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01.
arXiv (CS.AI) 2026-06-11

Can Open-Source LLM Agents Replace Static Application Security Testing Tools? An Empirical Assessment

arXiv:2606.11672v1 Announce Type: cross Abstract: This paper explores the value of agentic AI tools for cybersecurity purposes. We evaluate the efficacy of a general-purpose GenAI Large Language Model- (GenAI-) based agent when powered by three different Ollama-hosted general-purpose open source models. We assess each agent's performance using precision, recall, false positive count, and a calculated composite score based upon the interplay of the captured metrics, against the baseline performance of an existing, vetted Static Application Security Testing (SAST) tool, Bandit. Our findings refute the notion that a modern open-source GenAI LLM-based agent is currently suitable for the specialized task of SAST scanning under realistic conditions.

02.
arXiv (quant-ph) 2026-06-16

Information geometry and entanglement under phase-space deformation through nonsymplectic congruence transformation

arXiv:2505.02269v3 Announce Type: replace Abstract: The Fisher-Rao (FR) information matrix is a central object in multiparameter quantum estimation theory. The geometry of a quantum state can be envisaged through the Riemannian manifold generated by the FR-metric corresponding to the quantum state. Interestingly, any congruence transformation $GL(2n,\mathbb{R})$ in phase space leaves the FR-distance for Gaussian states invariant. In the present paper, we investigate whether this isometry affects the entanglement in the bipartite system. It turns out that the entanglement-generating congruent transformation depends upon the system and background space. To make our study relevant to physical systems, we choose Bopp's shift in phase space as an example of $GL(2n,\mathbb{R})$, so that the results can be interpreted in terms of noncommutative (NC) phase-space deformation. We provide an estimation of the measure of entangled states over separable states for bipartite Gaussian states under a Bopp's shift. Since the dynamics of free oscillators in background NC-space is mathematically equivalent to the dynamics of a charged particle under a homogeneous magnetic field, we provide an outline for a gedankenexperiment through photocurrent measurement in order to determine the effects of congruent transformation on the distinguishibility of Gaussian states.

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

Explaining RhythmFormer: A Systematic XAI Analysis of Periodic Sparse Attention for Remote Photoplethysmography

Remote photoplethysmography (rPPG) transformers achieve low heart-rate error on benchmarks, yet their decisions remain opaque–a growing concern as rPPG moves toward clinical heart rate estimation. Existing rPPG XAI is dominated by qualitative heatmap inspection without quantitative faithfulness metrics or physiology-grounded validation, leaving a gap between visual plausibility and auditable evidence. We address this gap. First, we adapt four attribution methods (raw attention, rollout, flow, Beyond Intuition) to RhythmFormer's bi-level routing attention with top-$k$ selection. Second, we introduce a skin coverage metric quantifying how much attribution mass falls on skin regions. Third, we adapt the SaCo faithfulness coefficient from its original classification setting to rPPG regression by using the MAE between original and perturbed predicted rPPG waveforms as the perturbation impact. Applying these tools, we quantify a multi-hop leakage effect under sparse top-$k$ routing: attention rollout and flow almost completely restores the connections that individual refined-attention layers explicitly set to zero. Beyond Intuition mitigates this via its value-projection-weighted rollout and gradient-supported mask, attaining the highest median refined skin coverage ($0.83$ vs. $0.57$ for vanilla rollout) and faithfulness ($F=0.92$) among the evaluated methods on UBFC-rPPG. Validation across diverse datasets and model variants is needed. A case study on a low-SaCo outlier further shows all four methods recovering consistently once an artefactual region is replaced, suggesting consistent SaCo behavior across attribution families in this illustrative case. Together, these metrics move XAI for rPPG toward auditable numerical evidence about spatial alignment and perturbation faithfulness, i.e. trustworthy rPPG XAI.

04.
arXiv (math.PR) 2026-06-25

Localized Centered Second-Chaos Operator

arXiv:2606.26065v1 Announce Type: new Abstract: We prove a localized continuous-frequency operator estimate for centered Gaussian chaoses of order two. The result applies to operator-valued centered second chaoses, including Wick-centered same-family variants, between Hilbert spaces. In the model, two Gaussian frequency legs at scale $N$, an input leg at scale $Q$, and an output leg at scale $M$ are coupled through a soft incidence kernel; non-orthogonal Gaussian profiles are represented by covariance synthesis maps. The proof combines four oriented flattenings, rectangular non-commutative Khintchine inequalities, soft-incidence Schatten bounds, and Sobolev–Besov dyadic summation. The time lift gives $L^p$ operator convergence, while a Galerkin stabilization hypothesis gives pathwise full-cutoff convergence by the first Borel–Cantelli lemma. Under $\mathcal G(N)\lesssim N^{-\Gamma}$ one obtains the window \[ \Gamma>\frac d2, \qquad s

05.
arXiv (CS.CL) 2026-06-18

Trust Region On-Policy Distillation

On-Policy Distillation (OPD) is a fundamental technique for efficient post-training of large language models (LLMs), with broad applications in agent learning, multi-task enhancement, and model compression. However, OPD training becomes unstable when the teacher and student distributions differ substantially, as teacher supervision on student-generated tokens may yield unreliable policy gradients and even cause optimization failure. This work addresses reliable on-policy token-level supervision through credit assignment strategies, and proposes Trust Region On-Policy Distillation, TrOPD. It features the following characteristics: 1) Trust-Region On-Policy Learning: TrOPD performs OPD only in regions where the teacher provides reliable supervision, mitigating the optimization difficulty of the K1 reverse-KL estimator under distribution mismatch. 2) Outlier Estimation: For outlier regions, we explore gradient clipping, masking, and forward-KL estimation to reduce the adverse effects of unreliable supervision. 3) Off-Policy Guidance: The student continues generation from teacher prefixes and uses forward KL to imitate off-policy guidance, encouraging on-policy exploration toward reliable regions. Experiments show that TrOPD consistently outperforms SoTA OPD baselines, including OPD, EOPD, and REOPOLD, across mathematical reasoning, code generation, and general-domain benchmarks.

06.
Nature (Science) 2026-06-24

Zero-shot design of drug-binding proteins via neural iterative selection−expansion

作者:

The design of proteins that bind to small molecules has been challenging because it requires simultaneous optimization of the protein sequence, protein structure and ligand conformation1–7. Current deep-learning algorithms have struggled to navigate this landscape, precluding the zero-shot design of binders. Here we show that by combining two neural networks in an iterative design algorithm, small-molecule binding proteins can be created from scratch with high accuracy. We trained a graph neural network—ligand-aware sequence engineering message-passing neural network (LASErMPNN)—to design compatible protein sequences for an input protein backbone and docked ligand. We paired  LASErMPNN with a structure predictor that models a three-dimensional protein–ligand complex for an input protein sequence and ligand identity. The closed-loop iteration of these reciprocal networks optimized sequence–structure–ligand compatibility, and outperformed a comparable design loop using a physics-based energy function. We used our strategy, termed neural iterative selection–expansion (NISE), to design proteins that, using different folds, specifically bind to two chemically distinct small-molecule drugs, exatecan and apixaban, with success rates of 100% and 83%, respectively. The tightest NISE binders had nanomolar-to-picomolar affinities, surpassing those of the next-leading method by 70-fold for exatecan and nearly 10,000-fold for apixaban. LASErMPNN then suggested two amino-acid substitutions that improved the affinity of the tightest exatecan binder by 100-fold without any experimental input. The optimized binder protected the labile lactone ring of exatecan from hydrolysis for days. Our work describes a general recipe for using neural networks to automate the design of small-molecule binding proteins for applications in drug delivery, sensing and catalysis.  By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing promise for applications in drug delivery and sequestration.

07.
arXiv (CS.AI) 2026-06-18

Forecasting what Matters: Decision-Focused RL for Controlled EV Charging with Unknown Departure Times

arXiv:2606.19199v1 Announce Type: cross Abstract: The recent growth of EV adoption poses challenges for power systems, including increased peak demand and potential grid instability. Smart control of EV charging – e.g., based on reinforcement learning (RL) – can alleviate these issues by learning temporal and contextual patterns from historical data. Yet, in real-world scenarios, key features, such as departure time, often are unavailable. This, in turn, makes it harder for an RL agent to learn and execute an effective charging policy. To mitigate this uncertainty, a trained forecaster can approximate the unknown features from available data. However, since these forecasting models are typically trained for accuracy (rather than their impact on a downstream agent's decision quality), their errors may propagate and hinder the overall performance of a controller that is using the forecasts. To avoid this, we propose a decision-focused RL (DF-RL) framework in which the forecaster is trained end-to-end, i.e., with feedback from the charging policy actions taken by the RL agent. Such joint training of both the forecaster and controller ultimately results in higher-quality actions: our proposed DF-RL method yields superior charging decisions compared to other baselines, achieving up to a 14% improvement in total reward and a 55% reduction of unsupplied energy (i.e., charging that failed to happen because the EV already left), relative to the RL method without departure time forecasting.

08.
Nature (Science) 2026-06-10

A 5.3-million-year-old deep-sea whale necropolis in the Diamantina Zone

Whale falls are biodiversity oases at seabeds1–6, yet their record from the oceans has remained sparse and fragmentary6,7. Here we report the discovery of a vast whale necropolis in the Diamantina Zone (4,616- to 7,001-m depth), extending about 1,200 km along the sea floor of the southeastern Indian Ocean. This area has a deep and extensive accumulation comprising five modern natural whale-fall communities and 476 fossil cetaceans recorded. We show that carcasses host specialized communities dominated by brittle stars, bone-boring worms and chemosynthesis-based bivalves and that the fossil record in this area comprises both extant and extinct deep-diving beaked whales. Isotopic dating shows that whale falls in this region have occurred since at least 5.3 million years ago. These findings reshape the understanding of the limits and biogeography of whale-fall ecosystems and establish some deep sea floors as a fossil archive for tracing cetacean evolution over geological time. Researchers uncovered an enormous deep-sea accumulation of whale remains in the southeastern Indian Ocean, showing long-term, specialized ecosystems and an extensive fossil record that offers new insight into deep-ocean biodiversity and whale evolutionary history.

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

How Do Instructions Shape Speech? Cross-Attention Attribution for Style-Captioned Text-to-Speech

arXiv:2606.20532v1 Announce Type: new Abstract: Style-captioned text-to-speech systems use natural language to control voice characteristics, but how individual words influence acoustic output remains unclear. Understanding this is critical for diagnosing failure modes and improving controllability in expressive TTS. We propose cross-attention attribution for speech diffusion models, adapting the DAAM framework to the speech domain for the first time, and apply it to CapSpeech-TTS. Our method extracts per-token heatmaps across 25 layers and 24 ODE steps. We analyze 3,600 (style caption, text transcript) combinations comprising 120 style captions conditioning the generation of 30 text transcripts each, revealing how caption tokens shape waveforms. Results show: (1) style tokens have lower temporal variance than content/function tokens, confirming global conditioning; (2) style attention correlates with F0 and energy; (3) style conditioning peaks in early steps and deep layers; (4) attention entropy reaches its minimum at layer 17, co-occurring with the style importance peak, indicating maximal network selectivity at the most style-critical stage. This is the first study of how natural language influences cross-attention in speech diffusion models

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

Runtime Analysis of Cartesian Genetic Programming in Evolving Boolean Functions

arXiv:2606.15923v1 Announce Type: cross Abstract: Cartesian Genetic Programming (CGP) is among the practical and popular forms of Genetic Programming as it uses a graph-based representation of programs. This paper presents a first runtime analysis of CGP in evolving Boolean functions using complete training sets. We prove an asymptotic bound $O(n D^5)$ for the expected number of fitness evaluations of CGP to construct a conjunction of $n$ inputs using at most $D \geq n-1$ binary gates, a minimal function set, and even with a strict survival selection. When the non-strict selection is used, the bound is improved to $O(n D^4)$. Our analysis reveals interesting characteristics of CGP induced search, which have been only observed empirically. In particular, enabling the acceptance of equally good solutions, including those with connected gates non-contributing to fitness, can lead to a speedup, and consequently a better asymptotic time bound. In contrast to conjunctions, we also prove a negative result which shows that CGP requires exponential time to evolve an exclusive disjunction. Experiments evolving conjunctions complement our theoretical findings. The use of incomplete training sets is found to further reduce the average number of fitness evaluations while maintaining a good level of generalisation.

11.
PLOS Computational Biology 2026-06-18

A comparison of contact patterns derived from the population structure in agent-based models and empirical contact survey data

作者:

by Janik Suer, Johannes Ponge, Michael Brüggemann, Jan Pablo Burgard, Vitaly Belik, Bernd Hellingrath, Alejandra Rincón Hidalgo, Andrzej K. Jarynowski, Richard Pastor, Huynh Thi Phuong, Steven Schulz, Ashish Thampi, Chao Xu, Marlli Zambrano, Rafael Mikolajczyk, André Karch, Veronika K. Jaeger, on behalf of the OptimAgent Consortium Agent-based models (ABMs) are powerful tools for simulating disease spread, relying on individual-level interaction rules from which emergent dynamics arise. An important component in ABMs is contact behaviour. To reduce computational complexity, contact behaviour in ABMs is often assumed as random mixing within structurally defined settings (as, e.g., workplaces). with setting composition typically based on empirical data such as census information. However, the validity of this approach to represent contacts remains unclear. To address this gap, we compare the contact structure derived through this approach in a large-scale ABM with empirical contact survey data with respect to age contact matrices for households, schools, workplaces, all remaining contact settings, and all contacts combined (based on difference matrices and sum of squared errors (SSE)). Our results demonstrate that random mixing in settings with known age compositions like households (SSE:0.7(95%CI0.4–0.9)), schools (SSE:0.7(95%CI:0.3–1.1)) and workplaces (SSE:0.5(95%CI:0.2-0.7)), captures basic interaction patterns but fails to account for age-related variation in contact numbers. The largest differences arise for contacts outside these settings (SSE:3.8(95%CI:1.2–6.5)), as ABMs typically use random regional contacts that do not capture age-structured behaviour observed in contact surveys. Applying contact matrices from both approaches to an age-structured compartmental model, leads to noticeable differences in simulated epidemic outcomes regarding reproduction numbers and spreading dynamics between age groups. Our results suggest that naïve approaches to represent contact behaviour in ABMs based on population structure can be valid in settings with defined age-structures while settings with low a priori structure require more advanced methods to represent contact behaviour observed in contact surveys.

12.
arXiv (CS.CV) 2026-06-17

ActWorld: From Explorable to Interactive World Model via Action-Aware Memory

Interactive world models aim to simulate environment dynamics under real-time user actions. However, their action vocabulary is largely confined to navigation: most actions correspond to motion (e.g., walk, turn, look around), while interaction with objects in the scene (e.g., pick up plates, open doors, or trigger physical responses) is either absent, restricted to game domains, or relegated to prompt-to-full-video scenarios. The resulting worlds are visually explorable but not truly actionable. In this work, we present ActWorld, an interactive world model that extends prior navigation-centric generators to support mid-rollout object interaction within a chunk-autoregressive framework. We argue that the navigation-interaction gap stems from two bottlenecks. First, a data bottleneck: the lack of human-object interaction data with accurate, dense labels. Second, a memory bottleneck: recency-biased history compression in existing world models discards the event-transition frames that causally determine subsequent object states, leading to an action-forgetting pathology. On the data side, we construct a 100K interaction video dataset, each annotated with per-chunk captions via chain-of-thought reasoning. On the model side, we introduce a hierarchical action-aware memory design that routes history compression by interaction importance, complemented by a persistent memory bank that maintains event-update and object-identity tokens across long rollouts. Experiments show that ActWorld supports both flexible navigation and rich object interaction within a single model, substantially improving interaction fidelity over navigation-only baselines without sacrificing viewpoint control. Project page is available at https://interactwm.github.io/ActWorld.

13.
bioRxiv (Bioinfo) 2026-06-11

inquiSTR: a toolkit for accurate and efficient population-scale tandem repeat genotyping and analysis

Tandem repeats are highly mutable genomic elements linked to human traits and diseases. Profiling large catalogs of tandem repeats from population-scale long-read sequencing data requires accurate and efficient tools. We introduce inquiSTR, a command-line toolkit for fast genome-wide tandem repeat length genotyping. inquiSTR, with efficient parallel processing and low-memory streaming algorithms, genotypes a genome-wide repeat catalog of 1.78 million loci in less than two minutes. Benchmarking shows high accuracy and significantly faster performance compared to existing tools and truth sets. inquiSTR also provides methods for downstream analyses such as population structure inference, association testing, and outlier detection.

14.
arXiv (quant-ph) 2026-06-11

Exact Entanglement Dynamics Beyond Nearest-Neighbor Dual-Unitary Floquet Systems

作者:

arXiv:2606.11311v1 Announce Type: new Abstract: Exact results using dual-unitarity largely rely on nearest-neighbor structures, while finite-range interactions typically lead to complications. Going beyond the usual nearest-neighbor setting, we introduce an analytically tractable family of finite-range kicked Ising models that admit exact closed-form entanglement dynamics. The construction is based on a staggered structure in which dual-unitarity is present on sublattices that are then coupled to each other. The central observation is that these inter-sublattice couplings do not obstruct the dual-unitarity of the resulting model. For the minimal interaction range of $r= 2$, we derive exact expressions for all the $n-$Rényi entanglement entropies at all times and show that the result is the sum of the two coupled sublattice contributions. Our framework extends naturally to larger finite interaction ranges and to systems with heterogeneous local Hilbert spaces, without additional assumptions. It thus provides a controlled setting for studying exact entanglement growth beyond strictly nearest-neighbor dual-unitary models.

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

Learning Directional Semantic Transitions for Longitudinal Chest X-ray Analysis

Chest X-ray (CXR) interpretation often requires longitudinal comparison to assess disease progression. Existing approaches typically rely on temporal feature fusion or inter-study discrepancy modeling, yet remain limited in capturing subtle progression semantics and overlook the inherently directional nature of disease trajectories. In this paper, we propose ProTrans, a novel vision-language pretraining framework that formulates disease progression as a directional semantic transition between paired CXR studies. ProTrans leverages radiology reports to anchor individual CXR representations within interpretable disease states, and introduces a learnable progression feature map to explicitly encode semantic shifts between states, aligned with report-derived progression descriptions. To enforce direction-aware perception, ProTrans incorporates a reversed temporal modeling process and imposes bidirectional reconstruction consistency across states and transitions, thereby disentangling directional semantics and promoting coherent trajectory modeling. Extensive experiments on longitudinal downstream tasks, including disease progression classification and progression captioning, demonstrate that ProTrans consistently outperforms existing methods, establishing a unified pretraining framework for longitudinal CXR understanding. https://github.com/RPIDIAL/ProTrans

16.
arXiv (CS.AI) 2026-06-19

FlowFake: Liquid Networks for Audio Deepfake Detection

arXiv:2606.19579v1 Announce Type: cross Abstract: Audio deepfakes generated by neural text-to-speech and voice-cloning systems threaten speaker verification and public discourse at scale. The core challenge is cross-dataset generalization: detectors trained on one synthesis pipeline collapse on unseen forgeries. We argue that this failure is primarily because of structural synthetic speech artifacts which are multi-timescale trajectory anomalies. Though every existing detector aggregates a fixed-window frame statistics, this misaligns the architecture with the signal. We propose FlowFake, a Liquid Time-Constant (LTC) architecture whose hidden state evolves via a learned ODE, with per-neuron adaptive time constants simultaneously resolving spectral (10ms) and prosodic (2s) cues. At only 34K parameters FlowFake achieves formal BIBO stability and O(dt^4) integration error. On a four-dataset cross domain benchmark (ASVspoof2019-LA, FakeOrReal, InTheWild, MLAAD), FlowFake reaches 75.29% on ASVspoof2019 trained only on FakeOrReal and 79.97% trained only on MLAAD. It outperforms RawGAT-ST and Whisper-DF on every evaluated pair and matching SSL Wav2vec2 (300x larger) at 0.01% of its parameter count. The source code is available on : https://github.com/GhostRider2023/FlowFake

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

The Program Is Still There: A Conservation Law for Program Discovery

arXiv:2606.13799v1 Announce Type: cross Abstract: Finding the shortest program that generates a sequence is uncomputable, and for six decades that fact has been mistaken for a wall around finding any generating program. It is not a wall but a price, and this paper measures it. For every algorithm that learns about a candidate program only through its score, a class spanning Levin search, evolutionary methods, simulated annealing, and the cross-entropy method, we define the coupling width of a search problem and prove an unconditional worst-case lower bound, exponential in that width with base one less than the domain size. From it follows a conservation law: structural knowledge injected into a search trades one for one against the search it removes, and their sum can never fall below the length of the program sought. Levin's 1973 upper bound and the lower bound proved here are the two ends of one conserved quantity, closing on each other as the instruction set grows. The only escape is to read a candidate's structure rather than its score, and its price, which we prove for generic targets, is incompleteness. A deterministic engine built on this theory recovers a generating program, certified by compressing its data and predicting an unseen continuation, for 2,383 of 3,914 sequences across four independent populations, including 244 of the 256 elementary cellular automata, with measured discovery cost rising along program length more than an order of magnitude inside the score-oracle worst case.

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

Optimizing Incomplete, Large-Scale and Sparse Multi-Graph Matching in Bioimaging

Multi-graph matching is a fundamental problem in computer vision. Our work is motivated by a challenging application in bioimaging, where dozens or even hundreds of 3D microscopy images of worms must be brought into correspondence. Existing datasets do not cover this large-scale regime, and virtually all existing methods are inapplicable because they assume a complete or dense problem setting. To support further research, our first contribution is a new large-scale dataset based on problem instances from bioimaging. Our second contribution is a comprehensive analysis of the two main multi-graph matching paradigms: direct and permutation synchronization-based formulations. We argue, in part by proof, that practical large-scale methods must explicitly address problem sparsity and incompleteness. Since standard permutation synchronization approaches fail in this setting, we further introduce a sparse permutation synchronization paradigm. Our final contribution is GREEDA, a general method for sparse and incomplete problems that can be instantiated across cost orders and paradigms. While our paper focuses on objective functions up to quadratic order, GREEDA is inherently generalizable to arbitrary orders. On larger, sparse instances, GREEDA outperforms competing methods in both objective value and runtime. For example, for moderately-sized problems based on 30 worm images GREEDA produces a high-quality solution within 2 minutes, whereas competitors require at least half an hour and yield far worse results. On smaller dense problems, GREEDA remains on par with leading methods while being an order of magnitude faster.

19.
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.

20.
medRxiv (Medicine) 2026-06-11

Genetic Susceptibility to Incisional Hernia: Evaluation of Hernia Polygenic Risk Scores

Objectives: Incisional hernia (IH) affects 13-30% of people after abdominal surgery, resulting in substantial morbidity and costs. While clinical risk factors have been studied extensively, genomic risk for IH is incompletely understood. We aimed to evaluate the impact of polygenic risk scores (PRS) on IH risk prediction. Methods] We created and evaluated three PRS for abdominal hernia, ventral hernia and latent hernia susceptibility for prediction of IH in an institutional biobank. The primary outcome was defined as the diagnosis or repair of an IH based on ICD-9/10-CM/PCS and CPT codes. Clinical covariates included age, sex, body mass index (BMI), smoking status, index procedure type, and perioperative surgical site infection. A phenome-wide association study (PheWAS) was performed to assess clinical associations with increased PRS. We then tested the ability of the PRS to improve prediction for IH by modeling clinical covariates with and without PRS in patients who underwent abdominal surgery. Model performance was assessed using 10 iterations of 5-fold cross-validation to estimate Brier scores and area under the receiver operating characteristic curve (AUROC), which were compared using cross-model Bayesian analysis of variance. Results: In 55,809 subjects, assessed PRS was significantly associated with incisional, umbilical, and ventral hernia on PheWAS, with 1.19 greater odds of developing IH per 1-SD increase in PRS (95% CI: 1.13-1.25, P < 0.001). Of 9,909 subjects who underwent qualifying abdominal surgery, 706 developed IH. In this cohort, the latent hernia susceptibility PRS was associated with a 16% increased hazard of developing IH per 1-SD increase (HR 1.16; 95% CI: 1.07-1.26; P < 0.001). Compared to a predictive model using clinical covariates (Brier score = 0.047, 95% CI: 0.046-0.048; AUROC = 0.660, 95% CI: 0.653-0.666), addition of the PRS showed similar Brier score and AUROC estimates (Brier score = 0.047, 95% CI: 0.046-0.048; AUROC: 0.667, 95% CI: 0.661-0.673) at five years. Cross-model Bayesian analysis demonstrated >99% probability of practical equivalence when trying to detect a difference of [&ge;] 0.02. Conclusion: All three PRS for hernia were independently associated with IH, suggesting that genomic factors contribute significantly to IH development. However, none of the three PRS meaningfully improved clinical IH risk prediction in patients who underwent abdominal surgery. This suggests that clinical comorbidities and surgical techniques may be equally as important as genomic architecture.

21.
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.

22.
arXiv (CS.LG) 2026-06-19

Alternating Direction Method of Multipliers for Nonlinear Matrix Decompositions

arXiv:2512.17473v3 Announce Type: replace-cross Abstract: We present an algorithm based on the alternating direction method of multipliers (ADMM) for solving nonlinear matrix decompositions (NMD). Given an input matrix $X \in \mathbb{R}^{m \times n}$ and a factorization rank $r \ll \min(m, n)$, NMD seeks matrices $W \in \mathbb{R}^{m \times r}$ and $H \in \mathbb{R}^{r \times n}$ such that $X \approx f(WH)$, where $f$ is an element-wise nonlinear function. We evaluate our method on several representative nonlinear models: the rectified linear unit activation $f(x) = \max(0, x)$, suitable for nonnegative sparse data approximation, the component-wise square $f(x) = x^2$, applicable to probabilistic circuit representation, and the MinMax transform $f(x) = \min(b, \max(a, x))$, relevant for recommender systems. The proposed framework flexibly supports diverse loss functions, including least squares, $\ell_1$ norm, and the Kullback-Leibler divergence, and can be readily extended to other nonlinearities and metrics. We illustrate the applicability, efficiency, and adaptability of the approach on real-world datasets, highlighting its potential for a broad range of applications.

23.
medRxiv (Medicine) 2026-06-11

Dissecting the functional landscape of rare diseases through genomic variation in a heterogeneous cohort of 11,000 patients

Rare diseases (RDs) remain a major diagnostic challenge. Genetic and phenotypic heterogeneity, incomplete knowledge of disease mechanisms, and limitations in variant clinical interpretation leave many patients without a molecular diagnosis. Meanwhile, the growing volume of genomic data generated in clinical practice offers an opportunity to develop data-driven methodologies for exploring disease mechanisms and improving the reanalysis of unsolved cases. We aggregated real-world genomic data from 11,084 unrelated patients with suspected RD. Patients were clinically classified into 122 diseases. We built a multi-disease genomic variant frequency database (FJD-DB), which enabled the development of variant and gene-disease association scores by means of case-control subcohort comparisons across 32 disease groups. Functional enrichment analyses were then used to highlight disease-associated protein domains, pathways, biological processes, and phenotypes. Finally, the resulting knowledge was integrated into a data-driven framework for the guided reanalysis of unsolved RD patients applied to Inherited Retinal Dystrophies (IRD) patients as first use case. FJD-DB contained more than 45 million unique variants, including ~185,000 potentially pathogenic variants. Disease-specific analyses identified disease-associated pathogenic variants and highlighted both established and candidate disease genes. We detected 179 significantly enriched protein domains across 23 diseases, 124 Human Phenotype Ontology terms across 13 diseases, 79 Reactome pathways across 10 diseases, and 72 Gene Ontology biological processes across 8 diseases, revealing highly disease-specific functional signatures. Integration of disease-specific variant, gene, and functional association signals enabled the development of a data-driven framework for guided reanalysis of unsolved RD cases. Applied to more than 1,100 unsolved IRD cases, the framework generated clinically relevant findings in 26 patients, including four molecular diagnoses, seven candidate diagnoses, and 15 cases upgraded from non-informative findings to variants of uncertain significance. Aggregated real-world genomic data can be leveraged to identify disease-associated molecular signals generating novel biological hypotheses. A unified analytical framework provides a scalable strategy for knowledge discovery and guided reanalysis, facilitating the identification of overlooked and potentially novel genetic causes of RDs.

24.
arXiv (CS.CV) 2026-06-25

Tensorion: A Tensor-Aware Generalization of the Muon Optimizer

Common first-order optimizers, such as Adam, implicitly treat each parameter block as an unstructured vector, which disregards the multilinear weight structure present in many modern machine learning models. Recent work has shown that exploiting matrix structure can improve optimization dynamics. A notable example is Muon, which performs steepest descent under the spectral norm constraint. We take the next step and introduce Tensorion, a tensor-aware optimizer that extends Muon's constrained optimization perspective from matrices to higher-order tensors. Tensorion is built around a linear minimization oracle (LMO) over a tensor norm ball. The norm is carefully chosen to balance two objectives: tightly bounding the tensor spectral norm, while still keeping the LMO tractable. This LMO becomes computable because it reduces to operations on adaptively selected unfolding matrices. Notably, when restricted to order-2 tensors (i.e., matrices), Tensorion recovers Muon exactly. Experiments on tensor-based computer vision problems suggest that Tensorion can offer improved convergence behavior and more stable gradient updates compared with Adam-based and existing tensor-aware baselines in the evaluated settings.

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

The Geometry of Admissible Short Selling in Discrete-Time Stochastic Portfolio Theory

arXiv:2606.11191v1 Announce Type: cross Abstract: While discrete-time Stochastic Portfolio Theory (SPT) provides a robust framework for market analysis, existing work on functional generation has predominantly focused on long-only portfolios defined on the entire unit simplex. This paper extends the geometric framework of functional generation to the broader class of bankruptcy-proof long-short portfolios defined on local market state spaces. We establish that, within this admissible setting, pseudo-arbitrage is fully characterized by the concavity of the generating function on the market state space, thereby relaxing the usual global domain requirement. A central contribution of this work is a geometric characterization of the short-selling mechanism. We prove that the presence of short selling is equivalent to the negativity of the maximal concave extension of the generating potential. This phenomenon is linked to the steepness of the logarithmic gradient as the market approaches a zero boundary nested inside the simplex. To systematically exploit this mechanism, we introduce the barycentric scaling transformation, a constructive methodology that maps classical long-only generating functions onto restricted domains to engineer admissible strategies with controlled short-selling exposure. Finally, through the analysis of specific shrunken portfolios, we identify a geometric phase transition: under suitable boundary conditions, admissible strategies exhibit a long-only core and a short-selling region in a qualitative sense (without asserting an exact partition of the state space). This provides a unified geometric perspective on relative arbitrage beyond the long-only constraint.