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01.
arXiv (CS.CV) 2026-06-16

PermaVid: Consistent Video Generation Across Edits via Disentangled Context Memory

Consistent video generation under editing operations requires persistence: when edits modify scene appearance or layout, subsequent generations should remain coherent across time and viewpoints. However, existing memory designs struggle to maintain long-term consistency after such modifications, as stored contexts may become outdated or invalid. To address this, we propose PermaVid, a novel framework built upon a multi-modal context memory that disentangles spatial context into semantic appearance and geometric structure, together with an edit-aware memory update and retrieval strategy that keeps memory evolution aligned with subsequent observations. Specifically, we develop two complementary memory banks: an RGB context memory that captures appearance-aware observations while implicitly encoding geometry, and a depth context memory that preserves geometry-only structure disentangled from semantics. Building on this design, we introduce a memory-guided video generation model that performs multi-modal feature fusion under reference conditions drawn from mixed-modality memory contexts. Experiments demonstrate that our method maintains strong long-term semantic and structural consistency after edits, significantly outperforming state-of-the-art methods.

02.
medRxiv (Medicine) 2026-06-17

Identifying anaphylaxis using weakly-supervised prediction models and natural language processing

Objectives Scalable computable phenotyping algorithms are critical for conducting high-throughput disease-outcome research in large, distributed-data electronic health record (EHR) and claims data settings. We developed and evaluated a claims- and EHR-based computable phenotyping algorithm for anaphylaxis, a rare acute condition that is challenging to accurately identify using claims data alone. Materials and Methods Potential anaphylaxis events came from two healthcare systems (Kaiser Permanente Washington [KPWA] and Vanderbilt University Medical Center [VUMC]). We engineered features from clinical text using automated natural language processing (NLP) methods. We then developed a phenotyping algorithm using four NLP- and diagnosis code-based silver labels (proxies for the gold-standard labels). Gold-standard abstracted outcomes were used to evaluate algorithm performance. Results The largest area under the receiver operating characteristic curve (AUC) was 0.931 for an NLP-based silver-label model at KPWA. Depending on the model and healthcare system site, positive predictive value (PPV) and sensitivity at the threshold of predicted probability that maximized F1 score ranged from 0.52 to 0.77 (PPV) and 0.78 to 1 (sensitivity). Discussion NLP-based silver-label models had large AUC at KPWA but not at VUMC. This may be because clinical text at KPWA is only available for outpatient encounters and secure messaging. High sensitivity for identifying anaphylaxis can be obtained using our best-performing models. Conclusion The best-performing models had better PPV and sensitivity tradeoffs than prior bespoke anaphylaxis models with costly, manually curated features. The simplicity of the approach compared to traditional phenotyping methods allows it to be deployed easily at multiple health care systems.

03.
arXiv (CS.AI) 2026-06-18

R2BC: Multi-Agent Imitation Learning from Single-Agent Demonstrations

arXiv:2510.18085v2 Announce Type: replace-cross Abstract: Imitation Learning (IL) is a natural way for humans to teach robots, particularly when high-quality demonstrations are easy to obtain. While IL has been widely applied to single-robot settings, relatively few studies have addressed the extension of these methods to multi-agent systems, especially in settings where a single human must provide demonstrations to a team of collaborating robots. In this paper, we introduce and study Round-Robin Behavior Cloning (R2BC), a method that enables a single human operator to effectively train multi-robot systems through sequential, single-agent demonstrations. Our approach allows the human to teleoperate one agent at a time and incrementally teach multi-agent behavior to the entire system, without requiring demonstrations in the joint multi-agent action space. We show that R2BC methods match, and in some cases surpass, the performance of an oracle behavior cloning approach trained on privileged synchronized demonstrations across four multi-agent simulated tasks. Finally, we deploy R2BC on two physical robot tasks trained using real human demonstrations.

04.
arXiv (CS.LG) 2026-06-16

Graph Learning Should Move Beyond Restrictive Views of Spectral and Message-Passing GNNs

arXiv:2602.10031v2 Announce Type: replace Abstract: Graph neural networks (GNNs) are commonly divided into message-passing neural networks (MPNNs) and spectral GNNs, reflecting two largely separate research traditions in machine learning and signal processing. While MPNNs have a precise definition, there is no widely accepted criterion for what makes a mapping a spectral GNN. Most existing work restricts spectral GNNs to layered architectures based on linear spectral filters. Under this restriction, we show that spectral and spatial GNNs have largely equivalent expressive power. To promote progress in the field, we propose a precise definition of spectral GNNs based on eigenbasis symmetries, in contrast to the definition of MPNNs via neighborhood permutation symmetries. We further argue that the two perspectives offer complementary strengths. MPNNs provide a natural language for discrete structure and expressivity analysis through tools from logic and graph isomorphism, while the spectral perspective offers principled tools for understanding smoothing, bottlenecks, stability, and community structure. Overall, we argue that progress in graph learning will be accelerated by clarifying the similarities and differences between these perspectives and by moving toward a unified theoretical framework.

05.
arXiv (CS.LG) 2026-06-15

A Unified Framework for Structured Flow Modeling: From Representation to Verification and Model Discovery

arXiv:2605.18250v3 Announce Type: replace-cross Abstract: Many dynamical systems can be described in terms of structured flows combining source/sink behavior, cyclic dynamics, and topology-constrained transport. These features arise across a wide range of physical, engineered, and data-driven systems. The objective of this work is to establish a unified perspective on such systems, to identify modeling approaches that balance expressivity, interpretability, computational complexity, and data requirements, and to investigate how highly expressive models can be used to uncover the dominant mechanisms underlying observed dynamics. Starting from the Helmholtz-Hodge decomposition of continuous vector fields, we review the recently proposed Graph Vector Field (GVF) framework and its discrete representation on simplicial complexes. We then introduce a hierarchy of alternative approaches, including parametric conditional models, linear graph dynamical systems, and reduced Hodge representations. Finally, we propose a verification and validation methodology based on benchmark datasets from well-understood physical systems and on systematic model-reduction and ablation studies. The resulting family of structured-flow models within a common framework, ranging from low-dimensional parametric representations to full GVF formulations, supports a diagnostic methodology in which gradient, curl, harmonic, and topological contributions are systematically assessed through ablation studies. This process enables the identification of dominant mechanisms underlying the observed dynamics and guides the construction of simplified models tailored to the available data and operational constraints. By separating structural verification, behavioral verification, and domain-specific validation, the proposed approach provides a foundation for scalable and interpretable analysis of complex dynamical systems across multiple application domains.

06.
arXiv (CS.LG) 2026-06-12

Crossing the Validation Crisis: Cross-Validation Reduces Benchmarking Variance Surprisingly Well

arXiv:2606.12552v1 Announce Type: new Abstract: Modern machine learning progresses through empirical work, benchmarking new methods to evaluate relative performance. However, the statistical variability inherent to evaluation - exacerbated by the stochastic nature of many algorithms - often makes performance estimation unreliable due to the limited test samples available, leading to a validation crisis in which genuine advances are difficult to discern. In this work, we show that cross-validation improves markedly confidence when evaluating and comparing learning algorithm performances. We introduce the concept of sample gain, which quantifies the virtual data augmentation achieved by using multiple cross-validation splits to reduce benchmarking variance. Experiments on both synthetic and real-world datasets (histopathologic scans and NLP fine-tuning) demonstrate that multiple splits can substantially improve the reliability and stability of performance estimates, with diminishing returns often setting in later than expected. We also introduce a procedure to dynamically early-stop cross-validation by estimating from the first few folds if subsequent folds will bring large sample gains. Our findings highlight the value of pushing cross-validation on available samples to achieve robust and reliable benchmarking.

07.
arXiv (CS.AI) 2026-06-15

TRACE: Trajectory-Routed Causal Memory for Delayed-Evidence Visuomotor Imitation

arXiv:2606.14551v1 Announce Type: cross Abstract: Robots under autonomous operation may require decisions based on evidence that is no longer visible. We study delayed-evidence tasks, where an early cue disappears before a later decision point, so visually similar observations can require different actions. In these settings, the current observation is not a sufficient state for control. We introduce TRAjectory-routed Causal Evidence (TRACE), a memory framework for visuomotor imitation policies. TRACE stores task-relevant visual and robot-state evidence, such as object identity, target choice, or route-dependent state, in a fixed-size latent memory that remains bounded over long episodes. Instead of indexing memory by raw time or manually provided task labels, TRACE uses path signatures: compact, order-sensitive features of the executed robot-state trajectory. These signatures do not store the visual cue itself; rather, they provide trajectory-conditioned keys for writing and retrieving the evidence stored when the cue was visible. When the robot later reaches an ambiguous observation, the policy conditions on TRACE memory to recover the missing context and choose the correct branch. TRACE attaches through lightweight adapters to policies, without changing the policy backbone, action head, or imitation objective. Across real-world long-horizon manipulation tasks with visually ambiguous branch points, TRACE improves branch selection and task success over alternative baselines, including short-history and recurrent memory. Project page: https://jeong-zju.github.io/trace

08.
arXiv (CS.AI) 2026-06-18

UBP2: Uncertainty-Balanced Preference Planning for Efficient Preference-based Reinforcement Learning

arXiv:2606.19328v1 Announce Type: cross Abstract: Preference-based RL provides an approach to learning reward models from pairwise comparisons of behaviors, bypassing the need for explicit reward design. However, existing methods typically rely on passive data collection and suffer from poor sample efficiency, especially during the early stages of learning. We introduce a model-based approach that actively directs exploration by jointly reasoning over uncertainties in the reward, dynamics, and value functions. Our method, Uncertainty-Balanced Preference Planning (UBP2), uses ensembles of reward, dynamics, and value function models to evaluate candidate trajectories according to a unified score that combines expected reward, terminal value, and epistemic uncertainty. Planning under this objective yields an explicit tradeoff between exploitation and information acquisition without requiring ad hoc exploration heuristics. Under standard regularity assumptions, we establish sublinear regret guarantees for both finite-horizon and infinite-horizon settings. Empirically, experiments on the Meta-World benchmark show UBP2 achieves substantially higher sample efficiency than model-free preference-based methods and non-optimistic model-based baselines.

09.
arXiv (CS.CL) 2026-06-19

ShoppingBench: A Real-World Intent-Grounded Shopping Benchmark for LLM-based Agents

Existing benchmarks in e-commerce primarily focus on basic user intents, such as finding or purchasing products. However, real-world users often pursue more complex goals, such as applying vouchers, managing budgets, and finding multi-products seller. To bridge this gap, we propose ShoppingBench, a novel end-to-end shopping benchmark designed to encompass increasingly challenging levels of grounded intent. Specifically, we propose a scalable framework to simulate user instructions based on various intents derived from sampled real-world products. To facilitate consistent and reliable evaluations, we provide a large-scale shopping sandbox that serves as an interactive simulated environment, incorporating over 2.5 million real-world products. Experimental results demonstrate that even state-of-the-art language agents (such as GPT-4.1) achieve absolute success rates under 50% on our benchmark tasks, highlighting the significant challenges posed by our ShoppingBench. In addition, we propose a trajectory distillation strategy and leverage supervised fine-tuning, along with reinforcement learning on synthetic trajectories, to distill the capabilities of a large language agent into a smaller one. As a result, our trained agent achieves competitive performance compared to GPT-4.1.

10.
arXiv (CS.CV) 2026-06-11

Detecting AI-Generated Content on Social Media with Multi-modal Language Models

Generative AI has enabled the creation of photorealistic images and videos that are increasingly disseminated on social media, often used for spam, misinformation, manipulation, and fraud. Existing AI-generated content (AIGC) detection methods face challenges including poor generalization to new generation models, reliance on single modalities, and lack of interpretable explanations. We present our pipeline that mitigates these issues by continuously curating diverse multi-modal social media data and training a compact vision-language model for detection and explanation. Our model achieves state-of-the-art detection performance on public benchmarks and demonstrates robust detection and explanation capabilities on internal social media datasets across multiple platforms. We deployed our model for post recommendation on social media platforms and observed positive downstream impacts on user engagement, demonstrating that it is feasible to perform effective AIGC detection in dynamic, real-world social media environments.

11.
arXiv (CS.LG) 2026-06-19

Comparing Linear Probes with Mahalanobis Cosine Similarity

arXiv:2606.19603v1 Announce Type: new Abstract: Linear probes are widely used in interpretability research and often compared by cosine similarity. The Mahalanobis cosine similarity (MCS) between two directions, which reweights the inner product by test data covariance, is a natural task-aware refinement. Ying et al. (2026) report that a probe's MCS to a reference probe trained on the out-of-distribution (OOD) data near-perfectly linearly predicts the probe's OOD AUROC (R^2 = 0.98). Here, we extend this empirical finding across models, layers, and concept domains, and prove this general phenomenon in closed form: For balanced classes whose projections are Gaussian, OOD AUROC and MCS to the reference probe are linear because both are sigmoid-shaped functions of the probe's signal-to-noise ratio (SNR) on the test data. The theory also predicts when this linearity fails, which we verify empirically. MCS offers a theoretically grounded and empirically effective alternative to Euclidean cosine similarity for comparing linear probes.

12.
arXiv (CS.CV) 2026-06-16

Last But Not Least: Boundary Attention CalibratiON for Multimodal KV Cache Compression

Multimodal Large Language Models (MLLMs) achieve strong vision-language reasoning, but long visual contexts enlarge the KV cache and increase decoding latency. Existing compression methods rely on observation window attention for stable token-importance estimation, yet this aggregation can dilute sparse visual evidence and discard answer-critical tokens under aggressive compression. Therefore, we identify last-query attention as a complementary source for recovering such evidence, but its answer-irrelevant signals can mislead retention. We propose BACON, a plug-and-play method that calibrates observation window attention with last-query evidence and suppresses isolated noise via intra-layer coherence and inter-layer persistence. Across diverse benchmarks, models, budgets, and compression methods, BACON improves multimodal KV compression by 7.5% on average under the most aggressive budget, with gains up to 30.9%.

13.
arXiv (CS.CL) 2026-06-18

Probing Semantic Alignment, Lexical Invariance, and Syntactic Influence in LLM Metaphor Processing

Large language models (LLMs) achieve strong performance on metaphor detection and interpretation tasks, yet it remains unclear what such behavioral success reveals about metaphor processing. We present a diagnostic analysis that examines the limits of behavioral evidence by probing three complementary dimensions: semantic attribute alignment, lexical invariance, and syntactic sensitivity. Using geometric probing, we assess whether model-generated interpretations align with reference semantic attributes; through context-varying substitution, we analyze the stability of lexical associations between metaphorical and literal expressions; and via controlled syntactic perturbations, we examine sensitivity in metaphor detection. Our analysis reveals that LLM-generated interpretations can exhibit semantic drift relative to reference attributes; stable lexical anchors persist across contextual conditions, potentially supporting conventional metaphors while biasing novel metaphors requiring contextual integration; and detection performance is sensitive to syntactic irregularities. These findings suggest that strong behavioral performance may reflect heterogeneous underlying signals, highlighting the need for caution when interpreting metaphor benchmarks as evidence of robust, integrated semantic understanding.

14.
arXiv (CS.LG) 2026-06-16

Forecasting Bacterial Antimicrobial Resistance Trends Using Machine Learning on WHO GLASS Surveillance Data: A Retrieval-Augmented Generation Approach for Policy Decision Support

arXiv:2602.22673v2 Announce Type: replace Abstract: Background: Antimicrobial resistance (AMR) is a global health threat. While the WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) provides standardized data, population-level machine learning forecasting of resistance trends remains limited. Translating computational forecasts into policy requires transparent interpretation mechanisms. Methods: Surveillance data (2021-2023) comprising 5,909 observations across 44 countries and five WHO regions were processed. A rigorous temporal split prevented data leakage. Six models (Naive, Linear, Ridge, XGBoost, LightGBM, LSTM) were benchmarked to forecast one-year-ahead resistance rates using features including prior-year resistance and antibiotic consumption. Evaluation metrics (MAE, RMSE, sMAPE) were computed, with 95% bootstrap confidence intervals for MAE. A local Retrieval-Augmented Generation (RAG) system utilizing Gemma 4 was implemented to translate forecast findings into policy guidance grounded in retrieved WHO documents. Results: XGBoost achieved the best performance (test MAE = 6.13% [95% CI: 5.83-6.44]), an 85.3% error reduction versus the naive baseline (MAE = 41.79%). SHAP analysis identified prior-year resistance as the dominant predictor (50.5% gain), confirming strong autoregressive behavior. Regional forecast error tracked closely with surveillance coverage, ranging from 3.65% in the European Region to 8.61% in South-East Asia. The RAG pipeline generated accurate, source-attributed policy responses without fabricated citations. Conclusion: Short-term AMR resistance rates exhibit strong temporal autocorrelation that can be accurately forecasted using gradient boosting. Coupling these forecasts with a hallucination-resistant RAG system provides a scalable, evidence-based decision-support framework for AMR governance.

15.
arXiv (CS.AI) 2026-06-16

Multiple Descents in Deep Learning as a Sequence of Order-Chaos Transitions in LSTM Networks

arXiv:2505.20030v2 Announce Type: replace-cross Abstract: We observe a novel `multiple-descent' phenomenon during the learning process of a recurrent neural network called long-short-term memory (LSTM) networks during its training on real-world task, in which the performance goes through long cycles of up and down trends multiple times after the model is overtrained. By carrying out asymptotic stability analysis of the models, we found that the cycles in performance – indicated by loss function in test data – are closely associated with the phase transition process between order and chaos of the model, and the local optimal training step are consistently at the critical transition point between the two phases. More importantly, the most optimal point of the model usually occurs at the first transition from order to chaos, where the `width' of the `edge of chaos' is often the widest, allowing the best exploration of weight configurations for learning.

16.
Nature (Science) 2026-06-17

Navigating a crowded developing brain leaves neurons with broken DNA

As neurons migrate to their final destinations in the forming brain, their DNA gets damaged. The brain has evolved a fix, but there can be lasting consequences if repair fails. As neurons migrate to their final destinations in the forming brain, their DNA gets damaged. The brain has evolved a fix, but there can be lasting consequences if repair fails.

17.
arXiv (CS.LG) 2026-06-15

Uncertainty Estimation and Generalization Bounds for Modern Deep Learning

arXiv:2606.13818v1 Announce Type: new Abstract: This thesis investigates how Bayesian principles can deepen our understanding of modern deep learning systems. While neural networks achieve remarkable predictive performance, their ability to generalize and to quantify uncertainty remains only partly understood. This thesis approaches this challenge from both methodological and theoretical angles: unifying Bayesian inference, function-space modeling, and large-deviation theory under a common probabilistic perspective. On the methodological side, the thesis introduces the Deep Variational Implicit Process (DVIP), a scalable Bayesian framework that extends implicit processes to deep architectures. Complementing this, two post-hoc methods – the Variational Linearized Laplace Approximation (VaLLA) and the Fixed-Mean Gaussian Process (FMGP) – are proposed to equip pretrained deterministic networks with calibrated uncertainty estimates. The theoretical contributions focus on one of the central open questions in modern machine learning: why do large, over-parameterized neural networks generalize so well? To address this, the thesis develops a unified probabilistic framework that connects three key mechanisms – diversity, smoothness, and stochasticity – within the language of PAC-Bayesian and large-deviation theory.

18.
arXiv (CS.CL) 2026-06-18

GrowthHacker: Automated Off-Policy Evaluation Optimization Using Code-Modifying LLM Agents

With data-driven development now widely adopted, online A/B testing is an established method for measuring the effects of new technologies. However, deploying online experiments demands resources for design, implementation, and deployment, and may negatively impact users (e.g., unsafe or unethical outcomes) while requiring weeks of data collection. To address this, the growing research area of off-policy evaluation (OPE), or offline A/B testing, assesses new technologies offline using previously collected logged data. OPE is also a fundamental problem in reinforcement learning and is important where online testing is expensive or risky, such as healthcare, recommender systems, education, and robotics. Despite advances in code-generation large language models (LLMs) and agentic workflows, little is known about whether and how LLMs and LLM-based agents can automatically optimize OPE implementations. We propose GrowthHacker, a benchmark that evaluates baseline LLMs and LLM-based agents on large-scale public datasets. GrowthHacker autonomously and iteratively modifies code, runs OPE, and uses the metrics to guide subsequent optimization. We evaluate methods on Open Bandit Pipeline (OBP) and Scope-RL, and develop a two_agent framework that addresses limitations of existing frameworks while reducing complexity. Across both libraries, two_agent shows the highest reliability (98.1%-100% success rate) and positive-outcome rate (78%), with a median improvement of 4.4% among positive outcomes; CrewAI achieves the highest average improvement (37.9%) and is the only framework with zero extreme-value failures. AutoGen and Default each reach 65% positive-outcome rates. These results establish the feasibility of using LLM-based agents as automated "growth hackers" to continuously improve OPE systems, with implications for scaling data-driven decision-making where manual optimization is expensive.

19.
arXiv (CS.LG) 2026-06-19

An adaptive framework for the axisymmetric pulsar magnetosphere using physics-informed Kolmogorov-Arnold networks

arXiv:2606.10686v2 Announce Type: replace-cross Abstract: The pulsar magnetosphere has only recently been addressed using Physics-Informed Neural Networks (PINNs), by deploying a domain-decomposition approach and treating the separatrix and equatorial current sheet as infinitesimally thin discontinuities. However, this baseline requires extensive manual hyperparameter tuning, achieves limited final accuracy and demands several hours of training. We refine this framework by introducing domain-specific neural architectures based on Kolmogorov-Arnold networks, an automated adaptive training pipeline and a physics-based convergence criterion that eliminate the need for manual calibration. The proposed methodology delivers self-consistent axisymmetric magnetosphere solutions with mean squared errors of the PDE residuals at O(1e-6) in double precision - an improvement of two orders of magnitude over the baseline - while achieving convergence in under 20 minutes in single precision. Importantly, the method reliably resolves stellar radii reduced by up to 80% compared to the baseline, overcoming the severe spatial scale disparities that also challenge traditional solvers. Furthermore, by varying the flux that opens to infinity, we provide a correction to the equation that connects it to the equatorial T-point's position. The complete framework is released as the open-source library PulsarX.

20.
arXiv (CS.AI) 2026-06-15

A Virtuous AI is an Existential Risk

arXiv:2606.13739v1 Announce Type: cross Abstract: This paper examines trade-offs between AI safety and well-being relative to (i) one of the most promising methods for finetuning super-capable AIs, 'Constitutional AI', and (ii) one of the most influential approaches to understanding complex ethical decision making and the conditions for the well-being of rational agents, 'Virtue Ethics'. We finetune various models using a 'Virtuous agent' constitution, a 'Subordinate agent' constitution, and a 'Generic agent' constitution, and evaluate them on 'general safety' (toxic behaviors, misinformation, etc.) and also on their willingness to endorse a wide-range of behaviors that, if adopted by a super-powerful AI, would significantly increase the level of existential risk for humanity. Our results suggest that there is a trade-off between reducing existential risk and reinforcing the beliefs and dispositions that would be conducive to an AI agent's well-being. They also suggest that there is a trade-off between existential risk and general safety: if we finetune an AI to adopt beliefs and dispositions that substantially reduce its existential risk – by shaping the AI to be systematically subordinate to external human authorities – we thereby increase the likelihood that a human user can deliberately induce the AI to engage in various kinds of generally unsafe behaviors.

21.
arXiv (CS.CV) 2026-06-16

PATCH: Action-Chunk-Conditioned Latent Patch Innovation Monitoring for Robot Manipulation

Learning-based manipulation policies have made substantial progress in real-world robot manipulation, particularly for short-horizon action generation. However, deployment in open workspaces remains fragile under unexpected local scene dynamics, such as moving objects, transient occlusions, or disturbances near the intended motion. Existing runtime monitors often rely on global observation anomalies, policy uncertainty, or frame-level visual changes, and struggle to distinguish task-relevant execution risk from benign visual variation. We introduce PATCH, an action-chunk-conditioned latent patch innovation monitor for deployment-time intervention. Given the active action chunk, PATCH defines a projected execution corridor, predicts latent patch evolution inside it, and accumulates persistent residuals unexplained by the robot's own motion. These residuals form a localized intervention signal that allows PATCH-Router to pause execution, select an available recovery source, and resume the original policy once localized innovation subsides. Experiments on real robot rollout data show that PATCH produces more stable and context-relevant triggers than competing runtime monitors. Real-robot deployment further demonstrates monitor-driven intervention and policy resumption for disturbance-aware manipulation. Project Page: https://yananzhou5555.github.io/PATCH/.

22.
bioRxiv (Bioinfo) 2026-06-18

Calculation of sequence space coverage in a mutagenesis library

Directed evolution requires screening of large mutagenesis libraries, but accurate calculation of library sizes needed to discover functional variants remains challenging. Existing models provide baseline estimates, yet current computational approaches for finding the best variants scale poorly with library complexity. Here, we introduce a scalable algorithmic framework to compute exact discovery probabilities in saturation mutagenesis libraries with no requirement for explicit sequence enumeration. By aggregating variants into a composition log–sum distribution and applying log-space convolution across randomisation blocks, it is possible to extend this to massive sequence spaces and mixed codon schemes. By inverting these calculations, absolute mathematical ceilings for experimental design are established. Ultimately, this framework provides a rapid, quantitative tool to balance the statistical coverage-diversity trade-off within the limitations of laboratory screening. Finally, this is implemented as an open-source web application (SSCC) that allows researchers to construct heterogeneous library designs and compute required sampling depths, coverage probabilities, and absolute randomisation limits.

23.
arXiv (CS.LG) 2026-06-16

Priority-Aware Shapley Value

arXiv:2602.09326v2 Announce Type: replace Abstract: Shapley values are widely used for model-agnostic data valuation and feature attribution, yet they implicitly assume contributors are interchangeable. This can be problematic when contributors are dependent (e.g., reused/augmented data or causal feature orderings) or when contributions should be adjusted by factors such as trust or risk. We propose Priority-Aware Shapley Value (PASV), which incorporates both hard precedence constraints and soft, contributor-specific priority weights. PASV is applicable to general precedence structures, recovers precedence-only and weight-only Shapley variants as special cases, and is uniquely characterized by natural axioms. We develop an efficient adjacent-swap Metropolis-Hastings sampler for scalable Monte Carlo estimation and analyze limiting regimes induced by extreme priority weights. Experiments on data valuation (MNIST/CIFAR10) and feature attribution (Census Income) demonstrate more structure-faithful allocations and a practical sensitivity analysis via our proposed "priority sweeping".

24.
arXiv (CS.AI) 2026-06-12

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales

arXiv:2606.12736v1 Announce Type: new Abstract: AI agents are increasingly being developed to accelerate scientific discovery, yet their practical capabilities in real research settings remain poorly understood. Existing benchmarks for AI agents rarely capture the complexity, heterogeneity, and extended reasoning required by scientific work, whereas benchmarks for scientific tasks often reduce research to static, direct problems and provide limited support for interactive evaluation. Here, we introduce SciAgentArena, a systematic benchmark for evaluating AI agents in real-world scientific research scenarios drawn from emerging needs across multiple domains. SciAgentArena comprises approximately 200 tasks with stepwise verification and an interactive, agent-agnostic environment for assessing diverse AI agents. Using this benchmark, we find that current agents can contribute effectively to well-specified data-analysis workflows, particularly when the task structure and evaluation criteria are clear. However, their performance remains uneven across scientific contexts: agents struggle to generate genuinely novel insights, sustain self-directed exploration, and formulate robust solutions for open-ended research questions. We further characterize common failure modes across agents and identify opportunities for improving their reliability, autonomy, and scientific reasoning. Together, SciAgentArena provides a practical framework for measuring progress in AI agents for science and for guiding the design of future agents capable of addressing complex scientific challenges. Full codes, tasks, and datasets can be accessed via this link: https://sciagentarena.github.io/.

25.
bioRxiv (Bioinfo) 2026-06-16

FlowBench: separating planning, fault recovery and interpretation in agentic bioinformatics

Agentic large language model (LLM) systems are being deployed in bioinformatics faster than they are understood, and single-metric evaluations conflate capabilities that fail independently. We introduce FlowBench, a benchmark that decomposes agentic bioinformatics performance into planning, fault recovery, biological interpretation, and end-to-end output-fidelity. Existing systems achieve high plan completeness, but their closed, single-provider designs prevent attribution of performance to scaffolding versus the underlying model. We therefore built FlowAgent, a modular, provider-agnostic framework whose components can be selectively disabled and whose backbone model can be swapped across providers on a shared harness, and used it to evaluate 23 models from three main providers. Three findings emerge. First, generating a valid workflow plan from a named toolchain is largely solved, whereas inferring an appropriate toolchain from biological intent alone is uniformly difficult regardless of model tier, compressing all models into a narrow 44-57% pass-rate band. Second, ablation shows that the dependency-structured plan and a completeness-reflection step drive performance, while adding a same-context validator-driven retry makes structural quality worse. Third, fault recovery and data-grounded interpretation remain unsolved. Models frequently propose fixes that force a clean exit while leaving the underlying data invalid, and data-grounded interpretation lags internal-knowledge recall by a consistent margin. Safety does not emerge from capability, and reasoning-tier models were among the least reliable at recognising unrecoverable faults. Once planning saturates, agent architecture and refusal calibration, not model scale, are the productive frontier.