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01.
arXiv (CS.AI) 2026-06-18

SciRisk-Bench: A Risk-Dimension-Aware Benchmark for AI4Science Safety

arXiv:2606.18936v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly embedded in AI for Science (AI4Science) workflows, from scientific question answering and literature analysis to laboratory planning and autonomous discovery. This progress creates an urgent need for safety benchmarks that evaluate not only scientific competence, but also whether models recognize and avoid risks in high-stakes scientific contexts. Existing AI4Science safety datasets cover several disciplines and task formats, leaving the underlying risk dimensions underspecified. We introduce SciRisk-Bench, a benchmark designed to evaluate AI4Science safety from two complementary perspectives: explicit risk dimensions and scientific disciplines. SciRisk-Bench covers 7 disciplines, 31 subdisciplines and 10 risk dimensions. In the experimental section, we evaluate both mainstream LLMs and science-oriented LLMs across risk dimensions, disciplines, and sub-disciplines, enabling fine-grained diagnosis of where scientific models remain unsafe.

02.
arXiv (CS.LG) 2026-06-12

Learning-Augmented Approximation for Unrelated-Machines Makespan Scheduling

arXiv:2606.13133v1 Announce Type: cross Abstract: Recently, Antoniadis et al. (ICLR 2025) proposed a framework for incorporating predictions to approximate NP-hard selection problems. Despite its simplicity, this approach tightly matches theoretical lower bounds, making its generalization highly compelling. We address an open question raised in the work of Antoniadis et al., concerning the extension of this approach to other important problems outside the class of selection problems, such as scheduling. We develop a learning-augmented algorithm for the makespan minimization problem on unrelated machines, denoted by $R\|C_{\max}$. By using predictions of heavy job assignments, we achieve a polynomial-time $(1+\varepsilon)$-approximation for accurate predictions that smoothly degrades to a worst-case 2-approximation as the error increases. We conclude our work with an empirical analysis of our method.

03.
Nature (Science) 2026-06-17

A mosaic of whole-body representations on the human precentral gyrus

Understanding how the body is represented in the motor cortex is key to understanding how the brain controls movement. Although the motor cortex has been mapped in animal models at a fine scale1–10, characterization in humans remains primarily limited to low-resolution recording11–16 and stimulation techniques17–20. Here we created a comprehensive map of the human motor cortex at single-neuron resolution, spanning microelectrode array recordings from 20 arrays across 8 individuals with paralysis from spinal cord injury, amyotrophic lateral sclerosis or brainstem stroke, all enrolled in brain–computer interface clinical trials. These arrays broadly sample the crown of the precentral gyrus (PCG; thought to be composed largely of the premotor cortex (Brodmann area 6)). We found that body parts were highly intermixed, such that the entire body was represented in all sampled locations of the PCG, although the relative strength of body parts was roughly consistent with the motor homunculus17,18. We also found two speech-preferential areas with a broadly tuned, orofacial-dominant area in between them. Throughout the PCG, movement representations of the four limbs were interlinked, with homologous movements of different limbs (for example, toe curl and hand close) having correlated representations. These data provide evidence consistent with an intermixed, interrelated and behaviour-centred organization of the motor cortex3,21. The resulting map also provides important targeting information for brain–computer interfaces that seek to restore motor function. A comprehensive map of the human motor cortex at single-neuron resolution is described.

04.
arXiv (quant-ph) 2026-06-16

Non-Gaussian Phase Transition and Cascade of Instabilities in the Dissipative Quantum Rabi Model

arXiv:2507.07092v3 Announce Type: replace Abstract: The open quantum Rabi model describes a two-level system coupled to a harmonic oscillator. A Gaussian phase transition for the nonequilibrium steady states has been predicted when the bosonic mode is soft and subject to damping. We show that oscillator dephasing is a relevant perturbation, which leads to a non-Gaussian phase transition and an intriguing cascade of instabilities for $k$-th order bosonic operators, as well as a jump in the steady-state qubit polarization. For the soft-mode limit, the equations of motion form a closed hierarchy and spectral properties can be efficiently studied. To this purpose, we establish a fruitful connection to non-Hermitian Hamiltonians. The results for the phase diagram, stability boundaries, and relevant observables are based on mean-field analysis, exact diagonalization, perturbation theory, and Keldysh field theory.

05.
arXiv (CS.CL) 2026-06-12

SkillChain: Closing the Loop on Skill Evolution for Image-Based E-Commerce AI Assistants

Image-based AI assistants are now deployed at production scale on e-commerce platforms, where a single uploaded image can trigger fundamentally different user intents: product search, style recommendation, visual encyclopedia, or utility tool calls, each demanding its own response format, tool invocation, and domain knowledge. Without per-intent behavioral constraints, LLM-based systems conflate these heterogeneous modes and fall short of domain quality standards, while the breadth and dynamism of the intent space render manual engineering infeasible. To address this, we present SkillChain, which closes the production feedback loop on Skill evolution, automating the lifecycle of Skills through three stages: Skill Creator for bootstrapping from task specs and trajectories, Route Optimizer for routing alignment, and Body Refiner for iterative Skill Body refinement via dual-path LLM-Judge evaluation. Deployed on a production-scale e-commerce image assistant, SkillChain substantially improves aggregate response quality, with the strongest gains on structural compliance and content quality; a one-week online A/B experiment further confirms significant gains in user engagement, content consumption, and long-term retention.

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

SciR: A Controllable Benchmark for Scientific Reasoning in LLMs

arXiv:2606.13020v1 Announce Type: new Abstract: Three paradigmatic forms of inference recur across scientific reasoning: deduction, induction, and causal abduction. Reliably evaluating LLMs on these in scientific settings is currently out of reach: scientific benchmarks built on human annotations are costly and lack mechanistic ground truth, while synthetic logical-reasoning benchmarks do not resemble real scientific documents. We introduce SciR, a benchmark that combines multi-paradigm reasoning with controllable scientific rendering, anchored on three paradigmatic scientific problems. Tasks are generated from formal objects (deduction tree, inductive rule hypothesis, causal graph) to guarantee verifiable answers, then rendered into multi-document scientific discourse via per-track domain-tuned genres. The construction lets us independently vary two difficulty axes: how hard it is to extract the key information needed for inference, and how hard the principled inference itself is. We test six models. Both axes hurt every model, and their effects compound. The rendering even hurts neurosymbolic pipelines, which hand inference to a verified solver. The two axes yield a per-model extraction-vs-inference profile: for instance, reasoning models like deepseek-r1 mostly surpass non-reasoning instruct models on the inference axis. To our knowledge, SciR is the first multi-paradigm scientific-reasoning benchmark with parametric control on both extraction and inference difficulty.

07.
arXiv (CS.CV) 2026-06-12

Spatially Grounded Concept Bottleneck Models via Part-Factorized Attention

Concept bottleneck models (CBMs) predict a layer of human-named attributes before predicting a class, which makes their decisions auditable. On fine-grained recognition tasks the concept heads are usually free to attend anywhere in the image, so a head named for one body region can be satisfied by evidence on another. This work studies a part-factorized CBM that removes that freedom by construction. The method has three components built on a frozen DINOv3 vision transformer. A learned foreground gate, trained on DINOv3 patch features, suppresses background patches inside the part attention. A set of part queries cross-attends to patch features and each of the 312 CUB attributes is routed, through a fixed concept-to-part map, to read only from the part token its name implies. A learnable two-dimensional Gaussian prior, injected additively in log space into the attention logits, breaks the permutation symmetry among part queries; its means are initialized from the dataset-average keypoint location of each part, which requires no per-image keypoint supervision at training or test time. On CUB-200-2011 the spatial-prior model matches a fully supervised baseline (88.85% versus 88.95% top-1) while raising pointing accuracy by 16 points (52.6% versus 36.4%). Replacing bounding-box supervision with a PCA foreground target and combining it with the Gaussian prior removes all per-image supervision and reaches 88.6% top-1 at about 70% pointing accuracy. A keypoint-fraction sweep shows that 0.5% of the training set (about 27 images) suffices to initialize the prior with no measurable loss. Removing part identity entirely is the harder case: without any spatial prior, pointing accuracy collapses to $2.9\%$.

08.
arXiv (CS.AI) 2026-06-17

Conservation Laws for Modern Neural Architectures

arXiv:2606.17816v1 Announce Type: cross Abstract: Understanding gradient descent dynamics is key to explaining the success of over-parameterized models, where implicit bias manifests through conservation laws in gradient flow. While such laws are well understood for linear and ReLU networks, they remain largely unexplored for modern architectures. This work develops a unified framework to characterize conservation laws for contemporary models, including feedforward networks with GELU, SiLU, and SwiGLU activations, multihead attention with sinusoidal and rotary positional encodings, and Mixture-of-Experts architectures under diverse gating designs. Our theoretical findings are supported by experiments that validate the predicted invariants.

09.
arXiv (CS.AI) 2026-06-16

CRC-Screen: Certified DNA-Synthesis Hazard Screening Under Taxonomic Shift

作者:

arXiv:2605.00074v2 Announce Type: replace-cross Abstract: DNA-synthesis providers screen incoming orders by searching the requested sequence against curated hazard lists. We show that this baseline collapses to a 100% false-flag rate when the hazardous sequence comes from a taxonomic family absent from the reference set: under Conformal Risk Control's certified miss-rate constraint, a low-discrimination signal forces the threshold below the entire test-benign mass. We compose three signals derived from a synthesis order's public annotation: $k$-mer Jaccard similarity to known toxins, the trimmed-mean score of a five-LLM judge panel, and cosine similarity to clustered embedding centroids. Fused under a monotone logistic aggregator and calibrated by Conformal Risk Control, the resulting screener certifies $\mathbb{E}[\mathrm{FNR}] \le \alpha + \mathrm{TV}$, where the additive term is the calibration-to-test distribution shift under family holdout (a certified ceiling of 24-49% across folds). Across ten leave-one-taxonomic-family-out folds at $\alpha=0.05$ on UniProt KW-0800 reviewed toxins, the calibrated screener achieves 0% empirical test miss rate on every fold and 0% test false-flag rate on nine of ten folds. The bound's finite-sample slack $1/(n_{\mathrm{cal}}+1)$ caps the certifiable miss rate at 1.77% on our 200-hazard subsample; reaching procurement-grade $\alpha=10^{-3}$ requires an $18\times$ larger calibration set, which the full reviewed UniProt KW-0800 corpus is large enough to deliver. The binding constraint on certifiable DNA-synthesis screening is calibration data, not algorithms. Code: https://github.com/najmulhasan-code/crc-screen

10.
arXiv (CS.AI) 2026-06-16

LLM-as-Code Agentic Programming for Agent Harness

arXiv:2606.15874v1 Announce Type: new Abstract: Every major LLM agent framework gives the LLM the role of orchestrator; the model decides what to do next, when to call tools, and when to stop. We argue that token explosion, control-flow hallucination, and unreliable completion are not implementation bugs but architectural consequences of assigning the deterministic work of looping, branching, and sequencing to a probabilistic system. A better prompt or a stronger model cannot guarantee the reliability of the LLM agent. We therefore propose Agentic Programming, in which the program governs all control flow, and the LLM is itself part of it, an adaptive component we call LLM-as-Code and invoke only where a task calls for reasoning or generation. Within each call the model keeps full flexibility, but it cannot alter the program's execution path. With control in the program, the LLM's context is built from the execution history's call tree and forms a directed acyclic graph (DAG). Each call's context length is then determined by its call depth rather than by accumulation over steps. A case study of computer-use agents shows that the design is practical, not just a theoretical stance, substantially improving the stability of long visual operation sequences.

11.
arXiv (CS.CV) 2026-06-15

Fusion of Pervasive RF Data with Spatial Images via Vision Transformers for Enhanced Mapping in Smart Cities

In this paper, we present a deep learning-based approach that integrates the DINOv2 architecture to improve building mapping by combining (possibly erroneous) maps from open-source platforms with pervasive radio frequency (RF) data collected from multiple wireless user equipments and base stations. Unlike prior methods, our approach leverages a vision transformer-based architecture to jointly process both RF and map modalities within a unified framework, effectively capturing spatial dependencies and structural priors for enhanced mapping accuracy. For the evaluation purposes, we employ a synthetic dataset co-produced by Huawei. To address the challenges associated with real-world data imperfections, we introduce controlled noise to its RF data so as to simulate real-world conditions. Additionally, we develop and train a model that leverages only aggregated path loss information to tackle the mapping problem. We measure the results according to three performance metrics: the Jaccard index (intersection over union, IoU), the Hausdorff distance, and the Chamfer distance. Our design achieves a macro IoU of 65.3%, significantly surpassing (i) the erroneous maps baseline, which yields 40.1%, (ii) an RF-only method from the literature, which yields 37.3%, and (iii) a non-AI fusion baseline that we designed which yields 42.2%. The comparative evaluation highlights the limitations of relying solely on RF data or on spatial data, as well as the effectiveness that AI can have on fusing data towards enhancing smart city mapping accuracy. We further validate our method on real-world data from the Oslo region, complementing the synthetic evaluation with a real deployment setting, where our best fusion model reaches 64.9% macro IoU. We additionally outline a strategy for deploying the model over larger areas by tiling the region with overlapping windows.

12.
medRxiv (Medicine) 2026-06-16

Adverse Childhood Experiences and Growth Outcomes in Childhood: A Longitudinal EHR-Based Study

Question Are adverse childhood experiences (ACEs) associated with altered growth trajectories in childhood? Findings In this cohort study of 412,549 children and adolescents, ACEs were associated with lower height throughout childhood, earlier pubertal timing, and shorter final stature. Height differences emerged approximately 2 years before ACE documentation and were greatest among those with earlier documentation. Meaning These findings suggest that early adversity affects physical growth in children and may serve as a measurable indicator of the biological consequences of early-life stress, especially in those with documentation of ACEs prior to the onset of typical pubertal growth. Importance Adverse childhood experiences (ACEs) are among the strongest risk factors for long-term mental and physical health complications, yet their impact on physical growth in childhood remains incompletely understood. Objective To determine the association of ACEs on childhood growth trajectories and growth dynamics. Design, Setting and Participants Retrospective cohort study using longitudinal electronic health record data. Data was collected from participants between February 1999 and August 2025. A large academic medical center biobank linked to deidentified electronic health records in the southeastern United States. A total of 412,549 individuals with at least 2 recorded height measurements between the ages of 2 and 20 were included in the primary analysis. Growth curve analyses were performed in a subset of 199,844 individuals with at least 3 height measurements spanning at least 2 years. Genetic analyses were performed in a subset of 10,114 individuals of primarily European ancestry. Exposure(s) Documented exposure to adverse childhood experiences before age 18 years identified through a natural language processing algorithm. Main Outcome(s) and Measure(s) Height-for-age z-scores across childhood, final attained height, and growth curve parameters estimated using SuperImposition by Translation and Rotation (SITAR) modeling. Results Among 412,549 participants, 18,502 (4.5%) had clinically documented ACEs during childhood. ACE documentation was associated with lower height-for-age z-scores throughout childhood and adolescence. Final attained height was significantly lower among ACE-documented individuals, with mean differences of -3.0 cm among males (174.0 cm vs 177.0 cm, p < 0.001) and -1.3 cm among females (161.8 cm vs 163.1 cm, p < 0.001). Height differences emerged approximately 2 years before clinical ACE documentation. Earlier age at first ACE documentation was associated with progressively shorter final attained height, with each year decrease in age at ACE documentation associated with a decrease in final height of -0.20 cm in females and -0.35 cm in males. Those with first ACE documented prior to pubertal age also showed the most pronounced growth dynamic differences, with males demonstrating a mean reduction in size of 5.25 cm (95% CI, -6.79 cm to -3.70 cm) and 1.26-year earlier pubertal timing (95% CI, -1.50 to -1.03 years), and females demonstrating a reduction in growth curve size of 3.62 cm (95% CI, -4.83 to -2.41 cm) and 1.14-year earlier pubertal timing (95% CI, -1.29 to -0.99 years). Conclusions and Relevance In this large clinical cohort, clinically documented ACEs were associated with time-dependent reductions in stature, earlier pubertal timing, and short final attained height. These findings suggest that early childhood adversity may have lasting effects on physical development and highlight growth trajectories as a potential marker of the biological consequences of early-life stress.

13.
arXiv (CS.AI) 2026-06-16

Input-Dependent Fisher Information for Local Sensitivity Analysis of Medical Image Classifiers

arXiv:2606.16362v1 Announce Type: cross Abstract: Deep neural networks have achieved strong performance in medical image classification, but often work like black-box. Commonly used post-hoc interpretation methods often provide heuristic visualizations whose relationship to the classifier's predictive distribution is indirect. This work introduces a local sensitivity analysis framework based on the input-dependent Fisher Information Matrix (iFIM) of a trained classifier. The iFIM characterizes how the classifier's predictive distribution changes under infinitesimal perturbations of the input image. By using a Gram-matrix formulation, the nonzero eigenspectrum of the iFIM can be recovered without explicitly forming the full image-dimensional Fisher matrix. The leading iFIM eigenspace is then used to project an input image into a high local-sensitivity component and its orthogonal component. These components provide a model-intrinsic description of local predictive sensitivity, rather than a conventional pixel-wise attribution heatmap or a causal segmentation of task-relevant anatomy. The framework is evaluated on controlled and clinical medical image classification tasks using multiple classifier architectures. Perturbation-based experiments show that high-sensitivity iFIM components are more strongly coupled to changes in predictive confidence and classification performance than lower-sensitivity complementary components. The results support the iFIM framework as a principled tool for analyzing local decision sensitivity and for complementing existing attribution-based interpretability methods in medical imaging.

14.
arXiv (CS.CL) 2026-06-19

Proactive Conversational Assistant for a Procedural Manual Task based on Audio and IMU

Real-time conversational assistants for procedural manual tasks often depend on video input, which can be computationally expensive and compromise user privacy. For the first time, we propose a real-time conversational assistant that provides comprehensive guidance for procedural manual tasks using only lightweight privacy-preserving modalities such as audio and IMU inputs from a user's wearable device to understand the context. Using a furniture assembly task and a cooking task, we show how this assistant proactively communicates step-by-step instructions to a user performing a procedural task, and answers user questions. We illustrate the data generation method and the system design to achieve such an assistant. On observing that an off-the-shelf language model is a talkative assistant but is not always able to answer questions correctly, we demonstrate how finetuning the model improves its ability to limit unnecessary dialogues with a 50% increase in the precision, while also improving its ability to answer questions correctly, measured by a 150% increase in the recall of answers. We further describe how such an assistant is implemented on an edge device with no dependence on the cloud.

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

Zone of Proximal Policy Optimization: Teacher in Prompts, Not Gradients

Knowledge distillation transfers a teacher's competence to a small student but is brittle in the small-student regime: forcing the student to imitate logits from a much larger teacher concentrates it on the teacher's sharpest modes, hurting generalization on benchmark families beyond the training corpus. Reinforcement learning (RL) avoids logit imitation by training on the student's own rollouts. However, on questions where every rollout fails-yielding zero advantage and being silently discarded-injecting a stronger teacher's response into the policy gradient breaks the on-policy assumption and induces drift. We introduce Zone of Proximal Policy Optimization (ZPPO), inspired by Vygotsky's zone of proximal development, which keeps the teacher inside the prompt rather than the policy gradient. On hard questions, ZPPO constructs two reformulated prompts: a Binary Candidate-included Question (BCQ) pairs one correct teacher response with one incorrect student response as anonymized candidates the student must discriminate, and a Negative Candidate-included Question (NCQ) aggregates the student's wrong rollouts into a single prompt to surface their shared failure modes. A prompt replay buffer recirculates each hard question until it either graduates-the student's mean rollout accuracy on it reaches half- or is FIFO-evicted under finite capacity, amplifying BCQ and NCQ inside the student's current zone of proximal development. On the Qwen3.5 family at four student scales (0.8B-9B) with a 27B teacher, post-trained as vision-language models and evaluated on a 31-benchmark suite (16 VLM, 10 LLM, 5 Video), ZPPO outperforms off/on-policy distillation and GRPO, with the largest gains at the smallest scale.

16.
arXiv (CS.CV) 2026-06-17

High-Fidelity 3D Geometric Reconstruction of Pelvic Organs from MRI: A Hybrid Deep Learning and Iterative Optimization Approach

Patient-specific 3D reconstruction of pelvic organ geometry from MRI is important for pelvic floor modeling and downstream patient-specific analysis. However, while previous studies have focused primarily on either image segmentation or downstream use of 3D models, the reconstruction of high-fidelity, high-quality geometries remains labor-intensive and poorly standardized. The study introduced a hybrid deformable shape modeling framework that integrates deep learning prediction with iterative optimization for the reconstruction of the bladder, uterus, and rectum. The framework consists of three core components: a geometry-aware multi-level deep learning architecture that preserves topological consistency of pelvic organs; a two-stage amortized optimization training strategy that balances global shape capture and local surface refinement; and a holistic synergy mechanism–where iterative optimization provides supervision for deep learning during the training phase, and during inference, deep learning rapidly predicts the global organ morphology, followed by iterative optimization to refine local surfaces and mesh quality. This framework demonstrated marked superiority in geometric fidelity than current mainstream deep learning-based organ reconstruction models. For individual anatomical structures, the reconstructed 3D geometries for the bladder, rectum, and uterus achieved significantly lower Chamfer Distance values and higher Dice Similarity Coefficient scores. In addition, while maintaining high computational efficiency, the proposed architecture yielded superior overall volumetric mesh quality. At the patient level, the framework achieved higher mean values for the 10 worst elements for both minSICN and minSIGE compared to traditional geometric post-processing algorithms.

17.
arXiv (CS.CL) 2026-06-17

EComAgentBench: Benchmarking Shopping Agents on Long-Horizon Tasks with Distributed Hidden Intent

As LLM-based shopping agents enter production, existing benchmarks fail to capture how a shopper's requirements arrive: stated implicitly in the query, recorded in a profile, or revealed only when the right question is asked. Benchmarks that expose full intent upfront and grade only the final choice can neither pose this long-horizon challenge nor explain which requirement an agent missed. To address this gap, we introduce EComAgentBench, a benchmark of 662 tasks grounded in real Amazon products and reviews. Each task scatters these requirements across a visible query, a tool-gated profile, and scripted clarification; an agent must uncover hidden intent, verify candidates against attributes and review evidence, and commit to a single product within 100 tool calls. Moreover, typed, source-tagged rubrics grade every task, attributing each failure to a requirement and its source. Construction is automated yet reliable, with every answer fixed in code before any text is generated and every sample validated. Our evaluation of seven models reveals that even the strongest attains only 57.1% overall accuracy, and rubric satisfaction degrades from visible to hidden sources. Overall, we believe EComAgentBench will serve as a reproducible foundation for moving shopping agents from single-query search toward dependable assistance over long horizons.

18.
arXiv (CS.AI) 2026-06-16

AI Contagion in Social Networks

arXiv:2606.15206v1 Announce Type: cross Abstract: We study how artificial intelligence (AI) interacts with social communication networks to shape the stability of collective knowledge. Agents exchange information through a network while receiving AI-generated content, and AI systems retrain on the aggregate social information they influence. This interaction generates two feedback forces: an AI contagion channel, through which distortions diffuse across the network, and an AI social distortion multiplier, through which retraining amplifies past errors. Despite the high dimensionality of the environment, we show that the long-run behavior of the system admits a two-dimensional representation whose spectral radius determines whether AI-mediated information systems are dynamically stable or unstable. We characterize a sharp regulatory frontier identifying the minimum filtering required for stability and show how network topology shapes systemic informational risk.

19.
arXiv (CS.CL) 2026-06-17

ProvenanceGuard: Source-Aware Factuality Verification for MCP-Based LLM Agents

Tool-using LLM agents increasingly use the Model Context Protocol (MCP) to answer from heterogeneous evidence sources, including search, APIs, databases, clinical records, and formulary tools. Standard factuality metrics usually test whether an answer is supported by pooled evidence, missing a provenance-sensitive failure mode: a claim may be supported somewhere while being attributed to the wrong source. We call this cross-source conflation. We introduce ProvenanceGuard, a source-aware verifier for MCP-grounded answers. It consumes captured MCP traces with stable tool IDs, source IDs, and raw outputs; decomposes answers into atomic claims; routes claims to source-specific evidence; checks support with NLI and a token-alignment proxy; compares stated attribution with the routed source; and returns per-claim verdicts plus an answer-level allow/block decision. Blocked answers can be repaired with retrieval-augmented answer revision and re-verified. We evaluate on 281 medical-domain MCP-agent traces. A 266-trace adjudicated subset yields 2,325 LLM-assisted claim labels split by trace; 361 held-out labels are human-verified. On the 40-trace held-out split, ProvenanceGuard achieves block F1 0.802 and source accuracy 0.858 over 260 source-eligible claims, outperforming source-blind baselines that do not emit claim-to-source IDs. On a harder multi-source benchmark it reaches block F1 0.846, while source-plus-relation accuracy drops to 0.229, showing that exact source ownership remains difficult with semantically close sources. Repair-and-reverify resolves all blocked answers in the full trace set, often via conservative fallback. In 50 controlled clinical conflation probes, ProvenanceGuard detects all injected attribution swaps with no retained wrong attribution. These results show that source attribution is an independent axis for factuality verification in MCP-based agents.

20.
arXiv (CS.AI) 2026-06-19

Thermodynamic Measure of Intelligence

arXiv:2606.20231v1 Announce Type: new Abstract: Can intelligence be measured? We propose that intelligence can be defined as the lawful amplification of rare but valid futures: a system increases the probability of outcomes that would be unlikely under passive dynamics but remain admissible under the constraints of the domain. We start with the premise that an intelligent system must model the world and its own place within it. Because the system is part of the world it models, this leads naturally to recursive self-simulation: the system represents futures in which its own actions are part of the trajectory. Our central results give a necessity statement and a conditional near-sufficiency statement connecting this architecture to a precise thermodynamic measure of lawful amplification of rare-valid futures: high rare-valid lift is impossible unless the internal simulation identifies rare-valid futures with high fidelity; conversely, when rare-valid fidelity is high and the simulation contains an effective policy, the achievable lift approaches the actuation-limited optimum. Thus recursive self-simulation is not merely a plausible feature of intelligence but, under the stated assumptions, is necessary and nearly sufficient for high thermodynamic intelligence. The resulting framework makes intelligence measurable on a universal scale, from passive matter and feedback controllers, large language models, and humans as text generators to Maxwell-demon-like information engines.

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

Exploding and vanishing gradients in deep neural networks: the effect of residual connections

arXiv:2606.17013v1 Announce Type: cross Abstract: The well known phenomenon of exploding and vanishing gradients in deep neural networks is analyzed using multiplicative ergodic theory. The effect of adding a residual connection is explained in this context. Specifically, a characterization of Liapunov exponents due to Furstenberg and Kifer is exploited in order to make a precise statement about the Liapunov spectrum and the effect of residual connections on it.

22.
arXiv (CS.CL) 2026-06-17

Position: Coding Benchmarks Are Misaligned with Agentic Software Engineering

Coding agents have become a major mode of software engineering, but the benchmarks we use to compare them were designed in a pre-agent era: they collapse model, harness, and environment into a single end-to-end score, typically computed against one reference solution, with no component-level signal for iteration. We argue that current coding benchmarks are misaligned with agentic software engineering. A coding agent in practice is not a model: it is a system harness – a composite of models, harnesses, contexts, environments, and feedback signals, any one of which can move the benchmark score by margins comparable to those between adjacent model generations. We discuss three symptoms: (i) benchmark scores conflate the model with the rest of the harness; (ii) grading against a single reference solution penalises equally valid alternatives; and (iii) the absence of signal at the level of individual harness components makes the end-to-end system score difficult to iterate on.

23.
arXiv (CS.AI) 2026-06-11

Bimanual Robot Manipulation via Multi-Agent In-Context Learning

arXiv:2604.20348v2 Announce Type: replace-cross Abstract: Language Models (LLMs) have emerged as powerful reasoning engines for embodied control. In particular, In-Context Learning (ICL) enables off-the-shelf, text-only LLMs to predict robot actions without any task-specific training while preserving their generalization capabilities. Applying ICL to bimanual manipulation remains challenging as the high-dimensional joint action space and tight inter-arm coordination constraints rapidly overwhelm standard context windows. To address this, we introduce BiCICLe (Bimanual Coordinated In-Context Learning), the first framework that enables standard LLMs to perform few-shot bimanual manipulation without fine-tuning. BiCICLe frames bimanual control as a multi-agent leader-follower problem, decoupling the action space into sequential, conditioned single-arm predictions. Evaluated on 13 tasks from the TWIN benchmark, BiCICLe achieves 70.5% average success rate, outperforming the best training-free baseline by 6.1 percentage points and surpassing most supervised methods. We also demonstrate superior real-world performance on 3 tasks without hardware-specific retraining.

24.
bioRxiv (Bioinfo) 2026-06-18

Accounting for allelic diversity and multicopy gene detection improves the accuracy of antibiotic resistance genotypic determination

Background Genomic prediction of antimicrobial resistance (AMR) relies on the accurate detection of resistance genes or allelic variants of core genes from raw or assembled genomes sequences. For several bacterial species and antibiotics, AMR genotype-phenotype discrepancies are common, indicating that important sources of error remain unresolved. For Enterococcus faecium, we focused on identifying the sources of discrepancies for tetracycline resistance, for which genotypic detection had shown particularly low accuracy. We investigated the effect of structural variation in antibiotic resistance genes (ARGs), including gene duplications, truncations, interruptions, and mixed configurations of complete and partial gene copies, as a source of genotype-phenotype discrepancies from short-read data. We conduct further extended investigations to other antibiotic families and into another bacterial species: Escherichia coli. Methods We analyzed collections of E. faecium and E. coli genomes, integrating high-quality complete assemblies, simulated Illumina short reads, and matched AMR phenotypic data. The integrity, copy number, and allelic diversity of ARGs were examined for multiple antibiotic classes, and their impact on ARG detection and accuracy of AMR determination was assessed using several commonly used bioinformatic tools (SRST2, ARIBA and AMRFinderPlus). Results For E. faecium, after ruling out the effect of specific tet allelic variants on tetracycline susceptibility, we found that the integrity and copy number of tet(M) had a major effect on detection accuracy. Duplicated and incomplete ARGs are also common in E. faecium genomes, particularly for macrolides (erm(B)) and aminoglycosides (ant(6)-Ia and aph(3')-IIIa). In E. coli, similar patterns were observed for tet(A), erm(B) and aminoglycoside-associated genes (aph(3')-IIIa and ant(6)-Ia). Across ARGs in both species, short-read mapping methods wrongly reported interrupted genes as complete in some instances, while assembly-based methods often failed to resolve complete copies of duplicated genes. Detection accuracy improved when tools were adapted to account for gene integrity and when extended AMR databases incorporating species-specific alleles were included. Conclusions Our findings reveal that bioinformatic limitations in dealing with ARG copy number and completeness, and in accounting for allelic variation, underly a substantial source of genotype-phenotype errors, highlighting the need for improved AMR databases and bioinformatic tools that consider these factors to achieve reliable genomic prediction of AMR.

25.
arXiv (CS.AI) 2026-06-15

DiffusionBlocks: Block-wise Neural Network Training via Diffusion Interpretation

arXiv:2506.14202v4 Announce Type: replace-cross Abstract: End-to-end backpropagation requires storing activations throughout all layers, creating memory bottlenecks that limit model scalability. Existing block-wise training methods offer means to alleviate this problem, but they rely on ad-hoc local objectives and remain largely unexplored beyond classification tasks. We propose $DiffusionBlocks$, a principled framework for transforming transformer-based networks into genuinely independent trainable blocks that maintain competitive performance with end-to-end training. Our key insight leverages the fact that residual connections naturally correspond to updates in a dynamical system. With minimal modifications to this system, we can convert the updates to those of a denoising process, where each block can be learned independently by leveraging the score matching objective. This independence enables training with gradients for only one block at a time, thereby reducing memory requirements in proportion to the number of blocks. Our experiments on a range of transformer architectures (vision, diffusion, autoregressive, recurrent-depth, and masked diffusion) demonstrate that DiffusionBlocks training matches the performance of end-to-end training while enabling scalable block-wise training on practical tasks beyond small-scale classification. DiffusionBlocks provides a theoretically grounded approach that successfully scales to modern generative tasks across diverse architectures. Code is available at https://github.com/SakanaAI/DiffusionBlocks .