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01.
arXiv (math.PR) 2026-06-11

Micro-macro population dynamics models of benthic algae with long-memory decay and generic growth

arXiv:2505.04289v4 Announce Type: replace Abstract: Benthic algae as a primary producer in riverine ecosystems develop biofilms on the riverbed. Their population dynamics involve growth and decay processes, the former owing to the balance between biological proliferation and mortality, while the latter to mechanical abrasion because of the transport of sediment particles. Contrary to the assumptions of previous studies, the decay has experimentally been found to exhibit long-memory behavior, where the population decreases at an algebraic rate. However, the origin and mathematical theory of this phenomenon remain unresolved. The objective of this study is to introduce a novel mathematical model employing spin processes to describe microscopic biofilm dynamics. A spin process is a continuous-time jump process transitioning between states 0 and 1, and the continuum limit of these processes captures the long-memory decay and generates generic growth. The proposed framework leverages heterogeneous spin rates, achieved by appropriately superposing spin processes with distinct rates, to reproduce the long-memory decay. Computational simulations demonstrate the behavior of the model, particularly emphasizing rate-induced tipping phenomena. This mathematical model provides a computationally tractable interpretation of benthic algae dynamics and their long-term prediction, relevant to river-engineering applications.

02.
medRxiv (Medicine) 2026-06-22

Genetic and Shared Environmental Influences on Cancer Risk and Cross-Cancer Associations in Nordic Twins

The relative contributions of genetic and shared environmental influences to cancer risk and cross-cancer associations remain poorly understood. We analyzed data from 222,530 same-sex twins from Denmark, Finland, Norway, and Sweden in the Nordic Twin Study of Cancer, including 43,060 incident cancers over a median follow-up of 41.6 years. Using a target trial framework, biometric modeling, and competing-risk adjustment, we estimated familial risk, heritability, and shared environmental contributions across 35 cancer sites. Lifetime cancer risk was 36.5%, increasing to 51.4% in monozygotic (MZ) twins and 45.3% in dizygotic (DZ) twins with an affected co-twin. Overall cancer risk was explained by heritable (28%) and shared environmental (40%) influences. Heritability was highest for prostate (42%), non-melanoma skin (24%), and breast (18%) cancers. Cross-cancer analyses revealed extensive overlap in the genetic and shared environmental factors across sites, consistent with widespread pleiotropy and shared environmental susceptibility. Prostate cancer exhibited the strongest genetic overlap with rectum/anus (12%) and kidney (11%) cancers, whereas co-shared environmental influences were most pronounced for breast-lung (11%), prostate-bladder (11%), and prostate-lung (12%) cancers. These findings show pervasive genetic overlap across cancers at different sites and emphasize the importance of incorporating familial shared environmental exposures into cancer risk prediction and prevention strategies.

03.
medRxiv (Medicine) 2026-06-18

Rare Coding Variants Reveal Distinct Genetic Architectures Across Multidimensional Sleep Phenotypes

Sleep and circadian traits have been widely studied using common variants, but the contribution of rare coding variation remains unclear. We analyzed rare coding variants in 397,065 whole-exome sequenced UK Biobank participants across 36 sleep phenotypes from self-report, diagnoses, sleep medication use and accelerometry, and meta-analyzed results with 171,536 whole-genome sequenced All of Us participants of diverse ancestries, with replication in the Mass General Brigham Biobank (N = 31,275). We identified 260 genes associated with sleep phenotypes, including novel associations with sleep medication use in 29 genes and 24 out of 29 have not previously been reported with any sleep phenotypes. We observed modest but significant rare variant heritability and strong genetic correlations between sleep medication use, insomnia and fatigue. Temporal gene expression trajectory analyses indicate that genes associated with self-reported sleep traits show constant high prenatal expression, whereas genes linked to sleep medication phenotypes exhibit peak expression in the late prenatal period. These findings highlight distinct biological mechanisms captured by different measurement sources of sleep phenotypes and reveal rare-variant-informed targets for therapeutic discovery.

04.
arXiv (CS.CL) 2026-06-16

TMASC: Transmasculine Attitude and Speech Corpus

作者:

We introduce the Transmasculine Attitudes and Speech Corpus (TMASC), a multimodal corpus of 196 transmasculine individuals, including questionnaire responses and 66 audio recordings. The questionnaire includes items exploring the vocal health of transmasculine individuals. The audio recordings include cough and throat-clearing samples, a reading passage, and additional session-specific questions. This paper outlines the development of this corpus and the data collection procedures. To illustrate the utility of this corpus, we present three case studies demonstrating how this crowd-sourced multimodal corpus can be used to support transmasculine individuals. These include the integration of perceptual and acoustic data, the identification of group-level characteristics, and the calibration of acoustic measurements.

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

Physics-Aware Auxiliary Losses Improve Out-of-Distribution Generalization of a GNN Synthesizability Filter

arXiv:2606.12651v1 Announce Type: new Abstract: Machine-learning drug-discovery pipelines increasingly rely on generative models that propose molecules far from the data used to train downstream synthesizability filters. Existing filters (SAScore, SCScore, RAscore, DeepSA) are purely statistical and degrade in exactly this out-of-distribution (OOD) regime. We ask whether cheap, closed-form physical priors, used as auxiliary supervision on a graph neural network (GNN), improve OOD generalization. We add two auxiliary losses to a GINE backbone: a topological complexity regression supervised by the Bertz index, and a strain-energy soft penalty supervised by MMFF94 force-field energy. On a 65,177-molecule corpus (HIV, Tox21, COCONUT) labeled by SAScore thresholds we reproduce a strong in-distribution baseline, then evaluate a 4-way ablation (baseline / +complexity / +strain / +both) on a single-source OOD split (train on drug-like HIV+Tox21, test on COCONUT natural products), repeated over 5 seeds with paired bootstrap confidence intervals. All three physics-aware variants give a small but statistically significant OOD improvement over the baseline (mean OOD AUC 0.9774): +complexity Delta = +0.0060 (95% CI [+0.0023, +0.0102]), +strain Delta = +0.0032 ([+0.0008, +0.0052]), +both Delta = +0.0066 ([+0.0038, +0.0093]); every interval excludes zero, and the combination is best. The variants are indistinguishable in-distribution, so the effect is visible only under OOD evaluation. We are explicit that the effects are modest, and we report a cautionary methodological finding: a single-seed version of this experiment produced a qualitatively different (non-monotone) story that did not survive multi-seed evaluation.

07.
arXiv (CS.LG) 2026-06-15

NeST: Neuron Selective Tuning for LLM Safety

arXiv:2602.16835v2 Announce Type: replace-cross Abstract: Safety alignment is essential for the responsible deployment of Large Language Models (LLMs). Yet, existing approaches often rely on heavyweight fine-tuning that is costly to update, audit, and maintain across model families. Full fine-tuning incurs substantial computational and storage overhead, while parameter-efficient methods, e.g., Low-Rank Adaptation (LoRA), trade efficiency for inconsistent safety gains and sensitivity to design choices. Safety intervention mechanisms reduce unsafe outputs without modifying model weights, but do not directly shape or preserve the internal representations that govern safety behavior. We present NeST, a Neuron-Selective Tuning framework for efficient post-hoc safety alignment. NeST identifies safety-relevant feed-forward neurons via activation probing on vanilla harmful and benign prompts, clusters neurons with similar activation profiles, and trains shared cluster-level updates while freezing the rest of the model. Importantly, NeST is trained only on vanilla malicious prompts, without using jailbreak-specific attack data, yet generalizes robustly to diverse jailbreaks. The learned updates are then folded into the original weights, incurring no inference-time overhead. Evaluated on 14 open-weight language and multimodal models, NeST outperforms lightweight baselines and approaches full fine-tuning robustness with significantly fewer trainable parameters. On text-only models, NeST reduces average jailbreak attack success rate from 44.5% to 1.1% while training only 0.4M parameters on average. Across multimodal settings, it reduces ASR from 55.3% to 1.1%, and for downstream fine-tuned variants, it restores safety by reducing ASR from 53.8% to 0.8%. These results show that robust, maintainable safety alignment can be achieved by concentrating adaptation on localized, functionally coherent safety structures.

08.
arXiv (quant-ph) 2026-06-11

Entanglement preservation and Clauser-Horne nonlocality in electromagnetically induced transparency quantum memories

arXiv:2507.15453v4 Announce Type: replace Abstract: Entanglement preservation in noisy quantum memories represents a central challenge in quantum information science. While experiments have shown that electromagnetically induced transparency (EIT) memories can store entangled photons, a quantitative theoretical analysis of whether nonlocal quantum correlations can survive storage loss induced by ground-state decoherence remains limited. Here we combine the dark-state polariton formalism with a reduced density-operator treatment to derive an EIT-specific effective pure-loss description for the retrieved photonic state in the ground-state-decoherence-limited regime. The analysis reveals that decoherence transforms an initially pure Bell state into a mixed state with a vacuum component and predicts a protocol-dependent storage-efficiency benchmark of 89.7% for violating the chosen unconditional Clauser-Horne (CH) inequality. Above this benchmark, the retrieved photonic state violates the CH inequality without post-selection, whereas below it, this unconditional CH violation is no longer obtained. This framework provides a quantitative theoretical description of entanglement retention, retrieved photonic density operators, and protocol-dependent Bell-test benchmarks in EIT quantum memories.

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

Scaling LLM Reasoning from Minimal Labels: A Semi-Supervised Framework with a Lightweight Verifier

For the development of Large language models (LLMs), recent approaches to generating pseudo intermediate reasoning have shown remarkable progress. But they typically rely on large numbers of correctly annotated answers to assess reasoning quality. This paper presents a semi-supervised framework that scales reasoning learning from minimal supervision, turning reasoning verification itself into a data creation mechanism. We train a lightweight reasoning-correctness classifier on only a few labeled samples, which judges whether intermediate reasoning traces generated by an LLM are valid. Furthermore, an entropy-based confidence threshold filters out unreliable samples, and the remaining high-confidence reasoning traces are used to fine-tune the model. Experiments on Verifiable Math Problems (Orca-Math subset) and Question Answering on Image Scene Graphs (GQA) with Visual Programming show that our method achieves accuracy comparable to using 10-15x more labeled data. Ablation analyses confirm that both the classifier and entropy filtering are essential for scalable and noise-resistant pseudo-labeling. By replacing expensive answer-level supervision with lightweight reasoning verification, our method provides a practical path toward constructing large-scale reasoning resources and paves the way for future autonomous reasoning systems that learn from minimal human input.

10.
arXiv (CS.CL) 2026-06-11

Gumbel-BEARD: Automatic Layer Selection for Self-Supervised Adaptation of Whisper in Low-Resource Domains

Speech foundation models often struggle in low-resource domains due to domain mismatch and data scarcity. We propose Gumbel-BEARD, a domain adaptation framework that automates Whisper encoder layer selection via an end-to-end trainable hard Gumbel-Softmax selector. It enables self-supervised adaptation with a BEST-RQ objective that dynamically adapts to target acoustic characteristics without manual tuning. Experiments on the MyST child speech corpus demonstrate efficiency and scalability: with 10 h of labeled data for fine-tuning, our method matches a fully supervised baseline trained on the complete 133 h labeled set. We establish new state-of-the-art word error rates (WERs) of 8.21% using Whisper-medium on MyST and 11.06% using Whisper-small on the OGI Spontaneous dataset. Evaluation on CORAAL further confirms robustness to adult dialectal domain shifts, with up to 6% relative WER reduction, highlighting the generalizability of our approach to diverse low-resource conditions.

11.
arXiv (CS.CV) 2026-06-16

InfoGeo: Information-Theoretic Object-Centric Learning for Cross-View Generalizable UAV Geo-Localization

Cross-view geo-localization (CVGL) is fundamental for precise localization and navigation in GPS-denied environments, aiming to match ground or UAV imagery with satellite views. Existing approaches often rely on global feature alignment, but they suffer from substantial domain shifts induced by varying regional textures and weather conditions. This issue becomes even more pronounced in UAV-based scenarios, where the broader perspective inevitably introduces dense, fine-grained objects, creating significant visual clutter. To address this, we draw inspiration from Object-Centric Learning (OCL) and propose InfoGeo, an information-theoretic framework designed to enhance robustness and generalization. InfoGeo reformulates the optimization as an information bottleneck process with two core objectives: (i) maximizing view-invariant information by aligning the object-centric structural relations across views, and (ii) minimizing view-specific noisy signals through cross-view knowledge constraints. Extensive evaluations across diverse benchmarks and challenging scenarios demonstrate that InfoGeo significantly outperforms state-of-the-art methods.

12.
arXiv (CS.CV) 2026-06-19

DeepForestVisionV2: Ecology-Driven Taxonomy Expansion for Camera-Trap Monitoring in African Tropical Forests

Camera-trap monitoring in African tropical forests increasingly extends beyond closed-canopy interiors to riverbanks, clearings, and park edges. Among available open tools for African forest camera-trap classification, DeepForestVision is the only one providing a matched offline workflow for both photographs and videos, and previous work showed that it outperformed other available baselines on a comparable benchmark. However, it was designed for closed-canopy, ground-level forest interiors and uses a 35-class prediction space that becomes too coarse when deployments encounter arboreal primates, birds, semi-aquatic taxa, or human-associated confounders such as livestock. We present DeepForestVisionV2, an ecology-driven expansion from 35 to 64 prediction classes (61 animal classes plus human, vehicle, and blank) designed to address three recurrent deployment gradients: vertical stratification, scene openness, and anthropogenic interfaces. DeepForestVisionV2 retains the same offline workflow and is trained on 1,535,010 photographs and 243,354 videos from multi-country African tropical-forest projects. Evaluation combines a cross-country cropped-photo validation set, used to assess robustness across sites and camera-trap settings, with three held-out Uganda video benchmarks spanning the targeted gradients. On the validation set, DeepForestVisionV2 reaches 0.86 accuracy, 0.82 macro-F1, and 0.81 balanced accuracy. On the deployment benchmarks, it preserves or improves baseline accuracy despite its harder classification task, while increasing the number of identified taxa from 22 to 29 in forest-interior videos and from 4 to 9 at riverbanks. In the park-edge use case, it raises accuracy from 0.62 to 0.86 and reduces false alarms from 11 to 0. These results show that DeepForestVisionV2 materially improves field utility while preserving robustness across sites, habitats, and camera-trap settings.

13.
arXiv (CS.LG) 2026-06-18

MOLAR: Learning Multimodal Molecular Representations from Noisy Labels

arXiv:2606.18390v1 Announce Type: new Abstract: Motivation: Noisy labels are a common challenge in molecular property prediction because molecular annotations are often obtained from assays, curated databases, or weak annotation pipelines rather than directly observed clean biological states. Treating recorded labels as reliable supervision can cause models to memorize corrupted observations and learn misleading molecular evidence. In multimodal molecular representation learning, this issue can be amplified by graph-text fusion or alignment, which may propagate label-induced errors across modalities. Results: We propose MOLAR, a noise-aware framework for learning multimodal molecular representations from noisy labels. MOLAR separates latent clean-property inference from recorded-label observation: graph and text views contribute residual evidence to a clean-property distribution, and a categorical label-observation channel maps this distribution to recorded labels for training. This formulation derives posterior label reliability and modality-specific molecular evidence from the model. Experiments on naturally noisy molecular benchmarks and controlled label-flipping benchmarks show that MOLAR consistently outperforms representative baselines. Visualization analyses further show that MOLAR provides interpretable reliability and modality-evidence diagnostics.

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

Deep-Unfolded Coordination

arXiv:2606.19920v1 Announce Type: cross Abstract: Distributed optimization is a highly scalable and structurally transparent technique to solve multi-agent robotics problems; however, such methods often suffer from the need for highly-specialized, problem-specific hyperparameter tunings. In this work, we propose Deep Coordinator, a deep-unfolding framework that learns to dynamically adjust the hyperparameters of ADMM-DDP, a popular distributed solver for robotics tasks, at solve-time in response to optimizer performance. Our architecture consists of unrolling a fixed number of ADMM-DDP iterations into a neural network with learnable functions between layers mapping the optimizer state to the next hyperparameters. To the best of our knowledge, Deep Coordinator is the first deep-unfolding framework to adapt the penalty parameters of a non-convex optimizer at solve-time; we show that the mainstream supervised approach can yield degenerate solutions when training such models, and propose an unsupervised learning scheme. On simulations with fleets of cars and quadrotors, Deep Coordinator produces trajectories of comparable quality 6.18-9.44x faster than conventional solvers. Furthermore, Deep Coordinator retains its performance benefits when deployed to systems up to 8x larger than trained on.

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

Probing Dec-POMDP Reasoning in Cooperative MARL

arXiv:2602.20804v2 Announce Type: replace Abstract: Cooperative multi-agent reinforcement learning (MARL) is typically framed as a decentralised partially observable Markov decision process (Dec-POMDP), a setting whose hardness stems from two key challenges: partial observability and decentralised coordination. Genuinely solving such tasks requires Dec-POMDP reasoning, where agents use history to infer hidden states and coordinate based on local information. Yet it remains unclear whether popular benchmarks actually demand this reasoning or permit success via simpler strategies. We introduce a diagnostic suite combining statistically grounded performance comparisons and information-theoretic probes to audit the behavioural complexity of baseline policies (IPPO and MAPPO) across 37 scenarios spanning MPE, SMAX, Overcooked, Hanabi, and MaBrax. Our diagnostics reveal that success on these benchmarks rarely requires genuine Dec-POMDP reasoning. Reactive policies match the performance of memory-based agents in over half the scenarios, and emergent coordination frequently relies on brittle, synchronous action coupling rather than robust temporal influence. These findings suggest that some widely used benchmarks may not adequately test core Dec-POMDP assumptions under current training paradigms, potentially leading to over-optimistic assessments of progress. We release our diagnostic tooling to support more rigorous environment design and evaluation in cooperative MARL.

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

Extracting Semantics: LLM-Guided Automatic Population of Robot Ontology from URDF

arXiv:2606.17073v1 Announce Type: cross Abstract: While commonsense knowledge may suffice for virtual agents, embodied robots interacting with humans require grounded and semantically rich representations of both their environment and their own physical embodiment. In cognitive robotics, ontologies are effective for integrating such heterogeneous knowledge to enable explainable reasoning, even during continuous knowledge updates. Yet, their manual construction remains a bottleneck. We present a preliminary approach for the automatic generation of robot semantic abstractions by transforming Unified Robot Description Format (URDF) models into populated ontologies. Although URDF files provide structural and kinematic descriptions, their identifiers often require commonsense interpretation to recover meaningful semantics, a task at which Large Language Models (LLMs) excel. Our pipeline leverages LLMs to infer semantic relationships by prompting them with concepts from an existing ontology, ensuring the final classification remains aligned with the formal model. To improve reliability, the pipeline combines majority voting across multiple LLM queries along with syntactic and schema-level validation to ensure that generated outputs conform to the expected representation format and ontology constraints. We evaluate the approach on multiple robot descriptions and discuss the generated abstractions. Initial results indicate that the proposed method can effectively bridge the gap between low-level robot descriptions and the structured, grounded knowledge representations required for human-robot interaction.

17.
arXiv (quant-ph) 2026-06-16

Experimental Observation of Dynamical Phase Transitions in a Dephased Photonic Quantum Walk

arXiv:2606.15935v1 Announce Type: new Abstract: Dynamical phase transitions in open quantum systems govern how non-equilibrium states relax toward a stationary state. We study these transitions experimentally using a discrete-time photonic quantum walk on a three-node graph. A tunable synthetic gauge flux and calibrated dephasing allow us to control time-reversal symmetry and the detailed balance properties of the effective Markovian dynamics. With detailed balance, we observe a first-order dynamical phase transition marked by a crossing of real Liouvillian eigenvalues. When detailed balance is broken, we observe a second-order dynamical phase transition at an exceptional point where eigenvalues and eigenvectors coalesce. By progressively reducing the dephasing strength, we track the crossover toward the quantum-coherent regime and determine that the transitions persist down to a finite threshold. Our results link Liouvillian spectral topology to relaxation criticality and demonstrate a controllable platform for engineered dissipative dynamics.

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

Expanding SPHERE-JEPA: A Family of Statistical Regularizers for the Hypersphere

arXiv:2606.17603v1 Announce Type: new Abstract: In Self-Supervised Learning (SSL), preventing representation collapse by explicitly enforcing a uniform distribution on the unit hypersphere has proven to be effective. However, current frameworks typically rely on sliced statistical regularizers such as SIGReg (used in LeJEPA) and SUSReg (used in SPHERE-JEPA), which approximate this continuous objective via Monte Carlo sampling along random 1D directions. This stochasticity injects projection variance into the training gradients, destabilizing optimization, and hindering convergence. In this work, we first show that analytically integrating out these random projections natively yields a deterministic Maximum Mean Discrepancy (MMD), bypassing the variance of sliced methods. Motivated by this equivalence, we formulate full-dimensional objectives for MMD, Kernel Stein Discrepancy (KSD), and Kullback-Leibler (KL) divergence directly on the sphere to enforce a uniform distribution. To prevent spatial bias, we equip these tests with rotationally invariant kernels constructed via spectral theory, systematically evaluating two canonical families: smooth exponential decay (Heat) and strict frequency cutoff (Bandlimited) filters. Empirically, removing projection-induced noise results in more stable optimization, faster convergence, and consistent improvements over stochastic sliced regularizers on ImageNet and Galaxy10. Furthermore, we reveal that the choice of the statistical test shapes the geometry of the learned latent space: MMD and KSD favor locally clustered organization suitable for object-centric domains, whereas the continuous KDE-based KL divergence promotes fine-grained instance separation, yielding the strongest results on unclustered procedural texture retrieval.

19.
arXiv (CS.CV) 2026-06-11

Tac-DINO: Learning Vision-Tactile Features with Patch Alignment

Touch is the primary medium through which humans interact with the environment. Currently, tactile learning mainly focuses on image-level pretraining or alignment. However, tactile signals correspond to local object contact, while research into scale alignment and holographic matching remains limited and proper datasets and benchmarks also lack. To bridge this gap, we first construct a data collection system to acquire a large-scale tactile dataset, with over 20 K tactile contacts from 505 real-world objects. Building on this dataset, we design a Vis-Tac Holographic Matching Benchmark to evaluate vision-tactile local-to-global alignment ability. Then we propose Vision-Tactile Patch Alignment (VTPA) methods for vision-tactile representation learning. Experiments demonstrate that these exceed the performance of methods without alignment and align with whole-object images.

20.
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.

21.
arXiv (CS.LG) 2026-06-17

Multi-Source Cybersecurity Logs: An ATT&CK-Labeled Dataset and SLM Evaluation

arXiv:2606.18190v1 Announce Type: cross Abstract: Multi-stage cyberattacks span system, network, and browser logs. Detecting them requires correlating events across all three sources. Machine learning methods can learn these cross-source patterns, but they need labeled multi-source data. Existing public datasets fall short. Network-only datasets such as CICIDS and UNSW-NB15 miss host and browser activity. Host-focused datasets such as LMDG and CICAPT-IIoT lack browser telemetry. ATLAS includes all three sources but labels events only as malicious or benign, without MITRE Adversarial Tactics, Techniques, and Common Knowledge (ATT&CK) technique granularity. No public dataset combines all three sources with per-entry ATT&CK technique labels. We close the gap by building a multi-source log dataset of 870 sessions (70 attack, 800 benign) and approximately 2.3 million events. We captured system, network, and browser activity simultaneously on Windows endpoints. We labeled malicious events with ATT&CK technique IDs, covering 12 tactics and 53 techniques. We generated all attack data using real tools, including Remote Access Trojan (RAT), Command and Control (C2) tunnels, and cloud exfiltration. To demonstrate learnability, we fine-tuned three Small Language Models (SLMs) (Qwen2.5-1.5B, Llama-3.2-3B, Phi-4-Mini) using Low-Rank Adaptation (LoRA). We compared each against its base variant across ten metrics on two tasks: chunk classification and ATT&CK technique identification. Fine-tuning improved every model on every metric. Chunk classification accuracy rose from approximately 8% in the base variants to between 90% and 97% after fine-tuning. Technique identification remained challenging, with the best exact-match accuracy at 42%, although high partial-match scores show the models captured most of the underlying reasoning.

22.
PLOS Computational Biology 2026-05-29

Structural and dynamic basis of NOD2 tandem CARD association and NOD1/2–RIP2 signaling complexes

by Jitendra Maharana, Aritra Bej, Debasish Biswal, Debashis Panda, Arjun Sharma NOD1 and NOD2, founding members of the NOD-like receptor (NLR) family, play a crucial role in host defense against bacterial infections. Recognition of peptidoglycan-derived ligands triggers ATP-dependent oligomerization of the NACHT domain, exposing the CARD domains that recruit the adaptor protein RIP2 via CARD–CARD interactions to activate the NF-κB signaling cascade. Although NOD1/2-RIP2 interactions and RIP2CARD filament assembly are established, the precise interfaces that stabilize hetero–CARD filaments remain poorly defined. Here, we integrate in silico structural modeling with molecular dynamics (MD) simulations to elucidate structurally compatible arrangements of NOD1–RIP2 and NOD2–RIP2 hetero–CARD filaments. Our results reveal that NOD1CARD subunits form a structurally compatible homomeric scaffold via canonical (type-I–III) interfaces, accommodating multiple tiers of RIP2CARD rings at both filament termini. Meanwhile, the NOD2 tandem CARDs adopt multiple discrete conformations, reflecting a more intricate structural mechanism. In stable filament conformations, tandem CARDs converge at the type-II interface, with RIP2CARD rings stacking onto CARDa (top-down) and CARDb (bottom-up) interfaces, highlighting the structural role of NOD2CARDb in RIP2-mediated CARD–CARD interaction. In silico mutagenesis, involving charge-reversal and alanine scanning of key interfacial residues, disrupts NOD1–RIP2 and NOD2–RIP2 interactions at both top-down and bottom-up interfaces, leading to rapid interface destabilization within 0.1–0.4 μs of simulation. Together, these results reveal conserved and receptor-specific mechanisms governing NOD1/2–RIP2 CARD–CARD interactions and provide deeper structural and dynamic insights into the complex structural mechanisms for NLR-mediated inflammatory signaling.

23.
medRxiv (Medicine) 2026-06-19

Reassessing Instrument Strength in Two-Sample Mendelian Randomization Analysis

Mendelian randomization (MR) analysis is widely used to estimate causal relationships between risk factors and outcomes of interest. Two-sample MR approaches have gained increasing attention in genetic epidemiology due to the growing availability of Genome-Wide Association Study (GWAS) summary statistics from public databases. A critical step in two-sample MR is the selection of genetic variants as instrumental variables (IVs). Although genome-wide significant variants are typically preferred, the inclusion of variants with weaker association p-values is considered, as they may potentially improve power through an increased instrument number of instruments, while they may introduce weak instrument bias and attenuate effect estimates towards the null. Our simulation results show that even modest levels of pleiotropy substantially increase the variability of causal effect estimates, while the inclusion of weak IVs does not substantially affect the direction and variability of causal effect estimates in most cases. In real data analyses, we used two released versions of FinnGen GWAS summary statistics with different sample sizes as exposure GWASs to assess the influence of weak IVs. Here, the inclusion of IVs with higher exposure-association p-values resulted in weakened estimated effect sizes, particularly when the exposure GWAS sample size was small. These findings suggest that incorporating weak IVs is reasonable when the exposure GWAS sample size is large, but it poses a risk of falsely concluding null associations when the exposure GWAS sample size is small.

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

Beyond Classification: A Cough Regression Benchmark for Respiratory Acoustic Foundation Models

arXiv:2606.15436v1 Announce Type: cross Abstract: Respiratory acoustic foundation models (FMs) excel at cough classification, yet their ability to predict continuous health quantities from cough audio remains largely unexplored, despite the clinical value of passive age, BMI, and disease probability estimation in settings where physical measurements are unavailable. We introduce the multi-model, multi-target cough regression benchmark evaluating five FMs (OPERA-CT, OPERA-CE, OPERA-GT, HeAR, M2D+Resp) across six targets on three datasets under subject-disjoint protocols, comparing linear, MLP-small, and full MLP regression heads. MLP-small beats the mean-predictor baseline on all tasks and linear probing in 23 of 30 model x task cases, with full MLP overfitting on small clinical data but recovering on larger sets, revealing a dataset size x head-capacity trade-off. HeAR leads within-dataset age regression on Coswara (9.12 yr MAE); its CIDRZ result is excluded from headline claims owing to possible HeAR-CIDRZ pretraining overlap. OPERA-GT is favored over OPERA-CT on age in all three datasets, with the CIDRZ margin within seed variance, extending a generative-pretraining advantage from breath to cough. HeAR and M2D+Resp reach near-full performance at N = 50 samples while OPERA models require N = 400. Cross-dataset transfer is strongly asymmetric as large diverse data generalises to small clinical populations (CoughVID to CIDRZ: -0.17 yr) but not vice versa (CIDRZ to Coswara: +2.43 yr, +26.6%).

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

PaperJury: Due-Process Review for Bounded LaTeX Revision

Pre-submission hardening of human-authored LaTeX computer science papers differs from drafting assistance because it requires adversarial whole-paper review, explicit no-fix outcomes, and bounded artifact-safe revision. Existing writing assistants, critique generators, and judge-centered loops lack durable issue identity across rounds, deterministic routing from critique to adjudication, and manuscript control that can reject invalid concerns or defer author-dependent ones. We present PaperJury, a closed-loop review-verdict-revise-verify system built on a deterministic-versus-semantic split: deterministic orchestration manages decomposition, a frozen claim spine, a durable ledger, routing, stopping, and exact-once patch application, while semantic agents are limited to bounded review, judgment, and repair. PaperJury combines bounded holistic review, contestability-based routing, a due-process trial, and risk-proportional guard chains for anchor-bounded edits, yielding terminal outcomes of invalid-drop, valid-fixable, and author-required. In a two-arm expert-review evaluation on held-out Vision, natural language processing, and machine learning papers against four baselines, we assess issue quality, verdict and routing quality, edit safety, convergence behavior, and cost, supporting the thesis that load-bearing safety and completion logic should reside in deterministic orchestration rather than model discretion. PaperJury is available at https://github.com/u7079256/paperjury.