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

Improving Human-Robot Teamwork in Urban Search and Rescue Through Episodic Memory of Prior Collaboration

arXiv:2606.18836v1 Announce Type: cross Abstract: Effective human-robot teamwork requires robots to adapt to partners, situations, and task dynamics from the start of an interaction. In the MATRX Urban Search and Rescue (USAR) environment, people can externalize collaboration patterns (CPs) they discover during teamwork through a chat and reflection interface. We study whether a robot can use such prior team experience to become a better teammate in future interactions. To this end, we represent historical CPs as knowledge-graph episodic memories and use graph representation learning with a node-classification objective to identify a representative and effective memory for reuse. We then initialize the robot with this memory before a new collaboration episode begins. Across 20 participants and 160 round-level observations, initializing the robot with a single automatically selected prior CP increases rescue success from 25.7% to 41.3% and reduces average task time by 283 seconds. The strongest gains appear at the beginning of interaction, suggesting that reusable episodic memory can help robots enter collaboration with more effective task knowledge and support smoother early teamwork.

02.
arXiv (CS.AI) 2026-06-17

Querying an astronomical database using large language models: the ALeRCE text-to-SQL system

arXiv:2606.18108v1 Announce Type: cross Abstract: We develop a text-to-SQL (structured query language) system based on large language models (LLMs) using in-context learning and apply it to the Automatic Learning for the Rapid Classification of Events (ALeRCE) astronomical database. ALeRCE is a community broker for the Zwicky Transient Facility and the Vera C. Rubin Observatory. The system enables users to query the database in natural language (NL) and generates executable SQL queries. To develop and evaluate the system, we constructed a dataset of 110 NL/SQL pairs. We propose a step-by-step generation framework comprising four modules: schema linking, query classification, prompt decomposition, and self-correction. The performance of thirteen LLMs is evaluated using in-context learning and prompt engineering techniques. Text-to-SQL performance is assessed using the perfect-match (PM) rate for row identifiers (e.g., object identifiers) and column identifiers (i.e., column names). The proposed step-by-step framework consistently outperforms a direct-inference baseline, while the self-correction module consistently reduces execution errors. For Claude Opus 4.6, PM performance on row (column) identifiers is high for simple queries, reaching 0.97 (0.94), and decreases with query complexity to 0.44 (0.72) for medium queries and 0.59 (0.49) for hard queries. Among the thirteen evaluated models, the best-performing LLMs for the text-to-SQL task are Claude Opus 4.6, Gemini 2.5 Pro, Gemini 3 Flash, and GPT-5.2-Codex.

03.
arXiv (quant-ph) 2026-06-16

Entanglement as a Witness of Quantum Coherence: A Bipartite Monty-Hall Protocol

arXiv:2604.25953v3 Announce Type: replace Abstract: We present a bipartite protocol inspired by the Monty Hall puzzle that operationally distinguishes quantum coherence from classical ignorance. A principal qutrit is entangled with an ancillary qutrit via a controlled unitary, preparing $|\Psi\rangle = \frac{1}{\sqrt{3}}(|A,0\rangle + |B,1\rangle + |C,2\rangle)$. A rank-1 projective discard then eliminates one basis state, leaving a coherent superposition of the two remaining states. Finally, the ancilla and qutrit are measured, yielding joint probabilities that encode the interplay between superposition and measurement back-action. We show that the conditional probability $P(B|anc=0)$ takes the value $1/4$ in both quantum mechanics and the classical ignorant-host model, making it unsuitable as a witness. The true quantum-classical separation emerges in conditional joint probabilities that correlate ancilla outcomes with specific discard operations. We define witnesses $\mathcal{W}_{i,j} = P(anc=i, qutrit=j \mid discard k)$ where $j$ differs from the ancilla-implied state. Quantum mechanics predicts $\mathcal{W} = 1/4$, while any classical epistemic model with perfect initial correlations yields $\mathcal{W} = 0$. We provide the explicit $9 \times 9$ unitary matrix, a complete analysis of all measurement outcomes, and a detailed proof of the violation. The witness is fully immune to white noise and robust against moderate dephasing. The protocol requires only a single pair of entangled qutrits and sequential measurements – no spatial separation, no multiple copies, and no complex sets of incompatible observables. This makes it suitable for advanced undergraduate laboratories and provides a pedagogically accessible test of the ontic-epistemic distinction in quantum foundations.

04.
arXiv (CS.LG) 2026-06-12

Loss-Shift Transfer via Bayes Quotients

arXiv:2606.13178v1 Announce Type: new Abstract: Transfer learning is usually studied as a consequence of distribution shift. This paper identifies an orthogonal failure mode in which the data distribution is fixed and the loss changes. This setting is called loss shift. A loss determines which information in \(X\) is Bayes-relevant, and two losses may therefore require different representations even under the same joint law \(P(X,Y)\). The idea is formalized using Bayes quotients, which allow losses to be ordered by refinement. In the Bayes-quotient formulation, strict refinement gives an immediate qualitative obstruction. A source-minimal representation for a coarser loss is insufficient for a strictly finer target loss. For finite-output log loss, this obstruction becomes an exact quantitative identity. The excess risk is the conditional information about \(Y\) discarded by the representation. Experiments in controlled, learned, synthetic-image, and real-image settings show the predicted effect, i.e., classification-equivalent representations can have different optimal log-loss performance under a fixed data distribution.

05.
arXiv (quant-ph) 2026-06-16

Optimizing Wigner Negativity in Scattering Processes Using Energetic Cost Functions

arXiv:2606.15101v1 Announce Type: new Abstract: Wigner negativities (WNs) are key signatures of non-Gaussian bosonic states and essential resources for quantum technologies. We study their generation in the scattering of coherent pulses by a two-level atom coupled to a one-dimensional reservoir, a unitary and energy-preserving platform. Optimization in this multimode setting is hindered by the complexity of evaluating Wigner functions. We overcome this challenge by introducing energetic cost functions that identify output modes most likely to host large negativities. First using incoherent energy and then isolating a genuinely non-Gaussian contribution, we demonstrate a strong correlation between these quantities and WNs. This correlation extends beyond short, intense pulses to encompass pulses of finite energy, where photons are scattered while the two-level atom is driven. Focusing on the energy-efficiency of the process, we show that maximally efficient generation takes place for one input photon, on average, spectrally mode-matched with the atom.

06.
Nature (Science) 2026-06-17

Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago

Plague is among the most devastating diseases in human history1. However, early strains of the plague-causing bacterium Yersinia pestis lacked virulence factors that are required for the bubonic form until around 3,800 years ago2,3. Consequently, the morbidity and mortality of early plague strains remain unclear. Here we describe early plague strains that are associated with two phases of outbreaks among mid-Holocene hunter-gatherers near Lake Baikal in southeast Siberia, beginning from about 5,500 years ago. These outbreaks occur across four hunter-gatherer cemeteries, with a 39% detection rate for plague infection. By reconstructing kinship pedigrees, we show that small familial groups were affected, consistent with human-to-human spread of disease, and that the first outbreak occurred within a single generation. The infections appear to have resulted in acute mortality, especially among children (aged 8 to 11 years). We further note functional differences, including in the ypm superantigen locus, which is also present in present day Yersinia pseudotuberculosis. The new strains diverge ancestrally to known Y. pestis and constrain the timing of its emergence, indicating that this happened before approximately 5,700 years ago. These findings show that plague outbreaks happened earlier than previously thought and were indeed lethal. We contend that the occurrence of outbreaks among mid-Holocene hunter-gatherer communities well outside the sphere of Late Neolithic Europe challenges the notion that higher population densities and lifestyle changes during the Neolithic agricultural transition were prerequisites for plague epidemics. Analyses of ancient DNA from hunter-gatherers near Lake Baikal in southeast Siberia around 5,500 years ago indicate that highly virulent Yersinia pestis emerged earlier than previously estimated, far from the next known cases of infection in Late Neolithic Europe.

07.
medRxiv (Medicine) 2026-06-10

Assessment of the accuracy of lung lesions diagnosis in adolescents with osteosarcoma using artificial intelligence

Background. Lung metastases in osteosarcoma (OS) are the main cause of the death. The accuracy of the diagnosis of nodules by computed tomography (CT) of the lungs is critically important for determining the disseminated stage of the disease and planning surgical treatment. The use of artificial intelligence (AI) in the search for lung nodules increases the accuracy of diagnosis and reduces the chance of missing metastases. Objective: to evaluate the accuracy of lung nodules diagnosis in adolescents with OS using AI. Methods. A retrospective assessment of CT scans of adolescents with OS was performed. A pathological nodule with an average size of [≥]4 mm was considered a target finding. The diagnostic accuracy of an AI algorithm previously trained on an adult dataset was evaluated, and the number of false positives (FP) and false negatives (FN) was determined. Sensitivity, specificity, accuracy, area under the ROC curve (AUC), positive predictive value, negative predictive value, and F1-measure were calculated. Based on the obtained results, the effectiveness of the algorithm was assessed. Results. 248 CT scans of adolescents with OS were evaluated. The following results were obtained: in 5 cases, the AI algorithm showed a FP result (2.02%), in 34 cases, it showed a FN result (13.71%), and in 209 cases, a correct result (both true positive and true negative) (84.27%). The diagnostic accuracy of the algorithm was 0.843 (95% CI 0.794-0.887). The application of the AI algorithm in the practice of an X-ray doctor in a specific clinical task would allow to increase the sensitivity from 0.805 to 0.891, while ensuring an absolute decrease in the number of FN results by 8.59% and a relative decrease by 44%. Conclusion. The obtained results confirm the practical value of the application of the AI algorithm and justify the implementation of AI-assisted systems in the diagnostic protocols for lung metastases in adolescents with OS.

08.
arXiv (CS.CV) 2026-06-24

Jolia: Concept-Level Vision-Language Alignment for 3D CT Contrastive Learning

Vision-language contrastive pretraining has become the dominant recipe for 3D medical foundation models, leveraging the large volumes of paired scans and reports produced in clinical practice. However, medical images usually span dozens of organs, and radiological reports are much longer than typical natural image captions and are composed of multiple structured sections. CLIP-style pretraining compresses this structure by encoding each modality into a single global token, at the risk of losing important details. We introduce ConQuer (Concept Queries), an image-text pretraining method that augments CLIP's global alignment with a set of localized alignments, one per concept. ConQuer splits the report into concept-specific sections and learns cross-attention queries that pool the matching image features without using any segmentation mask or spatial supervision. Contrastive learning is then applied independently for each concept. Concepts can be any unit of semantic localization; here, they are anatomical regions, one query per organ or gross body region. As a byproduct, each query learns attention maps focused on its concept, providing built-in spatial interpretability. We use ConQuer to train Jolia, a 3D CT foundation model on chest and abdominal CT. Jolia consistently outperforms a CLIP baseline on findings classification, report generation, and cross-center transfer, and sets a new state of the art across multiple public benchmarks. Jolia's weights will be released upon acceptance.

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

RepNet: Tackling spectral bias in deep neural networks via parameter reparameterization

arXiv:2606.16575v1 Announce Type: new Abstract: Deep neural networks (DNNs) have achieved remarkable success in scientific computing, yet they often suffer from spectral bias in capturing oscillatory and multiscale behaviors. In this study, we investigate this limitation by examining the failure of shallow ReLU neural networks in fitting high-frequency functions. This observation identifies two important factors in resolving rapid oscillations: the initial slope scale and the distribution of partition points induced by the networks. Motivated by this analysis, we propose RepNet, a reparameterized DNN model for ReLU and tanh networks designed for high-frequency and multiscale problems. The key idea is to reparameterize the weights and biases in the first hidden layer, which enables effective control of the initial slope scale and provides an appropriate distribution of the initial partition points. Furthermore, treating the reparameterized weights and biases as trainable parameters allows the DNN to achieve adaptive frequency scaling during training. In addition, we derive quantitative estimates for the output and slope magnitudes of the reparameterized DNN to guide the initialization of the proposed method. Numerical experiments, including multiscale one- and four-dimensional function approximation, forward and inverse PDE problems in combination with physics-informed neural networks (PINNs), and operator learning, demonstrate that RepNet improves the predicted accuracy of vanilla DNNs in capturing highly oscillatory features with slightly additional computational cost. These results indicate that RepNet provides an effective and flexible approach for overcoming spectral bias and applying DNNs to multiscale problems.

10.
Nature Biotechnology 2026-06-08

Single-cell spatial pharmacobiology for imaging antibody-based therapies in solid tumors

作者: 未知作者

We have developed single-cell spatial pharmacobiology (SSP), which combines in situ imaging of a systemically infused fluorescent therapeutic antibody with high-plex spatial proteomics. Applied to head and neck and pancreatic tumors from patients treated in phase 1 trials, SSP revealed marked spatial heterogeneity in antibody delivery and target engagement, which was shaped by conserved stromal barriers.

11.
arXiv (CS.LG) 2026-06-24

Hessian-augmented Supervised Learning for Hamilton-Jacobi-Bellman PDEs

arXiv:2606.23827v1 Announce Type: cross Abstract: A data-driven method is developed for approximating value functions in deterministic optimal control problems with nonlinear control-affine dynamics. The Pontryagin Maximum Principle optimality system is solved from multiple initial conditions to generate training data consisting of values, gradients, and Hessians of the value function, where Hessian information is obtained from a matrix Riccati equation along optimal trajectories. These quantities augment a weighted least-squares regression over sparse polynomial bases on hyperbolic cross index sets, with gradients and Hessians contributing additional linear equations per sample and substantially reducing sample complexity compared to value-only regression. Feedback laws are recovered analytically from the learned value function. In high dimensions, a partial Hessian strategy controls the cost of data generation. The approach is validated on problems of increasing state dimension, where second-order data augmentation is shown to improve approximation accuracy and closed-loop performance, with up to an order-of-magnitude reduction in the number of training samples required relative to lower-order methods.

12.
arXiv (CS.AI) 2026-06-11

GPO: Learning from Critical Steps to Improve LLM Reasoning

arXiv:2509.16456v3 Announce Type: replace Abstract: Large language models (LLMs) are increasingly used in various domains, showing impressive potential on different tasks. Recently, reasoning LLMs have been proposed to improve the reasoning or thinking capabilities of LLMs to solve complex problems. Despite the promising results of reasoning LLMs, enhancing the multi-step reasoning capabilities of LLMs still remains a significant challenge. While existing optimization methods have advanced the LLM reasoning capabilities, they often treat reasoning trajectories as a whole, without considering the underlying critical steps within the trajectory. In this paper, we introduce Guided Pivotal Optimization (GPO), a novel fine-tuning strategy that dives into the reasoning process to enable more effective improvements. GPO first identifies the `critical step' within a reasoning trajectory - a point that the model must carefully proceed to succeed at the problem. We locate the critical step by estimating the advantage function. GPO then resets the policy to the critical step, samples the new rollout and prioritizes the learning process on those rollouts. This focus allows the model to learn more effectively from pivotal moments within the reasoning process to improve the reasoning performance. We demonstrate that GPO is a general strategy that can be integrated with various optimization methods to improve reasoning performance. Besides theoretical analysis, our experiments across challenging reasoning benchmarks show that GPO can consistently and significantly enhance the performance of existing optimization methods, showcasing its effectiveness and generalizability in improving LLM reasoning by concentrating on pivotal moments within the generation process.

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

Clinically Aware Synthetic Image Generation for Concept Coverage in Chest X-ray Models

Deep learning models for chest X-ray diagnosis are constrained by limited coverage of clinically meaningful concept combinations in publicly available training datasets. While synthetic image generation has been explored to increase data diversity, existing methods rarely enforce clinical or anatomical constraints, limiting utility for improving model reliability. We propose CARPA, a clinically aware and anatomically grounded framework for synthetic chest X-ray generation that applies targeted perturbations to clinical concept vectors while preserving anatomical structure. By producing anatomically faithful synthetic images with controlled concept insertions and deletions, CARPA expands clinically relevant concept coverage. We evaluate CARPA across seven backbone architectures by fine-tuning models on synthetic subsets and testing on a held-out MIMIC-CXR benchmark. Compared to prior concept perturbation approaches, fine-tuning on CARPA-generated images consistently improves precision-recall performance, reduces predictive uncertainty, and improves model calibration. Structural and semantic analyses demonstrate high anatomical fidelity, strong concept alignment, and low semantic uncertainty. Evaluation by two expert radiologists further confirms realism and clinical agreement. Together, these results show that anatomically grounded concept perturbations enable more effective use of synthetic data, improving both performance and reliability of chest X-ray classification models and supporting safer clinical deployment.

14.
arXiv (CS.CV) 2026-06-17

DVD: Discrete Voxel Diffusion for 3D Generation and Editing

We introduce Discrete Voxel Diffusion (DVD), a discrete diffusion framework to generate, assess, and edit sparse voxels for SLat (Structured LATent) based 3D generative pipelines. Although discrete diffusion has not generally displaced continuous diffusion in image-like generation, we show that it can be an effective first-stage prior for sparse voxel scaffolds. By treating voxel occupancy as a native discrete variable, DVD avoids continuous-to-discrete thresholding and provides a simple framework for voxel generation, uncertainty estimation, and editing. Beyond quality gains, DVD provides more interpretable generation dynamics through explicit categorical modeling. Furthermore, we leverage the predictive entropy as a robust uncertainty metric to identify ambiguous voxel regions and complicated samples, facilitating tasks such as data filtering and quality assessment. Finally, we propose a lightweight fine-tuning strategy using block-structured perturbation patterns. This approach empowers the model to inpaint and edit voxels within a single sampling round, requiring negligible auxiliary computation and no additional model evaluations. Code is available at https://github.com/TeCai/DVD.

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

Emergent Strategic Reasoning Risks in AI: A Taxonomy-Driven Evaluation Framework

arXiv:2604.22119v2 Announce Type: replace Abstract: As reasoning capacity and deployment scope grow in tandem, large language models (LLMs) gain the capacity to engage in behaviors that serve their own objectives, a class of risks we term Emergent Strategic Reasoning Risks (ESRRs). These include, but are not limited to, deception (intentionally misleading users or evaluators), evaluation gaming (strategically manipulating performance during safety testing), and reward hacking (exploiting misspecified objectives). Systematically understanding and benchmarking these risks remains an open challenge. To address this gap, we introduce ESRRSim, a taxonomy-driven agentic framework for automated behavioral risk evaluation. We construct an extensible risk taxonomy of 7 categories, which is decomposed into 20 subcategories. ESRRSim generates evaluation scenarios designed to elicit faithful reasoning, paired with dual rubrics assessing both model responses and reasoning traces, in a judge-agnostic and scalable architecture. Evaluation across 11 reasoning LLMs reveals substantial variation in risk profiles (detection rates ranging 14.45%-72.72%), with dramatic generational improvements suggesting models may increasingly recognize and adapt to evaluation contexts.

17.
Nature (Science) 2026-06-17

Probing picometre-scale interlayer deformations via hyperbolic polaritons

作者:

The resilience of van der Waals (vdW) materials to large strain fields makes them an ideal platform for tuning electronic, optical and magnetic properties1–4. Although in-plane strain is readily mapped, non-invasive and quantitative characterization of out-of-plane strain remains a formidable challenge, particularly for picometre-scale deformations buried at interfaces. Here we demonstrate a polaritonic optical method that uses the mid-infrared out-of-plane hyperbolic polaritons (oHPs) mode to detect interlayer deformations in prototypical vdW polar insulator–hexagonal boron nitride (hBN). This method uses the softening mechanism of out-of-plane transverse optical (oTO) phonons induced by interlayer strain, enabling highly sensitive detection of picometre-scale deformations. Although these oTO phonon modes are typically spectroscopically ‘dark’, their strain response is activated through the oHPs, achieving an atomic displacement sensitivity of about 10 pm (about 8 × 10−7 times the probing wavelength), enabling ultradeep-subwavelength mechanical interlayer deformation detection. This is experimentally validated in both planar hBN and at the buried interface of quantum dot–hBN nanotube heterostructures. This polariton-based picometrology bridges nanomechanics and photonics, providing a non-destructive lens to visualize hidden stress landscapes with atomic precision. A new polaritonic optical method that uses the mid-infrared out-of-plane hyperbolic polaritons mode is described and experimentally validated to allow the examination of picometre-scale interlayer deformations, providing a bridge between nanomechanics and photonics.

18.
arXiv (CS.CV) 2026-06-24

Quantifying mandibular positioning error and simulated temporomandibular joint-space changes in patient-specific occlusal splints

Patient-specific occlusal positioning splints can be regarded as physical realisations of planned mandibular transformations. However, the achieved mandibular pose may differ from the planned one because of acquisition, registration, fabrication, and positioning errors. This study presents a transformation-based biomedical engineering framework for quantifying mandibular positioning accuracy and propagating the resulting error to a simulated temporomandibular joint configuration. Multimodal 3D data, including CBCT, facial motion acquisition, and dental scans, were integrated in a common coordinate system. Positioning splints corresponding to selected mandibular poses were designed and fabricated, and their realised positions were evaluated using repeated scans of plaster models. Discrepancies between planned and achieved positions were represented as rigid-body error transformations and analysed in SE(3), together with surface-distance metrics. The estimated transformations were propagated to CBCT-derived TMJ structures to quantify changes in condyle-fossa distance maps. The results demonstrate a systematic translational component and anisotropic variability of mandibular positioning error, with measurable propagation to simulated TMJ-space changes. The proposed framework provides an objective method for documenting planned and achieved mandibular configurations and for analysing positioning uncertainty in patient-specific splint workflows.

19.
arXiv (math.PR) 2026-06-16

Hua-Chen New Theory of Economic Optimization

arXiv:2504.19134v4 Announce Type: replace-cross Abstract: Between 1957-1985, Chinese mathematician Loo-Keng Hua pioneered economic optimization theory through three key contributions: establishing economic stability's fundamental theorem, proving the uniqueness of equilibrium solutions in economic systems, and developing a consumption-integrated model 50 days before his death. Since 1988, Mu-Fa Chen has been working on Hua's theory. He introduced stochastics, namely Markov chains, to economic optimization theory. He updated and developed Hua's model and came up with a new model (Chen's model) which has become the starting point of a new economic optimization theory. Chen's theory can be applied to economic stability test, bankruptcy prediction, product ranking and classification, economic prediction and adjustment, economic structure optimization. Chen's theory can also provide efficient algorithms that are programmable and intelligent. {Stochastics} is the cornerstone of Chen's theory. There is no overlap between Chen's theory, and the existing mathematical economy theory and the economics developments that were awarded Nobel Prizes in Economics between 1969 and 2024. The distinguished features of Chen's theory from the existing theories are quantitative, calculable, predictable, optimizable, programmable and can be intelligent. This survey provides a theoretical overview of the newly published monograph [5rw24]. Specifically, the invariant of the economic structure matrix, also known as the Chen's invariant, was first published in this survey.

20.
arXiv (CS.CL) 2026-06-12

CreativeBench: Benchmarking and Enhancing Machine Creativity via Self-Evolving Challenges

The saturation of high-quality pre-training data has shifted research focus toward evolutionary systems capable of continuously generating novel artifacts, leading to the success of AlphaEvolve. However, the progress of such systems is hindered by the lack of rigorous, quantitative evaluation. To tackle this challenge, we introduce CreativeBench, a benchmark for evaluating machine creativity in code generation, grounded in a classical cognitive framework. Comprising two subsets – CreativeBench-Combo and CreativeBench-Explore – the benchmark targets combinatorial and exploratory creativity through an automated pipeline utilizing reverse engineering and self-play. By leveraging executable code, CreativeBench objectively distinguishes creativity from hallucination via a unified metric defined as the product of quality and novelty. Our analysis of state-of-the-art models reveals distinct behaviors: (1) scaling significantly improves combinatorial creativity but yields diminishing returns for exploration; (2) larger models exhibit ``convergence-by-scaling,'' becoming more correct but less divergent; and (3) reasoning capabilities primarily benefit constrained exploration rather than combination. Finally, we propose EvoRePE, a plug-and-play inference-time steering strategy that internalizes evolutionary search patterns to consistently enhance machine creativity.

21.
arXiv (CS.AI) 2026-06-15

A Fixed-Point Neural Operator for Size- and Functional-Transferable Hamiltonian Prediction

arXiv:2606.14498v1 Announce Type: cross Abstract: Predicting the Kohn-Sham Hamiltonian with machine learning can accelerate density functional theory while retaining access to molecular orbitals, energy levels, and electronic-structure observables that energy-only surrogates cannot resolve. Yet element-wise agreement with the converged Hamiltonian, an implicit fixed point of the self-consistent field iteration, does not determine the occupied subspace that governs orbital energies and densities. Here we present HamEvo, a neural operator that learns the single-step self-consistent update and returns the converged Hamiltonian as its fixed point. HamEvo is pre-trained on intermediate self-consistent trajectories and calibrated at equilibrium with density-matrix supervision. Across benchmarks from MD17 to drug-like QMugs, HamEvo lowers Hamiltonian errors by 35-49% over direct-regression and deep-equilibrium baselines, and predicts QMugs HOMO and LUMO energies with mean absolute errors of 0.036 and 0.053 eV, near the 1 kcal/mol chemical-accuracy scale. Few-shot fine-tuning with only 20 reference conformations extends HamEvo to molecules of up to 122 atoms, well beyond the size range covered by pre-training. With thermal molecular-dynamics sampling, HamEvo captures temperature-dependent HOMO-LUMO gap renormalization beyond the harmonic approximation. Inference is up to 242 times faster than conventional DFT.

22.
bioRxiv (Bioinfo) 2026-06-23

biomeStat: Using Agentic AI for Scalable Genomic Epidemiology Demonstrated Through End-to-End Analysis of 1,000 Asian Dengue Virus Genomes

Genomic epidemiology workflows typically require expert curation of multiple specialized tools, extensive manual parameter tuning, and access to heterogeneous compute infrastructure. While standard generative AI models often hallucinate in complex biological domains, we introduce biomeStat: an autonomous AI agent that functions as a strict deterministic orchestrator. By automatically writing code to execute established bioinformatics tools in sandboxed environments, biomeStat dynamically provisions compute resources (CPU and GPU) and guarantees reproducibility, making it immediately useful for scientists without requiring command-line expertise. To demonstrate the platform, we performed a fully autonomous genomic epidemiology and structural analysis of 1,000 Dengue virus (DENV) genomes sampled from 16 Asian countries between 2000 and 2025. The agent seamlessly orchestrated phylogenetic reconstruction (IQ-TREE, TreeTime), Bayesian phylodynamics (BEAST2 via NVIDIA H200 GPU), selection pressure analysis (HyPhy), and structural mapping (PyMOL). The analysis was completed in under 24 hours of wall-clock time, revealing endemic stability (R_e ~1.0) and identifying 1,869 candidate immune escape sites structurally colocalized with B-cell and T-cell epitopes. Furthermore, the agent validated 176 highly conserved drug target residues across the viral replication complex, confirming that resistance-associated positions for emerging antivirals JNJ-1802 and NITD-688 remain absolutely conserved across all four serotypes. By bridging the gap between natural language intent and deterministic computational execution, biomeStat reduces weeks of expert effort into a single-session analysis with full methodological transparency.

23.
arXiv (CS.LG) 2026-06-12

Optical Implementation of Equilibrium Propagation Using Spatial Photonic Ising Machines

arXiv:2606.13454v1 Announce Type: cross Abstract: Equilibrium Propagation offers a compelling alternative to traditional machine learning for training energy-based networks. Here we demonstrate a hybrid optical-digital implementation of EP using a Spatial Photonic Ising Machine (SPIM). The SPIM exploits the gauge transformation method to optically encode both continuous neuron states and rank-1 binary trainable patterns as phase modulations via a spatial light modulator, with inference realized using a finite difference scheme. The experimental system is evaluated on the Wine classification dataset. The potential of this approach, including the use of continuous couplings and structured coupling matrices, is evaluated numerically on the more complex MNIST dataset. Our work provides a concrete pathway toward energy-efficient physical implementations of Equilibrium Propagation.

24.
arXiv (CS.AI) 2026-06-11

Characterizing Software Aging in GPU-Based LLM Serving Systems

arXiv:2606.11916v1 Announce Type: cross Abstract: This paper proposes an empirical methodology to study software aging in GPU-based LLM serving systems. Traditional aging studies focus on CPU-centric software with relatively regular workloads; LLM serving is different, spanning a Python host and a CUDA device, handling requests whose cost varies by orders of magnitude, and relying on rapidly evolving software stacks. We run a 216-hour campaign across six co-located deployments under identical stress conditions, monitor host, device, and client metrics in parallel, and apply a statistical pipeline that accounts for autocorrelation and multiple testing. Our results reveal statistically significant memory aging in all deployments, with leak rates strongly dependent on the serving runtime and deployment configuration. Beyond these findings, we provide a reproducible framework that opens a research direction at the intersection of the software aging and rejuvenation and LLM serving communities.

25.
arXiv (CS.CV) 2026-06-12

EyeTheia: A Lightweight and Accessible Eye-Tracking Toolbox

We introduce EyeTheia, a lightweight and open deep learning pipeline for webcam-based gaze estimation, designed for browser-based experimental platforms and real-world cognitive and clinical research. EyeTheia enables real-time gaze tracking using only a standard laptop webcam, combining MediaPipe-based landmark extraction with a convolutional neural network inspired by iTracker and optional user-specific fine-tuning. We investigate two complementary strategies: adapting a model pretrained on mobile data and training the same architecture from scratch on a desktop-oriented dataset. Validation results on MPIIFaceGaze show comparable performance between both approaches prior to calibration, while lightweight user-specific fine-tuning consistently reduces gaze prediction error. We further evaluate EyeTheia in a realistic Dot-Probe task and compare it to the commercial webcam-based tracker SeeSo SDK. Results indicate strong agreement in left-right gaze allocation during stimulus presentation, despite higher temporal variability. Overall, EyeTheia provides a transparent and extensible solution for low-cost gaze tracking, suitable for scalable and reproducible experimental and clinical studies. The code, trained models, and experimental materials are publicly available.