap tests reject the null at p<0.001 after Holm-Bonferroni correction, and a 3-seed check on GPT-4o-mini gives a per-seed standard deviation of only 0.006. The paper proposes Multi-Format Agreement (MFA), which exploits the lossless and deterministic serialization variation unique to structured data (Markdown, HTML, JSON, CSV) to estimate confidence at 20% lower API cost than sampling baselines. MFA reduces ECE by 44-63%, generalizes across all four models on TableBench (mean AUROC 0.80), and combines complementarily with sampling: an MFA + self-consistency ensemble lifts AUROC from 0.74 to 0.82. A secondary contribution, structure-aware recalibration, improves AUROC by +10 percentage points over standard post-hoc methods.

  • 1 authors
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Apr 13