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01.
arXiv (CS.AI) 2026-06-25

Evaluating AGENTS.md: Are Repository-Level Context Files Helpful for Coding Agents?

arXiv:2602.11988v2 Announce Type: replace-cross Abstract: A widespread practice in software development is to tailor coding agents to repositories using context files, such as AGENTS.md. Although this practice is strongly encouraged by agent developers, there is currently no rigorous investigation into whether such context files are actually effective for real-world tasks. In this work, we study this question and evaluate coding agents' task completion performance in two complementary settings: established SWE-bench tasks from popular repositories, with LLM-generated context files, and a novel collection of issues from repositories containing developer-committed context files. Surprisingly, we find that providing context files does not generally improve task success rates, while increasing inference cost by over 20% on average. This observation holds across different LLMs, coding agents, and for both LLM-generated and developer-committed context files. Specifically, we find that while instructions in the context files are well followed by coding agents, repository overviews, although popular and recommended by model providers, are not helpful. We conclude that while context files are useful for specifying non-standard coding practices, any attempts to improve performance should be rigorously evaluated before deployment.

02.
arXiv (quant-ph) 2026-06-25

Quantum Simulation of Non-Hermitian Special Functions and Dynamics via Contour-based Matrix Decomposition

arXiv:2511.10267v3 Announce Type: replace Abstract: Simulating non-Hermitian dynamics on quantum computers is often hindered by the decay of success probability and the instability of non-diagonalizable matrices. Here, we present contour-based matrix decomposition (CBMD), a rigorous and versatile quantum functional calculus framework for simulating non-Hermitian matrix functions. By generalizing the matrix Cauchy residue theorem, CBMD decomposes holomorphic non-Hermitian operators into an analytic infinite contour-residue identity, followed by finite truncation with controlled error to yield linear combinations of Hermitian components. For first-order dynamics, CBMD achieves optimal query complexity across all parameters, strictly matching the optimal performance bounds within the linear combination of Hamiltonian simulation (LCHS) paradigm. Beyond first-order systems, the framework naturally generalizes to complex operator functions, including second-order wave dynamics and non-Hermitian special functions such as Bessel and Airy evolutions. Furthermore, CBMD systematically suppresses the asymptotic growth of non-Hermitian components, yielding a significant reduction in the required number of amplitude amplifications compared to the naive scheme of combining monomials via linear combination of unitaries (LCU) after Taylor expansion. Notably, CBMD avoids explicit dependence on matrix diagonalizability, effectively mitigating the long-standing challenges associated with ill-conditioned eigenvectors and Jordan blocks. Our work establishes a systematic matrix calculus that bridges high-performance classical numerics and fault-tolerant quantum algorithms. It should be noted that CBMD inherits standard LCU overheads, and requires the target function to have a bounded growth order on the real axis.

03.
arXiv (CS.CV) 2026-06-12

An Improved Generative Adversarial Network for Micro-Resistivity Imaging Logging Restoration

An improved GAN-based imaging logging image restoration method is presented in this paper for solving the problem of partially missing micro-resistivity imaging logging images. The method uses FCN as the generative network infrastructure and adds a depth-separable convolutional residual block to learn and retain more effective pixel and semantic information; an Inception module is added to increase the multi-scale perceptual field of the network and reduce the number of parameters in the network; and a multi-scale feature extraction module and a spatial attention residual block are added to combine the channel attention. The multi-scale module adds a multi-scale feature extraction module and a spatial attention residual block, which combine the channel attention mechanism and the residual block to achieve multi-scale feature extraction. The global discriminative network and the local discriminative network are designed to gradually improve the content and semantic structure coherence between the restored parts and the whole image by playing off each other and the generative network. According to the experimental results, the average structural similarity measure of the five sets of imaged logging images with different sizes of missing regions in the test set is 0.903, which is an improvement of about 0.3 compared with other similar methods. It is shown that the method in this study can be used for the restoration of micro-resistivity imaging log images with good improvement in semantic structural coherence and texture details, thus providing a new deep learning method to ensure the smooth advancement of the subsequent interpretation of micro-resistivity imaging log images.

04.
medRxiv (Medicine) 2026-06-18

Effectiveness and Safety of Bempedoic Acid Across Clinically Relevant Subgroups: Insights from the CLEAR Taiwan Study

Background Despite available lipid-lowering therapies (LLT), many patients fail to achieve low-density lipoprotein cholesterol (LDL-C) targets. This gap persists across clinically relevant subgroups. Bempedoic acid has demonstrated effective LDL-C lowering with a favorable safety profile in the CLEAR Taiwan study; however, its effects across subgroups in Asian populations remains limited. Methods The phase IV CLEAR Taiwan study (NCT06925100) enrolled patients with inadequately controlled hypercholesterolemia who received bempedoic acid for 12 weeks in addition to background LLT. This analysis evaluated changes in lipid parameters, high-sensitivity C-reactive protein (hsCRP), and safety outcomes in clinically relevant subgroups, including cardiovascular risk, diabetes, age, statin tolerance, and sex. Results A total of 180 patients were included. Bempedoic acid achieved significant LDL-C reductions in all subgroups. Numerically greater LDL-C reductions were observed in primary prevention, statin-intolerant, younger (< 65 years), and female patients, while comparable reductions were observed across diabetes status. Reductions in non-high-density lipoprotein cholesterol, total cholesterol, and apolipoprotein B were consistent with LDL-C findings. Significant decreases in hsCRP were observed in all subgroups, with numerically greater reductions in patients aged < 65 years and those without diabetes. Bempedoic acid was well tolerated, with a low incidence of adverse events and no new safety signals identified. Changes in liver enzymes, renal function, and uric acid were minimal within subgroups. Conclusion Subgroup analyses from the CLEAR Taiwan study demonstrate consistent efficacy and safety of bempedoic acid across clinically relevant subgroups and support its use as a flexible option to address residual gaps in lipid management.

05.
arXiv (CS.AI) 2026-06-17

PIVOT: Bridging Black-Scholes Implied-Volatility and Price Objectives via Differentiable Jäckel Operator

arXiv:2606.17065v1 Announce Type: cross Abstract: Modern option-learning systems operate in two coordinates: price space, where markets quote and no-arbitrage constraints are most naturally enforced, and implied volatility (IV) space, where volatility surfaces are smoothed, regularized, and evaluated. The bottleneck is interface, not approximation: Jäckel's seminal "Let's Be Rational" (LBR) solver already inverts the Black-Scholes price to machine precision efficiently. What is missing is a differentiable layer that preserves LBR in the forward pass and avoids backpropagating through its branch logic. Such a layer must also confront the unavoidable singularity of the inverse map in the low-vega regime, where the sensitivity 1/vega diverges as vega -> 0. We close this gap with PIVOT, the Price-Implied-Volatility Objective Translator. PIVOT keeps the LBR forward pass intact and supplies the backward pass by implicit differentiation through the smooth Black-Scholes/Black-76 price map, with an explicit gating contract: invalid domains return NaN, well-conditioned rows receive the exact 1/vega gradient, and low-vega rows are attenuated rather than silently regularized. On a single H100, a fused Triton kernel reaches 1.79e9 IV/s at machine precision (9.3e-14 max relative error vs. the reference C solver); end-to-end label generation sustains 48.9M/s on synthetic chains and 16.6M/s on SPX OptionMetrics. In a HyperIV-style one-day reproduction on SPX, PIVOT-augmented objectives Pareto-dominate the baselines, reducing held-out price MAE by up to 43.4% and the strongest three-seed gated objective improving price MAE by 38.8% and IV MAE by 21.3% jointly; cross-asset results on RUT, VIX, and NDX show directional price-MAE gains of 40.1%, 24.2%, and 16.7%, while an ungated IV-roundtrip control collapses to a degenerate near-zero surface, confirming the gate as a correctness contract rather than a tuning knob.

06.
arXiv (CS.CV) 2026-06-25

Physics Question Scene Graph: Fine-grained Evaluation of Physical Plausibility in Text-to-Video Generation

Video generation models are increasingly capable of producing realistic videos, but they still struggle to generate videos that follow basic physical laws. Compounding this is a lack of reliable granular evaluation methods for localizing and specifying physical law violations in videos. We address this by introducing Physics Question Scene Graph (PQSG), a hierarchical question-based evaluation pipeline. PQSG evaluates generated videos by checking their faithfulness to a prompt across objects, actions, and adherence to physical laws using a graph-based hierarchy of questions generated by a vision-language model (VLM), guided by high-quality in-context examples. By representing questions as a graph, PQSG introduces logical dependencies within questions, ensuring that each query is contextually valid. Moreover, PQSG provides granular assessments of which qualities of the video violate physical plausibility constraints. We validate PQSG by creating FinePhyEval, a dataset with physics-based prompts and corresponding generated videos from diverse state-of-the-art video generation models (Sora 2, Veo 3, and Wan 2.1), with each video annotated across multiple categories by humans. Using FinePhyEval, we measure the correlation between PQSG's fine-grained scores and human judgments, showing higher overall correlations than prior work. We also find that PQSG ranks closed-source models higher than Wan 2.1 on physical realism. Lastly, we show that the annotations we provide in FinePhyEval can also be used for subtask evaluation: we benchmark two strong VLMs on generating and answering questions, finding that while models can create human-like questions, they still fall short of human performance in answering them.

07.
Nature (Science) 2026-06-24

The mutational landscape of STING-induced immunity

作者:

Stimulator of interferon genes (STING) is an evolutionary conserved immune signalling protein with key roles in host defence, cancer, senescence and inflammation1–3. Downstream of STING, type I interferon, inflammatory cytokine signalling and non-canonical autophagy are governed by a multilayered mechanism integrating ligand-induced structural transitions, protein–protein interactions and coordinated intracellular trafficking4–13. Despite its central role in immunity and relevance as therapeutic target14, the sequence elements that govern STING (in)activation in cells remain incompletely&nbsp;understood. Here we developed a massively parallel assay to systematically chart the sequence-function landscape of STING. Profiling thousands of single amino-acid variants, we identified structural and functional determinants that shape the&nbsp;immunostimulatory capacity of STING and its ability to translate ligand recognition into distinct signalling outputs. Cryogenic-electron microscopy structures of select STING hyperactive variants revealed new regulatory principles dictating conformational transition from inactive to signalling-competent states of STING. Mutational effects are widespread across the functional landscape and can sensitize STING towards the natural ligand 2′3′-cGAMP15–18 or decouple interferon induction from non-canonical autophagy, demonstrating a diversity of possible responses that can be accessed through single point substitutions. Finally, our data showed the clinical and evolutionary relevance of naturally occurring STING protein variants. Collectively, these findings define molecular principles that tune STING activity and chart the landscape of its functional potential across immune contexts. A massively parallel assay systematically charts the sequence-function landscape of the STING signalling protein, and the findings define molecular principles that tune STING activity and show its functional potential across immune contexts.

08.
arXiv (CS.CV) 2026-06-11

SCAIL-2: Unifying Controlled Character Animation with End-to-end In-Context Conditioning

Controlled character animation requires transferring motion from a driving sequence to a reference character. Prior works heavily rely on intermediate representations, including pose skeletons to represent motion or masked background to represent environment, which inevitably leads to information loss. To address this, we present SCAIL-2, a framework that bypasses those intermediates and achieves end-to-end character animation. By directly concatenating driving videos to the sequence, the model can obtain all the required visual information from the input video. To address the lack of end-to-end data, we unify sub-tasks of character animation with decoupled conditions and then curate a pipeline to synthesize MotionPair-60K, an end-to-end motion transfer dataset containing heterogeneous tasks of character animation. To achieve the unification, we utilize in-context mask conditioning and mode-specific RoPE as soft guidance beyond textual instructions and raw visual information. To address synthetic discrepancy in detailed regions, we propose Bias-Aware DPO to construct preference items to mitigate the errors. Extensive experiments demonstrate that our method substantially outperforms existing state-of-the-art approaches in various character animation tasks. A large subset of synthetic data as well as model weights will be released at our project page: https://teal024.github.io/SCAIL-2/.

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

What Makes Effective Supervision in Latent Chain-of-Thought: An Information-Theoretic Analysis

Latent Chain-of-Thought (CoT) internalizes reasoning within continuous hidden states, offering a promising alternative to verbose discrete reasoning traces. However, robust latent reasoning remains difficult because outcome supervision provides weak learning signals and leaves latent trajectories prone to semantic drift. In this work, we analyze Latent CoT from an information-theoretic perspective and identify this failure as a dual collapse: gradient attenuation along the optimization path and representational drift in the latent space. We further decompose process supervision into two complementary dimensions: Trajectory Supervision, which injects dense stepwise reasoning signals, and Space Supervision, which preserves the semantic structure of the latent manifold. Our analysis shows that rigid geometric compression can collapse the reasoning space, whereas generative reconstruction provides a more flexible semantic anchor that better preserves information capacity. To measure these effects, we introduce the Unified Latent Probe (ULP), which quantifies the mutual information between latent trajectories and explicit reasoning steps. Experiments reveal a clear Information-Performance Binding: reasoning accuracy depends on the information fidelity preserved in the latent chain. These findings provide a principled framework for latent reasoning supervision and suggest shifting from geometric imitation toward mutual information maximization. Our code is available at \href{https://github.com/EIT-NLP/Supervision-in-Latent-CoT}{this repository}.

10.
medRxiv (Medicine) 2026-06-24

ADVISE: A Machine Learning Framework for Early Recognition of a Surrogate Marker for Ventilator-Associated Pneumonia Using Routinely Collected Critical Care Data

Background Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in critical care, affecting 20-36% of mechanically ventilated patients. Early prediction is hampered by the absence of a reliable, objective diagnostic standard. We developed ADVISE (Automated Dudley Ventilation Infection Series Evaluation), a machine learning model to predict physiological deterioration consistent with developing VAP using routinely collected electronic health record data from a UK NHS intensive care unit. Methods Retrospective observational study of admissions at Russell's Hall Hospital ICU (2008-2026). Following National Data Opt-Out exclusion (158 admissions, 4.2%), 3,566 admissions generated 33,208 candidate 48-hour observation blocks. Six temporal variables - FiO2, ventilator mode, P:F ratio, procalcitonin (PCT), secretion amount, and secretion description - were extracted across the baseline window (hours 1-24). A composite VAP-surrogate outcome required concurrent P:F ratio decline (>=5%) and PCT rise (>=0.5 ng/mL) across the outcome window (hours 25-48). After sequential quality filters, 2,134 blocks (18 positive, 0.84% prevalence) were retained. An XGBoost classifier was trained using nested 5-fold cross-validation with scale_pos_weight=114.0 and ROC-based hyperparameter optimisation on 1,495 training blocks, evaluated on 639 held-out test blocks. Performance was assessed via AUROC, AUPRC, and calibration (Brier score). Bootstrap resampling (1,000 iterations) generated 95% confidence intervals. Results On the held-out test set (n=639, 5 positive outcomes), ADVISE achieved AUROC 0.874 [95% CI: 0.771-0.939] and AUPRC 0.031 [0.008-0.069], representing a 4.0-fold improvement over the no-skill baseline. Nested cross-validation mean AUROC was 0.844 +/- 0.078 (range 0.716-0.915). At the Youden-optimal threshold, sensitivity was 0% with specificity 97.8%, reflecting extreme class imbalance (0.78% test prevalence). A threshold targeting 80% sensitivity achieved sensitivity 80.0% [33.3-100.0%], specificity 87.4% [84.8-89.9%], positive predictive value 4.8% [1.1-9.9%], and negative predictive value 99.8% [99.4-100.0%], detecting 4 of 5 VAP cases with approximately 80 false alarms (12.6% false positive rate). Brier score was 0.0078. Feature importance identified baseline P:F ratio as the dominant predictor (41.3% total gain), followed by ventilator mode (26.1%), secretion amount (13.2%), secretion description (9.1%), procalcitonin (5.9%), and FiO2; (4.5%). Conclusions ADVISE demonstrates that baseline oxygenation trajectory and ventilatory support patterns - derived exclusively from routinely charted ICCA variables - can identify admissions at risk of VAP-related physiological deterioration with meaningful discrimination (AUROC 0.874) despite severe class imbalance. The 80% sensitivity operating point offers a clinically actionable alert rate (12.6% FPR), supporting integration into existing ICU workflows. This proof-of-concept study establishes feasibility; multi-site prospective validation is required before clinical deployment.

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

Enhancing Underwater Light Field Images via Global Geometry-aware Diffusion Process

This work studies the challenging problem of acquiring high-quality underwater images via 4-D light field (LF) imaging. To this end, we propose GeoDiff-LF, a novel diffusion-based framework built upon SD-Turbo to enhance underwater 4-D LF imaging by leveraging its spatial-angular structure. GeoDiff-LF consists of three key adaptations: (1) a modified U-Net architecture with convolutional and attention adapters to model geometric cues, (2) a geometry-guided loss function using tensor decomposition and progressive weighting to regularize global structure, and (3) an optimized sampling strategy with noise prediction to improve efficiency. By integrating diffusion priors and LF geometry, GeoDiff-LF effectively mitigates color distortion in underwater scenes. Extensive experiments demonstrate that our framework outperforms existing methods across both visual fidelity and quantitative performance, advancing the state-of-the-art in enhancing underwater imaging. The code will be publicly available at https://github.com/linlos1234/GeoDiff-LF.

12.
arXiv (math.PR) 2026-06-11

Exact Fourier dimensions of dyadic Mandelbrot cascades on curves of nonvanishing curvature under minimal integrability

arXiv:2606.11758v1 Announce Type: new Abstract: We prove an exact Fourier-dimension formula for scalar dyadic Mandelbrot cascades pushed forward to fixed C^2 Jordan curves with nonvanishing curvature. Let W be in the minimal Kahane-Peyriere regime, let the scalar dyadic cascade live on T = R/Z, and let gamma map T to R^2 be a fixed C^2 Jordan curve with nonvanishing curvature, parametrized at constant speed. For the push-forward measure mu_gamma, we prove that, almost surely on non-extinction, its Fourier dimension is A_loc(W), the usual local exponent obtained by optimizing over q>1 from the moment expression involving E[W^q]. The upper bound follows from the scalar circle local-dimension theorem, bi-Lipschitz transfer to the fixed curve, and a deterministic curved-support obstruction for Fourier dimension. The lower bound follows from a fixed-curve finite-r annular theorem, which gives summable annular Fourier decay under a single finite moment witness. The main analytic input is a deterministic phase-geometry package for fixed nondegenerate C^2 curves: stationary tubes, derivative bands, and phase-bin coefficient estimates replacing the explicit trigonometric structure available on the unit circle.

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

Understanding Latent Diffusability via Fisher Geometry

arXiv:2604.02751v2 Announce Type: replace Abstract: Diffusion models often degrade in latent spaces, yet the formal causes remain poorly understood. We quantify latent-space diffusability via the rate of change of the Minimum Mean Squared Error (MMSE) along the diffusion trajectory. Our framework decomposes this MMSE rate into contributions from Fisher Information (FI) and Fisher Information Rate (FIR). We demonstrate that while global isometry ensures FI alignment, FIR is governed by the interplay between encoder and data geometries. Our analysis decouples diffusion degradation into four penalties: dimensional compression, tangential distortion, high-frequency encoder curvature, and intrinsic data curvature. We derive theoretical conditions for FIR preservation to ensure stable diffusability. Experiments across diverse autoencoding architectures demonstrate the implications of our theoretical bounds. We establish FI and FIR as a comprehensive analytical framework for understanding latent diffusability.

14.
arXiv (quant-ph) 2026-06-24

Initial-state-dependent dephasing effect in non-Hermitian Su-Schrieffer-Heeger models

arXiv:2606.24185v1 Announce Type: new Abstract: Understanding the dynamical evolution of non-Hermitian systems under extra external dissipation is essential. Dephasing, a major realistic dissipation, is conventionally considered detrimental to information processing. However, its impact on non-Hermitian systems remains largely unexplored. Here, we focus on finite-sized non-Hermitian Su-Schrieffer-Heeger (SSH) lattice models with alternating gain and loss in real space and examine the dynamical evolution of the trace distance under pure dephasing. By tuning system parameters, this model supports phases with either parity-time or anti-parity-time symmetries, enabling us to explore the interplay between dephasing and different non-Hermitian symmetries. While the trace distance exhibits distinct dynamical behaviors across the different phases in the absence of dephasing, its response to dephasing is largely symmetry-independent but instead initial-state dependent. By varying initial states, we observe that increasing the dephasing strength can either merely accelerate the decay of the trace distance or stabilize it. Interestingly, we reveal two kinds of dephasing-induced stabilization that differ in the strong dephasing limit: a partial stabilization, where the trace distance approaches a finite value smaller than its initial value in the long-time limit, and a complete stabilization, where the trace distance remains at its initial value throughout the entire evolution. By analyzing the equation of motion, we attribute the initial-state dependent dephasing effect to the alternating gain and loss in the system and confirm its absence in Hermitian counterparts. Furthermore, in the anti-parity-time symmetry unbroken phase, we identify a continuous suppression-upon increasing the dephasing strength-of the otherwise exponential decay of the trace distance seen in the absence of dephasing.

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

Can LLM Coding Agents Reason About Time Series?

Large language models (LLMs) are increasingly being used for automated decision-making systems in finance, healthcare, or environmental monitoring. Time series data are ubiquitous in these fields, yet hard to process automatically. Can time series be analyzed by LLM agents? We examine three approaches: providing the agent with raw numerical data, using the LLM as a coding agent, or a combination of both. In the coding agent setup, the model iteratively queries the data using Python code. Using two time series understanding benchmarks, we show that agents with code access can outperform models processing raw data by up to 10%. However, even the best performing agent still answers about 22-34% of the questions incorrectly. To get insights into models' strategies and reasoning gaps, we analyze the model outputs with a strong LLM judge. Our analysis reveals that coding agents can select appropriate statistical tests, but often miss important nuances. Meanwhile, models with access to raw data can reach the right conclusions using back-of-the-envelope calculations.

16.
arXiv (CS.CL) 2026-06-25

RAS: Measuring LLM Safety Through Refusal Alignment

Safety evaluation of large language models (LLMs) is commonly performed by querying models with unsafe or jailbreak prompts and judging whether their outputs violate a safety policy. Although useful, output-level evaluation is expensive, sensitive to judge choice, and easily tied to fixed question banks. We propose **SafeVec**, a white-box evaluation procedure that measures safety from internal representations rather than generated answers. **SafeVec** first extracts layer-wise refusal directions from a safety-aligned reference model, then selects stable layer windows where safe and unsafe behaviors are separable, and finally scores a target model by measuring whether its hidden states align with these refusal directions under unsafe and jailbreak prompts. The resulting metric, **RAS** (**R**efusal **A**lignment **S**core), maps representation-level refusal alignment to a calibrated 0-100 safety score. Across `Llama`, `Gemma`, and `Qwen` model families, RAS separates aligned models from uncensored and abliterated variants, tracks output-level attack success rate, and is substantially faster than judge-based evaluation. These results suggest that refusal alignment provides a compact and efficient signal for white-box LLM safety evaluation.

17.
arXiv (quant-ph) 2026-06-19

Spatial Localization of Relativistic Quantum Systems: The Commutativity Requirement and the Locality Principle. Part II: A Model from Local QFT

arXiv:2604.04173v3 Announce Type: replace-cross Abstract: This paper is the second and final part of a two-part study. We construct positive-energy relativistic spatial localization observables in Minkowski spacetime within standard quantum field theory, using the stress–energy–momentum tensor smeared with suitable test functions. For each fixed timelike direction, the construction gives positive operator-valued measures (POVMs) on spacelike hypersurfaces, well defined on every $n$-particle sector and satisfying a relativistic causality condition excluding superluminal propagation of detection probabilities. The observables are built from local or quasi-local field-theoretic quantities, thus providing a rigorous version of earlier heuristic proposals. In the one-particle sector, the construction reduces to the observable previously introduced by the author, and its first moment gives the Newton–Wigner position operator under appropriate normalization and centering assumptions. Because the Reeh–Schlieder theorem prevents the normally ordered stress–energy–momentum tensor from being positive on the full Fock space, we use quantum energy inequalities to obtain lower bounds controlling deviations from positivity. This leads to regularized operator families, bounded from below, which approximate the localization effects. Finally, we define conditional localization observables for finite laboratories through modified local energy operators. By Haag duality, the corresponding conditional POVMs belong to local von Neumann algebras and commute for causally separated regions, in accordance with the Araki–Haag–Kastler framework. The results show how commutativity of localization observables is recovered for conditional measurements in finite spacetime regions.

18.
arXiv (CS.AI) 2026-06-12

APCyc: Property-Informed Design of Cyclic Peptides via Automated Cyclization

arXiv:2606.12991v1 Announce Type: new Abstract: Cyclic peptides represent a promising class of therapeutic compounds in modern drug discovery, often offering improved stability and binding affinity. However, the de novo design of cyclic peptides remains challenging because methods must identify pocket-adaptive cyclization patterns and linkage sites while simultaneously controlling drug-relevant properties. This challenge is particularly pronounced for recent generative models trained predominantly on linear peptide data, which may fail to capture cyclization-specific constraints. To address the limitation, we introduce APCyc, a target-aware de novo cyclic peptide generation framework that explicitly models cyclization and jointly optimizes multiple essential physicochemical properties. By using an expanded residue vocabulary and explicitly encoding cyclization-site and linkage-type information, APCyc learns cyclization-aware representations and leverages Bayesian posterior guidance to steer sampling toward cyclic peptides satisfying multiple property objectives. Experimental results demonstrate that our model learns target-dependent cyclization preferences, and enables effective and controllable multi-property optimization for cyclic peptide design. The source code of this paper is available at https://github.com/HKUSTGZ-ML4Health-Lab/APCyc.

19.
arXiv (CS.AI) 2026-06-25

BrainAgent: A Large Language Model-Driven Multi-Agent Framework for Autonomous Brain Signal Understanding

arXiv:2606.25400v1 Announce Type: new Abstract: Brain-Computer Interfaces (BCIs) and brain signal understanding are pivotal for clinical health and next-generation interactions. Despite this significance, its widespread adoption in real-world scenarios remains restricted, primarily because current analytical paradigms lack sufficient agentic intelligence. First, existing methodologies impose prohibitive technical barriers, requiring extensive specialized expertise. Second, they remain inherently static and task-specific, failing to execute the complex, long-horizon workflows essential for real-world deployment. To accelerate the democratization of brain signal understanding, we draw inspiration from Large Language Models (LLMs) to introduce BrainAgent, an LLM-driven multi-agent framework designed to ground abstract natural language intent into rigorous, executable, and end-to-end processing pipelines. BrainAgent employs a hierarchical architecture where a central supervisor orchestrates specialized sub-agents for adaptive task decomposition and execution. Furthermore, we establish a comprehensive, systematic benchmark for evaluating agentic systems in brain signal analysis. Empirical results demonstrate that BrainAgent effectively automates complex workflows with superior reliability, marking a paradigm shift toward democratized brain signal understanding.

20.
arXiv (CS.CV) 2026-06-24

EERLoss: A Novel Loss Function for Training Deep Biometric Models. A Case Study in Keystroke Dynamics

Deep learning approaches to biometric verification are commonly trained by optimizing indirect objectives, creating a misalignment between the optimization process and the primary evaluation metric, typically the Equal Error Rate (EER). This paper introduces EERLoss: a subdifferentiable, arbitrarily accurate approximation to EER for training deep biometric models. Furthermore, this framework has the potential to be adapted to optimize any specific operating point on the DET curve, enhancing its generalizability. To validate this approach, EERLoss is evaluated on a particularly demanding behavioral biometric modality: keystroke dynamics verification. This task is characterized by its high intra-class and low inter-class variability. Experiments are conducted on the large-scale KVC-onGoing benchmark, incorporating data from over 185,000 subjects across different scenarios. A comprehensive ablation study initially demonstrates the superiority of EERLoss in comparison to existing state-of-the-art loss functions. It also converges substantially faster compared to other losses, reducing the overall training cost. Additionally, a comparison is made between the proposed loss and the KVC-winning architecture by re-training it with EERLoss, demonstrating that the proposed approach significantly outperforms the original SoTA, achieving a relative EER reduction of up to approx. 30\%. This improvement on a challenging, large-scale benchmark validates the effectiveness of EERLoss as a task-aligned training objective specifically suited for high-variance biometric traits.

21.
arXiv (CS.LG) 2026-06-18

ThousandWorlds: A benchmark for climate emulation of potentially habitable exoplanets

arXiv:2606.18338v1 Announce Type: new Abstract: The search for life beyond Earth will depend on detecting faint signatures in the atmospheres of potentially habitable exoplanets. Interpreting those signatures requires understanding the host planet's climate: the same molecule may signal life on one planet and abiotic chemistry on another. Global climate models (GCMs) provide this understanding, but individual runs can require up to millions of core-hours and substantial domain expert time. Machine-learning emulators could remove this bottleneck, but progress has been limited by the absence of a curated, multi-model exoclimate dataset. We introduce ThousandWorlds, an ML-ready benchmark for exoclimate emulation and for the broader regime of low-data, multi-simulator, parameter-to-field regression. The dataset contains approximately 1800 simulations from five GCMs, mapping eight planet parameters to 3D atmospheric fields including temperature, humidity, winds, clouds, and radiation. Three nested subsets define progressively harder challenges: single-simulator regression, multi-simulator regression with complete observations, and multi-simulator regression with structured missingness. We propose two evaluation protocols: one for ranking methods, and one that measures performance relative to the disagreement between GCMs themselves. We evaluate seven baselines spanning simple methods, deep learning, and Gaussian processes. GP-based methods perform best, suggesting that ThousandWorlds exposes a regime where off-the-shelf deep learning does not yet succeed. Data: https://doi.org/10.57967/hf/8695. Code: https://github.com/edstevenson/ThousandWorlds.

22.
arXiv (CS.AI) 2026-06-18

RODS: Reward-Driven Online Data Synthesis for Multi-Turn Tool-Use Agents

arXiv:2606.19047v1 Announce Type: new Abstract: Multi-turn tool-use RL is bottlenecked by the rapid depletion of informative samples in static datasets. We observe that the gradient signal in GRPO concentrates on tasks with the highest rollout reward variance, a consequence of the Popoviciu upper bound. Consequently, samples near the agent's capability boundary – where successes and failures are roughly balanced – contribute disproportionately large policy gradients. As training progresses, this boundary continuously shifts, which gradually depletes the pool of informative samples in a static dataset. We propose RODS (Reward-driven Online Data Synthesis) to resolve this depletion. RODS closes the loop between RL training and data generation by repurposing the progress reward variance as a practical, zero-cost boundary detector that requires no extra inference beyond the rollouts already computed for training. It continuously identifies such boundary samples, synthesizes new multi-turn variants matching their structural complexity (e.g., API topology and dependency depth) via a skill-aligned resampling pipeline, and manages a dynamic replay buffer that co-evolves with the policy. Starting from 400 human seeds and maintaining an active training pool of ~800 samples, RODS achieves comparable performance to a 17K-sample offline pipeline while requiring roughly 20x fewer trajectories, and improves over fixed-data RL and environment augmentation in our controlled setting.

23.
arXiv (quant-ph) 2026-06-12

Quantum Otto engine powered by an anisotropic Heisenberg XYZ model under independent local magnetic fields

arXiv:2606.12877v1 Announce Type: new Abstract: We study a quantum Otto heat engine whose working substance is an anisotropic two-qubit Heisenberg XYZ model. Independent local magnetic fields are used to control each spin individually. The influence of the longitudinal coupling, anisotropy, transverse coupling, and local fields on the net work output and efficiency is systematically examined. Reducing the longitudinal coupling is found to markedly improve both the maximum work and the peak efficiency. The engine performance reaches an optimum at a particular value of the anisotropy parameter. A local work analysis clarifies how work is produced during the cycle. Because of the asymmetric local fields and the intrinsic spin-spin interaction, the two qubits play markedly different thermodynamic roles; the interaction term itself contributes crucially to the total work. We further analyze the variation of quantum entanglement, quantified by concurrence, along the cycle. The results indicate that a pronounced change in entanglement between the hot and cold isomagnetic strokes is closely correlated with the efficiency enhancement. This work offers new insight into the operating principles and control of quantum Otto heat engines.

24.
arXiv (CS.AI) 2026-06-16

Open-SWE-Traces: Advancing Dual-Mode Multilingual Distillation for Software Engineering Agents

arXiv:2606.16038v1 Announce Type: cross Abstract: The path toward autonomous software engineering is currently bottlenecked by a severe deficit of diverse, large-scale trajectory data. We address this by introducing \ourdataset, an expansive dataset of 207,489 agentic trajectories spanning nine programming languages (Python, Go, TS, JS, Rust, Java, PHP, C, C++). Sourced from 20,000 real-world PRs via OpenHands and SWE-agent harnesses, the dataset utilizes a hybrid-reasoning synthesis: Minimax-M2.5 generates trajectories with explicit "thinking" processes, while Qwen3.5-122B provides high-quality "non-thinking" traces. Filtered for permissive licenses (MIT, Apache, BSD) from SWE-rebench-V2, this data facilitates the training of models capable of long-horizon reasoning. We validate the dataset by fine-tuning the Qwen3-30B-A3B series (Thinking, Instruct, and Coder). The best performing model achieves resolve rates of 61.7% on SWE-bench Verified, 57.1% on SWE-bench Multilingual, and 36.8% on SWE-bench Pro. These results establish Open-SWE-Traces as a premier resource for distilling human-level software engineering capabilities into efficient, open-source agentic LLMs.

25.
arXiv (CS.AI) 2026-06-16

Medical Heuristic Learning: An LLM-Driven Framework for Interpretable and Auditable Clinical Decision Rules

arXiv:2606.16337v1 Announce Type: new Abstract: Predictive modeling for clinical tabular data is central to clinical decision support and therefore requires not only strong predictive performance but also transparent decision logic. Although deep learning and tree-based ensemble methods can achieve high accuracy, their black-box nature remains a major obstacle to clinical deployment. This challenge is further compounded by common characteristics of medical data, including limited sample sizes, severe class imbalance, and feature evolution arising from changes in diagnostic criteria and clinical documentation. To address these issues, we propose Medical Heuristic Learning (MHL), an instantiation of the learning-beyond-gradients paradigm for clinical tabular prediction. Instead of relying on neural network weight updates, MHL uses a large language model (LLM)-driven workflow that integrates statistical probes, medical knowledge probes, rule synthesis, and code-level iterative refinement to optimize a deterministic and executable decision system. The resulting model is expressed not as opaque parameters, but as versioned pure-Python decision rules that are explicitly interpretable, fully auditable, and clinically grounded. MHL also supports continual learning by starting from previously validated rules and iteratively revising them using updated feature information under data drift or feature evolution. Comprehensive experiments on medical datasets show that MHL achieves performance comparable to state-of-the-art methods while maintaining strong behavior in small-sample and highly imbalanced settings. The results further indicate that this explicit rule update mechanism can help alleviate catastrophic forgetting under feature evolution. Overall, these findings suggest that non-gradient-based heuristic systems offer a transparent and adaptable alternative for high-stakes clinical decision support.