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01.
arXiv (CS.LG) 2026-06-17

Recursive Scaling in Masked Diffusion Models

arXiv:2606.18022v1 Announce Type: new Abstract: Masked diffusion models (MDMs) have recently emerged as a promising paradigm for sequence generation. Scaling MDMs is conventionally achieved by increasing the parameter count or the number of denoising steps. We introduce Recursive Masked Diffusion Models (R-MDMs), which add recursive depth as a third scaling axis by repeatedly applying the same denoising transformer within each diffusion step. Recursion enables iterative refinement of the output through parameter reuse, increasing effective model depth without increasing parameter count. Across structured generation tasks, including Sudoku and Countdown, we show that R-MDMs achieve substantially improved parameter efficiency: a model with $L$ recursive iterations often matches the performance of non-recursive baselines with roughly $L\times$ more parameters. Moreover, recursive refinement can partially substitute for additional denoising steps, allowing recursive models to reach the same generation quality with fewer forward passes at inference time. These results suggest that recursive depth is a practically useful scaling mechanism for MDMs, improving both parameter efficiency and the allocation of test-time compute.

02.
arXiv (CS.LG) 2026-06-19

CAGE: Curvature-Aware Gradient Estimation For Accurate Quantization-Aware Training

arXiv:2510.18784v3 Announce Type: replace Abstract: Despite significant work on low-bit quantization-aware training (QAT), there is still an accuracy gap between such techniques and native training. To address this, we introduce CAGE (Curvature-Aware Gradient Estimation), a new QAT method that augments the straight-through estimator (STE) gradient with a curvature-aware correction designed to counteract the loss increase induced by quantization. CAGE is derived from a multi-objective view of QAT that balances loss minimization with the quantization constraints, yielding a principled correction term that depends on local curvature information. On the theoretical side, we introduce the notion of Pareto-optimal solutions for quantized optimization, and establish that CAGE yields strong convergence guarantees in the smooth non-convex setting. In terms of implementation, our approach is optimizer-agnostic, but we provide a highly-efficient implementation that leverages Adam statistics. CAGE significantly improves upon the prior state-of-the-art methods in terms of accuracy, for similar computational cost: for QAT fine-tuning, it halves the compression accuracy loss relative to the prior best method, while for QAT pre-training of Llama models, its accuracy for 3-bit weights-and-activations (W3A3) matches the accuracy achieved at 4-bits (W4A4) with the prior best method. The official implementation can be found over https://github.com/IST-DASLab/CAGE .

03.
arXiv (CS.LG) 2026-06-15

Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction

arXiv:2606.14217v1 Announce Type: new Abstract: Accurate prediction of protein-ligand binding affinity is essential for structure-based drug discovery. Recent geometric deep learning methods have achieved promising performance by representing protein-ligand complexes as three-dimensional graphs. However, most existing approaches mainly rely on static interaction geometry from a single bound conformation, while neglecting molecular flexibility and binding-induced conformational changes. To address this limitation, we propose a curvature-informed potential energy surface (CPES) graph neural network for protein-ligand binding affinity prediction, which incorporates physics-informed curvature representations to model conformational flexibility. CPES first derives curvature spectral descriptors from the Hessian of the potential energy surface evaluated at equilibrium configurations, whose eigenvalues define the local principal curvatures of the potential energy surface. It then uses spectral cross-attention to compare the unbound ligand and protein with the bound complex, thereby capturing binding-induced changes in conformational dynamics. In parallel, hierarchical protein-ligand interaction representations are learned from static structural features through geometry-aware message passing, soft clustering, and bidirectional cross-attention. Finally, CPES fuses the curvature-informed dynamic representations with static interaction representations for affinity regression. Extensive evaluations on multiple benchmark datasets demonstrate that CPES achieves improved predictive performance and offers physical interpretability.

04.
arXiv (CS.CV) 2026-06-17

Bounding Box Label Propagation for Re-Annotation of Document Layout Analysis Datasets

Datasets in practical document processing scenarios typically grow over time, and their class annotations undergo continuous refinement. This creates significant re-annotation efforts, which are time-consuming and costly. A promising remedy is to re-annotate only a small subset of available documents manually and apply semi-supervised learning techniques that leverage both labelled and unlabelled data. Although there are numerous approaches to tackle this problem for classification, there exists no adaptation for the problem of re-classifying object detection instances, e.g. for document layout analysis. To this end, we propose Bounding Box Label Propagation (BBLP), a pseudo-labelling framework for object detection. An object encoder integrates visual, textual, and positional embeddings from object detection samples to come up with a joint embedding that can be used for Label Propagation on partially annotated datasets in a plug-and-play fashion. Evaluation results indicate that the proposed approach produces high-quality class annotations of bounding boxes. In the D4LA layout analysis dataset, it achieves a mAP of 54.0%, corresponding to 81.6% of fully supervised performance, while using only 10% labelled data. Our work demonstrates the potential of Label Propagation for object detection and lays the groundwork for reducing manual annotation efforts in real-world document processing applications.

05.
arXiv (CS.LG) 2026-06-16

Drivers, Receivers, and Dynamic Linkages: The Directed Structure of SDG Interdependence, 2000–2024

arXiv:2601.20875v2 Announce Type: replace-cross Abstract: Governments with limited fiscal and administrative capacity need to know which Sustainable Development Goals (SDGs) propagate progress through the goal system and how quickly. We map the directed interdependence structure of all seventeen goals using a balanced panel of 114 countries observed annually from 2000 to 2024. The goal series are persistent, trending, and cross-sectionally dependent, so we apply two estimators matched to this regime: a Dumitrescu-Hurlin panel Granger non-causality test, run on first-differenced series, to recover the directed interaction network, and panel local projections with Driscoll-Kraay standard errors to measure the dynamic magnitude of 31 theory-derived indicator linkages. Of 272 directed goal pairs, 84 linkages survive false-discovery control (40 synergies, 44 trade-offs; network density 0.31). Synergies and trade-offs occur at comparable strength, so no single goal behaves as a universal accelerator, and the goal-level hierarchy itself is fragile. Driver-receiver rankings correlate weakly across lag orders and centrality metrics, and under a country bootstrap only two roles are distinguishable from zero: peace and strong institutions as the clearest net receiver, and poverty reduction as the most probable effect-size-weighted driver. The supported linkages are dynamic, accruing over four to five years: sanitation and poverty improvements are the strongest predictors of lower child mortality, and the education-child-health association is corroborated in independent World Development Indicators data across 183 countries. These results caution against rankings-based accelerator policy and support adaptive portfolios built on supported, time-lagged linkages monitored through constituent indicators.

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

Learning from almost nothing: How neural networks survive heavy input corruption

arXiv:2606.11319v1 Announce Type: new Abstract: Learning from imperfect data is a central theme in machine learning, connecting practical questions of robustness to fundamental questions of learnability. Here we examine attribute noise: learning from corrupted inputs while keeping the labels intact, a setting that has received considerably less analytical attention than its label-noise counterpart. We consider two types of corruption models: additive noise and replacement noise. Through experiments with multi-layer perceptrons (MLPs) on corrupted classification datasets, we find that neural networks remain robust, maintaining well-above-chance accuracy even when inputs are >90% corrupted – far beyond human recognition. To understand this robustness, we analyze infinite-width networks in the heavy-corruption regime using a mean-field-inspired approach and derive a leading-order decision rule for the classification outcome: the network implements a prototype rule, the nearest-class-mean, assigning each test point to the class whose training-set average it most closely resembles. This leading-order decision rule is universal across a broad range of MLP architectures, holding for any depth, as well as a wide class of activation functions and noise distributions. The same centroid mechanism closely matches finite-width network behavior in our experiments and provides an interpretable and analytically tractable account of why learning can succeed even when individual training examples carry almost no signal.

07.
arXiv (CS.AI) 2026-06-11

Artificial Intelligence in Ship Finance: Applications, Opportunities, and a Case Study in AI-Augmented Loan Origination

arXiv:2606.11238v1 Announce Type: cross Abstract: Ship finance is a data-intensive and document-heavy segment of asset-based lending, requiring the integration of financial, technical, contractual, and regulatory information from heterogeneous and largely unstructured sources. Increasing environmental regulation and ESG reporting requirements are adding further complexity to underwriting and loan-origination processes. Recent advances in artificial intelligence (AI), particularly large language models (LLMs), create new opportunities for processing and analysing such information. This paper reviews potential applications of AI in ship finance, with a particular focus on LLM-based systems for document comprehension, information extraction, and workflow automation. We present ShipFinance.ai, a modular agentic architecture to support loan application workflows in ship finance. The proposed system combines an LLM-based extraction module, financial analysis components, external maritime data services, and a controlled document-generation module with a chatbot interface to support the preparation of standardized financing applications. The paper discusses the key challenges for using such models in production. We argue that AI-assisted systems can support maritime finance professionals in managing increasingly complex information and reporting requirements.

08.
arXiv (quant-ph) 2026-06-19

$K$-Theoretic Obstructions to Linearizing QCA Representations

arXiv:2606.19657v1 Announce Type: cross Abstract: Projective representations arise naturally in physics and representation theory, and determining whether they can be linearized has been a fundamental problem. In this work, we study the analogous problem for quantum cellular automata (QCA) representations, which incorporate locality constraints imposed by a metric space $X$. Over an arbitrary field $\mathbb{F}$, we develop an obstruction theory for the linearization of QCA representations, using the algebraic $K$-theory spectrum of QCA constructed in previous work of the authors. The resulting obstructions are governed by the homotopy type of the QCA spaces, from which we extract universal obstruction classes to linearization. In the complex algebraic and unitary case, we also fully compute the homotopy types of the QCA spaces over a point, a line, and a plane.

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

How Much Do Reviews Really Contribute? A Study on Text-Enriched Matrix Factorization for Recommendations

arXiv:2606.16973v1 Announce Type: cross Abstract: Incorporating textual reviews into a Recommender System has become a prominent strategy for enriching collaborative signals with semantic information. However, the actual contribution of review-derived representations remains an open question, particularly when strong collaborative baselines are employed. In this work, we systematically investigate the impact of textual information on Matrix Factorization by introducing and comparing three enrichment strategies over a common collaborative backbone. First, we propose a learnable gating mechanism that adaptively balances collaborative and textual signals during training. This mechanism is applied to two distinct review representations: (i) aggregated topic profiles extracted from user and item histories, and (ii) full text embedding representations derived from reviews. Additionally, we explore a cross-attention mechanism that identifies and emphasizes the most informative dimensions of the textual representation before fusion with collaborative factors. We evaluate six variants: pure, enriched with topic profiles and text via gating; enriched with topics and text via gating; and enhanced with cross-attention over textual features. Experiments across multiple review-based datasets reveal that although adaptive fusion mechanisms improve representation flexibility, the marginal contribution of textual signals remains limited compared to the collaborative backbone. These findings suggest that, under typical rating-prediction settings, collaborative information continues to dominate performance, raising important considerations for the effective integration of semantic review signals into recommendation models.

10.
arXiv (CS.AI) 2026-06-17

Catastrophic Forgetting is Low-Rank: A Function-Space Theory for Continual Adaptation

arXiv:2606.18024v1 Announce Type: cross Abstract: Catastrophic forgetting in continual adaptation is usually studied through parameter drift, replay, or distillation, but these views do not identify which output-space directions are vulnerable. We give a function-space account in the NTK regime: new-task training induces old-task prediction drift through the cross-task kernel, yielding a closed-form predictor for the forgetting vector before any new-task gradient step. In frozen-backbone linear-head PEFT-CL, where the model is linear in the trainable parameters, the predictor is exact up to numerical precision; for nonlinear adapters/full fine-tuning, it is a local NTK approximation. The same expression reveals that forgetting concentrates in a small number of old-task NTK eigenmodes and under frozen linear heads gives a Kronecker scaling rule for the vulnerable rank. These results clarify the relation to prior NTK-overlap theory, explain why parameter-space regularizers can miss output-space interference, and motivate a targeted spectral regularizer.

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

A Temporal Planning Framework for Disruption Aware Dynamic Route Optimization in Heterogeneous Railway Systems

arXiv:2606.14582v1 Announce Type: new Abstract: Efficient route optimization play a vital role in ensuring both safety and punctuality in railway operations. It is very crucial particularly in heterogeneous multi-gauge railway networks with varying train speed, stopping pattern, infrastructure compatibility constraints increase coordination complexity. In single-track systems these challenges are further intensify due to all trains to share the same track and requires frequent track switching.Stochastic disruptions events including blocked tracks, blocked trains, engine failure and speed slowdowns introduces additional unpredictability in operations and deviate the timetable. However, existing studies predominantly focuses on high-level timetabling, omitting operational details such as track switching coordination. As a result leaving decision to human operators, increasing safety risks into railway operations. This study proposes a framework based on temporal planning for dynamic route optimization and disruption management in heterogeneous railway systems. The framework formulates railway operations as a temporal planning problem using PDDL 2.1 with explicitly modeling gauge compatibility constraints and diverse disruption scenarios. It generates conflict-free timestamped operational plans specifying both optimized schedules and executable action sequences. To evaluate the proposed framework, we developed a benchmark problem set with 200 instances using up to 1,000 track points and 120 trains. Two state-of-the-art temporal planners and a plan validator were employed to assessed the framework. The experimental results demonstrate that the framework effectively generates temporal operational plans for heterogeneous railway systems and handles multi-gauge constraints, disruptions, and reduces dependence on manual decision making.

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

CheXGenBench: A Unified Benchmark For Fidelity, Privacy and Utility of Synthetic Chest Radiographs

Structured benchmarks have advanced text-conditional image generation for real-world imagery, however, no such benchmark exists for synthetic radiograph generation. Despite being a highly active area of research, existing studies continue adopting inconsistent evaluation protocols and lack a unified assessment of the three most critical criteria: generative fidelity, privacy risk, and downstream utility. To address these limitations, we introduce CheXGenBench, the first unified evaluation framework for synthetic chest radiograph generation that simultaneously assesses fidelity, privacy risks, and downstream utility across frontier text-to-image (T2I) generative models. Our evaluation protocol, comprising over 20 quantitative metrics, covers 11 leading T2I architectures with plug-and-play integration for newer models. Through a rigorous and fair evaluation protocol, we establish comprehensive baseline state-of-the-art (SoTA) performances across all dimensions to guide future research. Furthermore, our results uncover several limitations of current generative models, which include first, even SoTA models struggle with long-tailed medical distributions; second, models pose high privacy risks regardless of fidelity quality; and third, while synthetic data already benefits downstream classification, it is of limited utility for downstream multimodal tasks. Drawing from these results, we propose concrete research directions to advance the field. The code is available at https://github.com/Raman1121/CheXGenBench

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

When the Same Musical Knowledge Forgets Differently: A Clean Probe of Pathway-Dependent Forgetting

A model can learn that the piano piece Für Elise is calm and reflective by listening to the audio or by reading a text description, but does it matter which route that knowledge took when it is later at risk of being forgotten? Forgetting research in multimodal models measures what knowledge is lost under adaptation, yet has not asked whether acquisition route affects how easily that knowledge is forgotten. We call this untested premise the Pathway-Invariant Assumption. Music understanding enables a clean test because a music clip and a canonical text description can be aligned to the same perceptual content, allowing the same knowledge unit to enter a model through listening or reading while the target remains fixed. Across multiple architecturally distinct audio-language models, we observe a consistent asymmetry: text-pathway knowledge is forgotten more than matched audio-pathway knowledge under identical adaptation pressure. To attribute this effect to route rather than confounds, we introduce the Paired Pathway Controlled Protocol (PPCP), a three-phase design that establishes matched pathway baselines, activates both pathways under symmetric supervision on the same knowledge pool, and applies identical forgetting pressure to both pathways. The gap is stable across models and gain-controlled analyses, persists when contradictory overwrite is replaced by correct-label cross-domain learning, remains under single-modality pressure, and is not removed by lightweight replay. Two independent routing-depth controls confirm that the effect is not explained by architectural depth, pointing to input representation as the dominant factor. Under PPCP, our results demonstrate that forgetting is highly route-dependent, establishing acquisition route as a new analytical dimension for forgetting research and multimodal system design.

14.
medRxiv (Medicine) 2026-06-17

Accounting for Human Movement to Improve Exposure-Health Models

Background. Current exposure-health models rely on averaged, residential-based environmental exposures, failing to account for human movement. This aggregation can lead to exposure misclassification and biased exposure-response estimates, potentially distorting our understanding of the true health effects of environmental conditions. We developed exposure disaggregation regression models that explicitly account for human movement when linking environmental exposures to health outcomes. Methods. By weighting pixel-level exposures according to distance from home as a simple proxy for human movement, our model linked disaggregated environmental exposures to individual-level health outcomes. Weights were either fixed a priori or derived from a latent distance-decay power parameter learned from the data. We additionally evaluated model performance under a nonlinear exposure-response relationship. Model performance was assessed across multiple sample sizes (N = 1,114; 50,000; and 100,000). A simulation study examined parameter recovery using bias, empirical standard error (EmpSE), and credible interval coverage. As a case study, Demographic and Health Surveys (DHS) data from Albania were used to link acute respiratory infection (ARI) outcomes among children under five to pixel-level NDVI within a 3 km buffer around DHS cluster centroids, and the proposed models were applied to these data. Results. Across all models (fixed-weight, learned-weight, and restricted cubic spline models), parameter recovery improved with increasing sample size. At N = 1,114, estimates were biased and imprecise, with incorrect effect direction for exposure-response parameters (e.g., learned-weight {beta}1 bias = - 0.79; EmpSE = 2.61; coverage = 0.88). In contrast, the models accurately recovered parameters at larger sample sizes, including the latent distance-decay parameter (bias = - 0.02; EmpSE = 0.15; coverage = 0.95 at N = 100,000), demonstrating their ability to reliably learn movement-based exposure weights when sufficient data were available. Conclusion. Instead of relying on arbitrarily-sized buffers, this statistical framework provides a novel method for studying environmental exposure-health relationships whilst accounting for human movement. With sufficiently large sample sizes, it can accurately estimate the influence of disaggregated environmental exposures on individual-level health and help address exposure misclassification arising from residential-only metrics. This methodological framework remains scalable, interpretable, and adaptable to other exposures and outcomes, offering a foundation for future work that integrates richer mobility-informed exposure-health research.

15.
arXiv (quant-ph) 2026-06-16

Intrinsic preservation of plasticity in continual quantum learning

arXiv:2511.17228v2 Announce Type: replace Abstract: Artificial intelligence in dynamic, real-world environments requires the capacity for continual learning. However, standard deep learning suffers from a fundamental issue: loss of plasticity, in which networks gradually lose their ability to learn from new data. Here we show that quantum learning models naturally overcome this limitation, preserving plasticity over long timescales. We demonstrate this advantage systematically across a broad spectrum of tasks from multiple learning paradigms, including supervised learning and reinforcement learning, and diverse data modalities, from classical high-dimensional images to quantum-native datasets. Although classical models exhibit performance degradation correlated with unbounded weight and gradient growth, quantum neural networks maintain consistent learning capabilities regardless of the data or task. We identify the origin of the advantage as the intrinsic physical constraints of quantum models. Unlike classical networks where unbounded weight growth leads to landscape ruggedness or saturation, the unitary constraints confine the optimization to a compact manifold. Our results suggest that the utility of quantum computing in machine learning extends beyond potential speedups, offering a robust pathway for building adaptive artificial intelligence and lifelong learners.

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

Entanglement-Rank Duality in Quadratic Phase Quantum States

arXiv:2605.05167v2 Announce Type: replace Abstract: Absolutely maximally entangled (AME) states are fundamental resources in quantum information theory, yet their construction and certification remain a nontrivial problem. Within the family of quadratic phase quantum states, defined by symmetric matrices $P$ over finite fields $\mathbb{F}_{p^m}$, we show that the Rank-Purity Duality $\operatorname{Tr}(\rho_S^2) = |\mathbb{F}|^{-\operatorname{rk}_{\mathbb{F}}(P_{S,\bar{S}})}$ follows from additive character orthogonality and holds over all $\mathbb{F}_{p^m}$, yielding a polynomial-time AME certification criterion. For square-free dimensions $d = p_1\cdots p_r$, the Chinese Remainder Theorem induces a prime-field factorisation. This implies additivity of Rényi-2 entropy and yields sharp obstruction criteria that rule out cases such as $\operatorname{AME}(4,6)$ and constrain the open case $\operatorname{AME}(8,6)$. As a proof of concept, we construct an explicit $\operatorname{AME}(17,10001)$ state, certified across all $65{,}535$ bipartitions, demonstrating that the framework scales to large systems and previously inaccessible local dimensions.

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

Tensor-based second-order causal discovery

arXiv:2606.18074v1 Announce Type: cross Abstract: Causal discovery seeks to uncover the causal dependencies among variables. For this purpose, we propose an algorithm called Tensor-based Second-order Causal Discovery (TSCD). Its input is a tensor obtained from the covariance matrices of observational and interventional data. Assuming the causal dependencies follow a linear structural equation model on a directed acyclic graph (DAG), TSCD outputs the DAG and the functions on its edges, requiring only that the noise variables are uncorrelated. We also implement a version of the approach for nonlinear models. Our focus on second-order statistics (via the covariance matrices) is motivated by their statistical and computational efficiency relative to higher-order moments, their identifiability relative to first-order statistics, and that they work regardless of whether the variables are Gaussian. We show that TSCD has identifiable causal order and parameters from a number of interventions that is logarithmic in the number of variables. Experiments show that TSCD is robust to noise, competitive with existing methods, and scales to hundreds of variables.

18.
arXiv (CS.CV) 2026-06-17

Structured Adversarial Camouflage via Voronoi Diagrams

Pixel-wise adversarial patches are computationally heavy and often visually detectable, limiting utility in security-critical systems. We present adversarial Voronoi camouflage that optimizes only seed-point locations under fixed, printable palettes using a soft assignment, producing structured, splinter camouflage-like patterns without additional regularization. Evaluated on person detection with COCO-style AP@[.5:.95], naive placement (Inria -> COCO) performs comparably bad, while garment-level application via segmentation mask (3DPeople) results in a significant AP drop. The attack transfers to out-of-domain backgrounds and across detector families (YOLOv9/10/11/12), indicating robustness in black-box settings. Repainting with different palettes largely nullifies the effect, and single-color tweaks show limited tolerance (

19.
arXiv (CS.LG) 2026-06-18

Latent-Conditioned Parameterized Quantum Circuits as Universal Approximators for Distributions over Quantum States

arXiv:2605.28690v3 Announce Type: replace-cross Abstract: Many applications in quantum simulation, quantum chemistry, and quantum machine learning require not a single quantum state but an ensemble of states characterizing the heterogeneity of a target system. Preparing such ensembles state-by-state is prohibitive in both variational and fault-tolerant settings, thereby motivating a generative modeling approach. We introduce latent-conditioned parameterized quantum circuits (LPQCs), a hybrid quantum-classical framework in which classical neural networks map a latent variable sampled from a prior distribution to the parameters of a parameterized quantum circuit. We prove that LPQCs are universal approximators for probability measures over density operators in the 1-Wasserstein distance, extending classical universal approximation theorems to the quantum-distribution setting. We additionally introduce a multimodal latent prior and a mixture-of-experts circuit architecture, and show empirically that the latent-conditioned parameterization alleviates the barren plateau problem during optimization, a behavior for which we provide rigorous partial guarantees. Numerical experiments validate the framework on a synthetic multi-cluster ensemble of mixed quantum states and on a QM9-derived ensemble of 3-D molecular structures. In these tasks, LPQC outperforms recent quantum generative baselines and matches the generation quality of a classical neural-network baseline, while requiring an output dimension that grows only linearly with the number of qubits rather than exponentially. By leveraging classical expressivity in the latent space, LPQCs offer a tractable route to quantum generative modeling.

20.
PLOS Computational Biology 2026-06-22

TCRBinder: Unified pre-trained language model with paired-chain synergy for predicting T-cell receptor binding specificity

Authors:

by Weihe Dong, Qiang Yang, Long Xu, Xiaokun Li, Kuanquan Wang, Suyu Dong, Gongning Luo, Xianyu Zhang, Tiansong Yang, Xin Gao, Guohua Wang Deciphering how human T cells recognise peptide-HLA (pHLA) complexes underpins next-generation vaccines and personalised immunotherapies, yet extreme sequence diversity and paired-chains interdependence still hamper reliable in silico prediction of T-cell receptor (TCR) specificity. To overcome these hurdles, we built TCRBinder, a paired-chain-aware deep model with a multi-branch encoder that routes each molecular component through dedicated transformer-based modules to capture contextual signals in both HLA pseudo-sequences and antigenic peptides while simultaneously processing the TCR α and β chains. This design captures the synergistic interaction between paired chains to emulate peptide-HLA-TCR (PHT) interactions and expose residue-level contact motifs. Across PHT and peptide-TCR (pTCR) benchmarks, the model delivered state-of-the-art performance (AUC-ROC = 0.911, AUPR = 0.791 for the PHT task) and remained superior on multiple independent datasets. We tracked the dynamics of clonal expansion and, in a large SARS-CoV-2 repertoire containing completely unseen peptides, improved the AUC-ROC by up to 16.3% over the leading alternatives. Moreover, TCRBinder provided mechanistic insights by pinpointing contact hotspots and quantifying residue contributions to binding probability. These capabilities position TCRBinder as a versatile tool for rational antigen discovery, immunotherapy stratification, and neoantigen vaccine design.

21.
Nature (Science) 2026-06-16

Mathematicians are developing rules for AI use — other fields should follow

Authors: Unknown Author

The mathematics community is right to call for transparency, integrity and fairness to be protected when AI tools are used. Researchers in other disciplines could learn from this approach. The mathematics community is right to call for transparency, integrity and fairness to be protected when AI tools are used. Researchers in other disciplines could learn from this approach.

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

A Reproducible Log-Driven AutoML Framework for Interpretable Pipeline Optimization in Healthcare Risk Prediction

arXiv:2605.21528v2 Announce Type: replace-cross Abstract: Accurate disease risk prediction is challenged by heterogeneous features, limited data, and class imbalance. This study presents yvsoucom-iterkit, a deterministic AutoML framework that models pipeline optimization as a configuration-level system with full reproducibility and traceable execution logs, enabling systematic analysis of component attribution, interactions, similarity, and cross-seed robustness. Experiments on the Pima Indians Diabetes and Stroke datasets across more than 18,000 pipeline configurations reveal a structured yet partially redundant search space, where performance is dominated by a small subset of interacting components. Ensemble models achieve stable performance, reaching a Weighted-F1 of 0.89 on Pima and 0.94 on Stroke. Macro-F1 reaches approximately 0.88 on Pima but drops to 0.6560 on Stroke due to severe imbalance. Cross-seed experiments show that ensembles reduce variance compared to single models. Friedman testing ($p < 0.05$) confirms significant ranking differences across configurations. Based on analysis of component attribution, interaction, and similarity, optimal configuration design reveals dataset-dependent behavior. For the Pima dataset, computational efficiency benefits from simplified search spaces where redundant components can be removed, with split ratio playing a key role. In contrast, the Stroke dataset requires enhanced imbalance-aware strategies, where RandomOverSampler improves Macro-F1 from 0.6560 to 0.6766. These findings demonstrate that effective AutoML optimization is achieved through optimal configuration design, where carefully constraining the search space to high-impact components can improve performance, stability, and interpretability while reducing unnecessary search complexity.

23.
bioRxiv (Bioinfo) 2026-06-10

Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins

Motivation: Spurious protein sequences, resulting from gene prediction errors, theoretically should not yield folded structures. AlphaFold2 was previously shown to predict short spurious sequences with high pLDDT scores and was therefore unlikely to distinguish between real proteins and spurious proteins which are usually short. We evaluate whether newer structure prediction methods (ESMFold and AlphaFold3) similarly predict short sequences with high pLDDT or if they better discriminate between spurious and real proteins. Results: All three structure prediction methods (ESMFold, AlphaFold2, and AlphaFold3) predict short spurious sequences from AntiFam with unexpectedly high pLDDT scores, however the discrimination between spurious and real proteins improves beyond 100 amino acids. By analysing sequences with disparate pTM and pLDDT scores, we identified two likely spurious shadow ORFs in Swiss-Prot and one potentially non-spurious AntiFam entry. Using the structure prediction scores, we developed a Gaussian Process Model and evaluated its performance on AlphaFold DB, identifying potential spurious proteins at scale. While limited on its own, this model can increase confidence in spurious protein identification when combined with other methods.

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

EyeMVP: OCT-Informed Fundus Representation Learning via Paired CFP–OCT Pretraining

Color fundus photography (CFP) is the mainstay for large-scale retinal screening, yet its diagnostic capacity is constrained by the lack of depth-resolved structural information. Optical coherence tomography (OCT) provides cross-sectional retinal anatomy, but is less accessible in population-level screening. Here, we present EyeMVP, a cross-modal retinal foundation model that uses paired CFP–OCT pretraining to learn OCT-informed CFP representations. EyeMVP is pretrained on 674,893 strict same-eye same-day paired CFP–OCT image triples from 112,642 patients across eight hospitals in China. The model uses cross-modal masked reconstruction to enrich CFP representations with OCT-associated supervision, while requiring only CFP images at inference. To accommodate the non-aligned imaging geometry between en-face CFP and cross-sectional OCT, EyeMVP combines source-constrained cross-attention with CFP-derived structural masks. Across 16 downstream tasks, including classification, segmentation, few-shot adaptation, and cross-modal retrieval, EyeMVP outperforms representative retinal foundation models and shows consistent gains on tasks involving macular and optic nerve structure. For CFP-challenging macular diseases, EyeMVP achieves an AUROC of 0.948 for macular edema (vs.~0.852 for EyeCLIP) and 0.825 for myopic macular schisis. In an exploratory reader study, EyeMVP exceeds junior and intermediate ophthalmologist groups but does not reach senior ophthalmologist performance on macular edema, while showing numerically higher balanced accuracy than all reader groups on myopic macular schisis. These results suggest that pixel-level cross-modal reconstruction can enrich CFP representations with OCT-associated supervision, providing a practical route toward stronger CFP-based retinal analysis in screening settings.

25.
arXiv (math.PR) 2026-06-11

On the Wasserstein distance between a hyperuniform point process and its mean

arXiv:2404.09549v3 Announce Type: replace Abstract: We study the existence of bounds on the expected $p$-Wasserstein distance between a random measure and its mean under the assumption that the $p$-th centered moments of the counting statistics are controlled uniformly in space. The average Wasserstein transport cost is shown to be bounded from above and from below by some multiples of the number of points. $D$-dimensional versions of those results are also obtained. As a corollary, we prove that for any value of $p\geq 1$ the Ginibre point process can be seen as a perturbed lattice with identically distributed perturbations with a finite $p$-th moment.