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01.
bioRxiv (Bioinfo) 2026-06-19

Children's DNA Methylation and Family Dynamics in a Congo Basin Subsistence Community: Links with Parental Conflict and Fathers' Caregiving

Family environments may contribute to children's long-term health through biological processes, including epigenetic regulation such as DNA methylation (DNAm). However, most studies in this area focus on Euro-American populations while also rarely including fathering data. The current study investigated children's blood DNAm associations with positive (father caregiving) and negative (parental conflict) family dynamics in a smaller-scale subsistence society living in the Congo Basin rainforest. We measured DNAm from dried blood spots of 54 children (mean age=8.48 years) and conducted three epigenome-wide association studies aimed at discovering differential co-methylated regions (CMRs) associated with family dynamics. Via path models, we investigated the health implications and shared contribution of family factors of the identified CMRs. Differential DNAm associated with family dynamics was localized to genes related to stress, immunology, development, and aging, thus possibly linking to children's physical health and were simultaneously connected to other family factors such as number of siblings. Our findings suggested similarities in biological embedding of family factors across socio-ecologically diverse contexts.

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

NAMESAKES: Probing Identity Memorization in Text-to-Image Models

Text-to-image (T2I) models generate realistic likenesses of some individuals when prompted with their names, raising privacy concerns. However, distinguishing whether a generated face is memorized or fabricated currently requires ground-truth photos, access to training data, or white-box access to model internals, limiting applicability. We introduce a fully black-box behavioral probe that distinguishes between these regimes while requiring no reference photos or prior knowledge of training data. To benchmark this task, we present the NAMESAKES dataset of over one thousand names and faces of public figures spanning a wide range of fame levels, along with perturbed, less famous names. Experiments on state-of-the-art T2I models show that our probe substantially predicts identity memorization and separates memorized from unrecognized names, with further insights into differences across model families.

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

The Metric Picks the Winner: Evaluation Choice Flips Model Rankings for Drug-Response Prediction in Unseen Chemistry

arXiv:2606.12639v1 Announce Type: new Abstract: Predicting how a cell's transcriptome responds to a drug it has never seen is a core, hard problem in computational cell biology: recent benchmarks show complex models often fail to beat trivial baselines once test compounds are held out by chemistry. We study one cell line and assay, THP-1 cells profiled by DRUG-seq, scored by the active-compound weighted MSE(wMSE) of the VCPI prediction contest. We propose a staged approach: dumb baselines (untreated control and mean training-compound response) that the field keeps failing to beat; non-parametric retrieval (a Tanimoto-weighted average of a held-out compound's nearest training compounds); and a fusion stage combining a frozen chemistry embedding with retrieval-support features to predict the residual over the mean, with an uncertainty head and gene programs. On the released VCPI THP-1 drug-seq data (14,026 training compounds), under a Bemis-Murcko scaffold split, the model ranking inverts depending on the metric. Under an inverse-variance per-gene proxy, a regularized linear regression on Morgan fingerprints appears to win over the deep models, retrieval, and ChemBERTa – the textbook "simple baselines win" result. But under the contest's true active-set metric (per-(gene, compound) Mejia weights, validated against the official scorer; mean baseline 0.535 vs the organizers' 0.507 reference), that reverses: the deep models win, our fusion decoder significantly beats the linear fingerprint baseline (-0.012 wMSE, paired bootstrap p < 10^-4), and the proxy's winner becomes the worst chemistry-aware predictor. Picking the metric picks the winner – to our knowledge the first demonstration on real held-out drug chemistry of the metric-calibration effect established largely on genetic perturbation. We release a reproducible pipeline wired to the official scorer that emits a valid submission over the real 1064 x 12,995 grid.

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

Policy Regret for Embedding Model Routing: Contextual Bandits with Low-Rank Experts

arXiv:2606.14929v1 Announce Type: cross Abstract: Modern recommendation systems increasingly rely on dynamically routing diverse queries to multiple embedding models. Despite its practical significance, this problem remains poorly understood under realistic conditions like adversarial queries, bandit feedback, and limited observability of models. We formalize embedding model routing as an adversarial contextual linear bandit with low-rank experts, where contexts are queries, actions are items, and experts are the embedding models working on low-rank latent representation spaces. We first establish that standard regret notions suffer from structural misspecification or statistical intractability, and we identify a log-quadratic policy class that is expressive enough to capture query-dependent model routing, yet structured enough to allow efficient online learning. Second, we propose a policy gradient algorithm called Hypentropy Policy Gradient (HPG). It provably adapts to the unknown low-rank structure under incomplete information and attains $\tilde{\mathcal O}(s\sqrt{M T})$ linearized policy regret – where $s, M$, and $T$ are the intrinsic rank of the experts, the number of models, and the number of rounds – thus avoiding a curse of dimensionality. Finally, we also provide an computationally efficient and parameter-free implementation of HPG.

05.
arXiv (CS.AI) 2026-06-19

Modeling Day-Long ECG Signals to Predict Heart Failure Risk with Explainable AI

arXiv:2601.00014v2 Announce Type: replace-cross Abstract: Heart failure (HF) affects 11.8% of adults aged 65 and older, reducing quality of life and longevity. Preventing HF can reduce morbidity and mortality. We hypothesized that artificial intelligence (AI) applied to 24-hour single-lead electrocardiogram (ECG) data could predict the risk of HF within five years. To research this, the Technion-Leumit Holter ECG (TLHE) dataset, including 69,663 recordings from 47,729 patients, collected over 20 years was used. Our deep learning model, DeepHHF, trained on 24-hour ECG recordings, achieved an area under the receiver operating characteristic curve of 0.80 that outperformed a model using 30-second segments and a clinical score. High-risk individuals identified by DeepHHF had a two-fold chance of hospitalization or death incidents. Explainability analysis showed DeepHHF focused on arrhythmias and heart abnormalities. This study highlights the feasibility of deep learning to model 24-hour continuous ECG data, capturing paroxysmal events essential for reliable risk prediction. Artificial intelligence applied to single-lead Holter ECG is non-invasive, inexpensive, and widely accessible, making it a promising tool for HF risk prediction.

06.
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.

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

Free Heavy-Tailed Lunch for Muon: A Theoretical Justification of Empirical Success

arXiv:2606.14560v1 Announce Type: cross Abstract: Non-Euclidean optimisation methods with matrix-valued updates, such as Muon and Scion, have recently shown strong empirical performance for training Transformer models, yet their theoretical advantages over Euclidean methods remain poorly understood. We address this gap in the heavy-tailed non-convex regime, where stochastic gradients have bounded $p$-th central moments, $p \in (1,2]$. We show that certain non-Euclidean methods achieve optimal sample complexity under stronger stationarity measures, while Euclidean methods incur additional dimension-dependent costs. As a consequence, for $m \times n$ matrices, Muon finds an $\varepsilon$-stationary point in nuclear norm within $\mathcal{O}\left(\min\{m, n\} \frac{\Delta_1 L}{\varepsilon^2} \left(\frac \sigma \varepsilon \right)^{\frac p {p-1}}\right)$ samples, absorbing heavy-tailed noise without extra dimension dependence, unlike Euclidean methods. We further prove this sample complexity, including its dimension dependence, is optimal for all first-order methods under nuclear-norm stationarity. Experiments on large language models support our theory. Surprisingly, our results suggest that other Schatten geometries beyond the spectral geometry of Muon can perform competitively in certain settings.

08.
arXiv (CS.CV) 2026-06-15

Memento: Reconstruct to Remember for Consistent Long Video Generation

Long-form video generation requires recurring subjects to remain consistent across various shots, viewpoints, motions, and scene transitions. Existing temporal decomposition methods improve scalability by generating videos shot by shot. However, they mainly focus on optimizing plausible next-shot continuations without verifying whether the historical memory preserves identity-critical subject evidence. Consequently, as generation proceeds, recurring subjects may be diluted, overwritten, or forgotten. In this paper, we propose Memento, a subject-reconstruction-guided framework that treats subject preservation as an explicit identity grounding problem, based on the premise that a memory bank faithfully preserving a subject should support reconstructing that subject from memory alone. Specifically, Memento jointly trains autoregressive next-shot generation with memory-based subject reconstruction, recovering target appearances using historical memory and global story captions. To disentangle long-range subject evidence from short-range cues, Memento introduces a dual-query memory mechanism, where one query retrieves identity-relevant memory and the other selects short-context keyframes for coherent continuation. Additionally, a subject-aware cinematic data pipeline provides precise reconstruction supervision via consistent, pronoun-free subject descriptions. Experiments demonstrate that Memento achieves state-of-the-art performance in long-term subject consistency, cross-shot coherence, and visual quality.

09.
arXiv (CS.CL) 2026-06-11

Toward Preference-aligned Large Language Models via Residual-based Model Steering

Preference alignment is a critical step in making Large Language Models (LLMs) useful and aligned with (human) preferences. Existing approaches such as Reinforcement Learning from Human Feedback or Direct Preference Optimization typically require curated data and expensive optimization over billions of parameters, and eventually lead to persistent task-specific models. In this work, we introduce Preference alignment of Large Language Models via Residual Steering (PaLRS), a training-free method that exploits preference signals encoded in the residual streams of LLMs. From as few as one hundred preference pairs, PaLRS extracts lightweight, plug-and-play steering vectors that can be applied at inference time to push models toward preferred behaviors. We evaluate PaLRS on various small-to-medium-scale open-source LLMs, showing that PaLRS-aligned models achieve consistent gains on mathematical reasoning and code generation benchmarks while preserving baseline general-purpose performance. Moreover, when compared to models aligned with DPO and SimPO, they perform better with great time-savings. Our findings highlight that PaLRS offers an effective, much more efficient and flexible alternative to standard preference optimization pipelines, offering a training-free, plug-and-play mechanism for alignment with minimal data.

10.
arXiv (quant-ph) 2026-06-11

Single Photon Cross-Phase Shifts Can Be Enhanced by Localization in both Frequency and Time

arXiv:2606.11516v1 Announce Type: new Abstract: Single-photon optical nonlinearities face a fundamental trade-off: maximum nonlinearity requires both spectral resonance (narrow bandwidth) and high peak intensity (short duration), constraints that are incompatible due to the time-energy uncertainty relation. We demonstrate experimentally that this limitation does not need to exist in cases involving post-selection. We measure a cross-phase shift (XPS) produced by a resonant photon from a narrow-band source that is first transmitted through a cold atomic cloud and then localized in time through detection. The peak size of this XPS is greatly enhanced compared to that of Gaussian single-photon-level pulses without post-selection, benefiting from the narrow bandwidth of the resonant prepared state and the high intensity of the post-selected state simultaneously. We measure enhancements in the peak XPS of 6$\pm$1 at an optical depth (OD) of 2.4$\pm$0.1, and our results are in qualitative agreement across a range of optical depths with the recently developed weak value theory of atomic excitation [Thompson et al., APL Quantum 2, 036108 (2025)] for such post-selected photons. This work uncovers new consequences of having simultaneous knowledge of frequency and time, raising new foundational questions about how a particle behaves, and interacts with other systems, when its preparation and post-selection are non-commuting.

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

Which Models Are Our Models Built On? Auditing Invisible Dependencies in Modern LLMs

Modern LLM training pipelines increasingly rely on other models to generate data, filter corpora, judge outputs, and guide development decisions. These dependencies are recursive: a model may depend on an upstream artifact whose own dependencies are documented only in separate releases and artifacts. As a result, the full dependency structure is fragmented across heterogeneous public artifacts, with complexity and recursive depth far outpacing humans' ability to trace. We introduce ModSleuth, an agentic system that recursively reconstructs LLM dependency graphs from public artifacts with source-grounded evidence. We find that the primary challenge is no longer information extraction, but defining what constitutes a dependency and reconciling artifact references across inconsistent documentation. We address these challenges through a formalization that distinguishes direct and indirect dependencies, represents heterogeneous pipeline roles through operation-centered relationships, and resolves artifact identities across names, versions, and repositories. Applying ModSleuth to four public-artifact-rich LLM releases, we recover 1,060 source-verified dependencies and construct large-scale dependency graphs of modern LLM development. These graphs reveal multi-hop license obligations, train-evaluation coupling, discrepancies between released and training-time artifacts, and documentation inconsistencies that would otherwise be difficult to uncover. We release ModSleuth and the resulting dependency graphs to support transparent analysis of the increasingly complex ecosystems underlying modern LLMs.

12.
arXiv (quant-ph) 2026-06-16

Magnetic control of an exciton-polariton condensate in a van der Waals magnet

arXiv:2506.06010v3 Announce Type: replace-cross Abstract: Quasiparticle condensates are among the most spectacular solid-state manifestations of quantum physics. Coupling macroscopic real-space wavefunctions to additional degrees of freedom, such as the electron spin, would add valuable control knobs for quantum applications. While creating spin-carrying superconducting condensates has attracted enormous attention, man-made condensates of light-matter hybrids known as exciton-polaritons have lacked an analogous spin-based perspective. Here we open a new door by demonstrating magnetically tunable exciton-polariton condensation in the van der Waals magnet CrSBr. Under photoexcitation, CrSBr microwires embedded in an optical cavity show the hallmarks of polariton condensation: a dramatic increase of the emission intensity from an excited laterally confined polariton state by multiple orders of magnitude, spectral narrowing of the emission line, and a continuous shift of the peak energy. Interferometry evidences an increase in spatial and temporal coherence. Owing to the strong coupling between the spin order and excitonic correlation, the energy of the condensate can be tuned by up to 10.5 meV by an external magnetic field of only 2 Tesla. Our results establish CrSBr microcavities as a powerful platform for exploring magnetic control of polariton condensates and mark a significant step toward spin-controlled coherent quantum light sources.

13.
arXiv (CS.CV) 2026-06-15

OmniVideo-100K: A Dataset for Audio-Visual Reasoning through Structured Scripts and Evidence Chains

Current automated pipelines for audio-visual Question Answering (QA) generally adopt a ``video-caption-QA'' paradigm. However, these methods typically segment videos into short clips and generate separate descriptions for audio and visual modalities. This decoupled processing severs inherent associations between sounds and their visual sources, while independent clip processing often causes inconsistent descriptions of the same entity across segments. Furthermore, coupling long-text comprehension and QA synthesis into a single step often restricts models to localized events, yielding questions lacking long-term temporal connections and deep cross-modal reasoning. To address these issues, we propose an automated data engine featuring two mechanisms: (1) Entity-Anchored Video Scripting transforms videos into structured scripts, comprising summaries, main entity lists, and segment-wise audio-visual descriptions. The entity list serves as a global prior to ensure cross-segment referential consistency and reconstruct audio-visual associations. (2) Clue-Guided QA Generation prompts models to first mine cross-segment, multimodal clues from the script, and subsequently generate QA pairs based on these high-value clues. Leveraging this pipeline, we construct the instruction-tuning dataset OmniVideo-100K and a human-verified test set, OmniVideo-Test. Fine-tuning VITA-1.5, Qwen2.5-Omni-7B and Qwen3-Omni-30B on OmniVideo-100K yields performance gains of up to 20.59% on OmniVideo-Test, demonstrating strong generalization (up to 12.64% improvements) across established benchmarks like Daily-Omni and JointAVBench.

14.
arXiv (CS.AI) 2026-06-11

Towards a Bridge Layer Between Bibliographic and Formalized Mathematical Knowledge

Authors:

arXiv:2606.11430v1 Announce Type: cross Abstract: Mathematical knowledge is split between bibliographic databases (e.g., MathSciNet, zbMATH Open) and formal proof libraries (e.g., Lean mathlib), preventing unified access between published results and their formalizations. We propose a relational bridge-database that aligns publication metadata with formal artifacts, providing an interoperability layer between mathematical literature and machine-verifiable proofs. We introduce a paper-level formalization score that measures how much of a publication is covered in formal systems. As a feasibility study, we show how such scores can be estimated via cross-document alignment between informal texts and Lean formalizations, enabling large-scale analysis of formalization coverage. This framework is a first step toward integrating bibliographic and formal mathematical ecosystems into scalable, machine-actionable knowledge graphs linking publications to formal proof objects.

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

Conformal Candidate Certification for Offline Model-Based Optimization

Authors:

arXiv:2606.15217v1 Announce Type: cross Abstract: Offline model-based optimization (MBO) proposes candidates by optimizing a surrogate trained on a fixed historical dataset. Because candidates are deliberately out-of-distribution, surrogate rankings are least reliable exactly where the optimizer is most aggressive, yet existing methods provide no per-candidate statistical certificate that a design meets a target threshold. We propose Conformal Candidate Certification (CCC), a post-hoc wrapper that attaches a calibrated one-sided lower bound to each candidate and advances only those whose bound exceeds the target. We show that entropy-regularized surrogate maximization induces a Gibbs-tilted proposal, so the same surrogate supplies importance weights for weighted conformal prediction without a separate density-ratio estimation step. In a controlled synthetic study, CCC certifies $16.7\%$ of an aggressive proposal pool with empirical coverage 0.990 at nominal 0.90, while standard conformal prediction ignoring the covariate shift collapses to 0.416 coverage.

16.
bioRxiv (Bioinfo) 2026-06-11

Machine Learning-Guided Discovery of Bacterial-Selective Membrane-Active Compounds Reveals Mechanistic Bias in Antibiotic Training Datasets

The rise of antibiotic resistance necessitates the discovery of antibacterial compounds with novel mechanisms of action (MoAs). Recent machine learning approaches have shown promise in antibacterial compound discovery, but often identify derivatives of known antibiotic classes rather than mechanistically novel compounds. Previous approaches applied Tanimoto similarity filters at the end of screening pipelines, but this method has substantial drawbacks: Tanimoto similarity can be misleading in chemical space, and post-hoc filtering does not influence what activity models learn to prioritize. Here, we present a machine learning pipeline that addresses chemical novelty upfront by employing an XGBoost-based MoA classifier to explicitly prioritize compounds predicted to have mechanisms distinct from known antibiotic classes, combined with graph neural networks for antibacterial activity and toxicity prediction. Applied to the Zinc20 database, our approach successfully identified non-toxic antibacterial compounds structurally distinct from known antibiotics. Notably, the majority of these hits exhibited membrane-targeting activity with selectivity for bacterial cells over mammalian cells, suggesting potential for next-generation membrane-active antibiotics. However, we did not identify compounds with novel protein targets. Systematic analysis revealed that this limitation stems from mechanistic bias in training data rather than model architecture. Specifically, our activity model learned to preferentially score compounds similar to specific groups in the training data, thus overrepresenting certain MoA classes including membrane-active compounds. Even substantial model architecture and training data enhancements did not overcome this constraint. Our findings demonstrate that the primary bottleneck for discovering mechanistically novel antibiotics is the scarcity of diverse, mechanistically-annotated training data. This work provides both a methodological framework for mechanism-aware screening and critical insights into data requirements for genuinely novel antibiotic discovery.

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

A Stationary (and Therefore Compatible) Representation is All You Need

arXiv:2606.12488v1 Announce Type: new Abstract: Learning compatible representations aims to learn feature representations that can be used interchangeably over time whenever a model undergoes updates. In this paper, we demonstrate that stationary representations learned by d-Simplex fixed classifiers imply compatibility as in its formal definition. This result establishes a foundation for future works and can be directly exploited in practical learning scenarios. We address the challenge of learning compatibility using $d$-Simplex fixed classifiers when the model is sequentially fine-tuned. Learning according to a d-Simplex fixed classifier with the cross-entropy loss aligns feature distributions at the first-order statistics. Consequently, it may not fully capture higher-order dependencies in the representation between model updates. To address this issue, we demonstrate that training the model using a $d$-Simplex fixed classifier through a convex combination of the cross-entropy loss and a contrastive loss not only captures higher-order dependencies, but is also equivalent to learning with the cross-entropy under the compatibility constraints. We confirm our findings with extensive experiments also considering a new scenario where a pre-trained model is sequentially fine-tuned and occasionally replaced with an improved model. We show that stationary representations enable uninterrupted retrieval services (without reprocessing gallery images) while improving performance during model updates and replacements, achieving state-of-the-art. Code at https://github.com/miccunifi/iamcl2r.

18.
arXiv (CS.CV) 2026-06-11

OpenMedReason: Scientific Reasoning Supervision for Medical Vision-Language Models

High-stakes clinical use of large vision-language models (LVLMs) requires reasoning that is grounded in visual evidence and clinical knowledge, not just correct final answers. We introduce OpenMedReason, a large-scale, open multimodal medical reasoning corpus comprising approximately 450K image-question-answer instances whose reasoning traces are primarily derived from curated biomedical, human-authored scientific articles. OpenMedReason provides high-fidelity supervision beyond synthetic chains of thought, covering diverse medical domain vision modalities such as radiological scans, microscopic images, visible light photographs, charts, and others. We complement it with OpenMedReason-Bench, a held-out benchmark that allows fine-grained evaluation of LVLMs along three complementary axes of capability, including perception, medical knowledge, and rationale, enabling diagnostic evaluation beyond final-answer accuracy. OpenMedReason is a rich training resource that exhibits its effectiveness in both supervised fine-tuning (SFT) and reinforcement-based alignment. Training with OpenMedReason yields a 20% average improvement in VQA accuracy over the base model and achieves performance within 4.2% of the strongest comparable-scale medical LVLMs. Fine-grained performance analysis confirms that the gains are not concentrated in any single axis: OpenMedReason improves perception, medical knowledge, and rationale jointly, and its reasoning traces are preferred over those of the base model in 86.1% of pairwise comparisons. We release the code and dataset at huggingface.co/datasets/neginb/OpenMedReason.

19.
arXiv (CS.AI) 2026-06-15

From Sorting Algorithms to Scalable Kernels: Bayesian Optimization in High-Dimensional Permutation Spaces

arXiv:2507.13263v4 Announce Type: replace-cross Abstract: Bayesian Optimization (BO) is a powerful tool for black-box optimization, but its application to high-dimensional permutation spaces is severely limited by the challenge of defining scalable representations. The current state-of-the-art BO approach for permutation spaces relies on an exhaustive $\Omega(n^2)$ pairwise comparison, inducing a dense representation that is impractical for large-scale permutations. To break this barrier, we introduce a novel framework for generating efficient permutation representations via kernel functions derived from sorting algorithms. Within this framework, the Mallows kernel can be viewed as a special instance derived from enumeration sort. Further, we introduce the Merge Kernel , which leverages the divide-and-conquer structure of merge sort to produce a compact, $\Theta(n\log n)$ to achieve the lowest possible complexity with no information loss and effectively capture permutation structure. Our central thesis is that the Merge Kernel performs competitively with the Mallows kernel in low-dimensional settings, but significantly outperforms it in both optimization performance and computational efficiency as the dimension $n$ grows. Extensive evaluations on various permutation optimization benchmarks confirm our hypothesis, demonstrating that the Merge Kernel provides a scalable and more effective solution for Bayesian optimization in high-dimensional permutation spaces, thereby unlocking the potential for tackling previously intractable problems such as large-scale feature ordering and combinatorial neural architecture search.

20.
arXiv (CS.LG) 2026-06-18

ChronoSurv: A Clinical Pathway-Guided Graph Framework for Multimodal Survival Analysis

arXiv:2606.19140v1 Announce Type: new Abstract: Accurate survival prediction is essential for personalized treatment planning in head and neck cancer, yet remains challenging due to the heterogeneous and high-dimensional nature of multimodal clinical data. While deep survival models have improved predictive performance over classical statistical approaches, existing methods typically rely on static fusion strategies or temporally agnostic modeling, limiting their ability to capture structured clinical workflows. In this work, we propose ChronoSurv, a heterogeneous hierarchical directed graph framework for multimodal survival analysis. ChronoSurv represents patient care as a progression-aware clinical trajectory using directed graphs aligned with key diagnostic steps. A hierarchical topology incorporates fine-grained, coarse, and global representations, further supporting flexible adaptation to missing modalities, while heterogeneous message passing models complex and asymmetric relationships across modalities and clinical steps. Experimental results on two public datasets demonstrate that ChronoSurv achieves state-of-the-art discriminative performance while maintaining statistically reliable calibration. Comprehensive ablation studies further confirm the contribution of each architectural component, highlighting the potential of trajectory-aware graph modeling for multimodal survival prediction.

21.
arXiv (CS.LG) 2026-06-16

Circuit Tracing in Autoregressive Protein Language Models

arXiv:2606.16044v1 Announce Type: new Abstract: Protein language models (pLMs) can generate novel protein sequences with properties beyond those observed in nature, yet the mechanisms underlying protein generation remain poorly understood. Existing mechanistic interpretability methods based on sparse autoencoders and transcoders primarily focus on protein representation learning models and do not capture the computation required for autoregressive generation. Here, we introduce ProGenMech, a mechanistic interpretability framework for generative protein language models that extends cross-layer transcoders (CLTs) to ProGen3, a sparse Mixture-of-Experts model trained for both causal generation and span infilling. Unlike per-layer approaches, CLTs reconstruct each layer using sparse latent variables from all preceding layers, enabling faithful recovery of inter-layer generative computation. We further develop a zero-shot circuit discovery framework to identify sparse latent circuits responsible for protein generation and fitness prediction. In causal generation and zero-shot fitness estimation tasks, ProGenMech outperforms local transcoder baselines in recovering ProGen3's probability distribution and functional scoring behavior, while matching the original model's generative distribution in span infilling tasks. Moreover, the recovered circuits reveal biologically meaningful motifs and functional regions associated with conserved sequence patterns and protein fitness landscapes, establishing a foundation for interpretable and steerable protein generation.

22.
arXiv (CS.CV) 2026-06-11

LAST: Bridging Vision-Language and Action Manifolds via Gromov-Wasserstein Alignment

We take a Gromov-Wasserstein perspective on Vision-Language-Action (VLA) learning, where the goal is to make the relational geometry of action representations compatible with the semantic geometry of VL embeddings. However, this alignment is non-trivial due to the mathematical heterogeneity between the domains: the semantic space of vision-language is topologically linear and isotropic, whereas the physical manifold of robotic action is non-Euclidean and anisotropic. Their disjoint metric structures render direct regression ill-posed. To resolve this incompatibility, we introduce LAST (Lie-algebraic Action Space Tokenizer), which reconstructs the action space to establish local metric compatibility with the VL modality via a two-stage transformation: (1) Global Topological Linearization: linearizing the action manifold via Lie-algebraic mapping, converting trajectories into a fixed-length, physically additive representation. (2) Local Metric Discretization: hierarchically discretizing the representation into schemas and whitened residuals, yielding approximately isotropic local charts that are statistically aligned with the semantic metric. By resolving the structural mismatch at both global and local levels, LAST enables VLA models with superior convergence and generalizability.

23.
arXiv (CS.CL) 2026-06-16

CoCoGEC: Counterfactual Generation for Robust Grammatical Error Correction

Grammatical error correction (GEC) systems are usually trained and evaluated on GEC benchmarks, but their performance often drops sharply once the surrounding context is slightly perturbed or extended. This indicates that the existing GEC models usually fail to understand the error patterns in the varying contexts. In this paper, we thoroughly investigate the counterfactuals for GEC tasks, where the subtle changes to the contexts could lead to the label flipping issue. We propose CoCoGEC, a counterfactual generation framework that creates copies of training instances with error-irrelevant contexts altered. Our framework systematically generates counterfactuals by (1) generating intra- and inter-sentence counterfactuals that maintain the error patterns as well as syntax of the original instances by altering the word-level and sentence-level contexts; (2) revising the generated counterfactuals by selecting the instances with flipped labels and high GEC Mutual Information (MI) coefficient. Extensive experiments show that our method substantially improves the stability of GEC models, outperforming a set of data augmentation baselines. Particularly, it could achieve absolute F0.5 gains of +9.9, +11.3, and +20.8 points on the perturbed BEA-19*,CoNLL-14*, and TEM-8* data set.Our code is released at https://github.com/Quinnok/CoCoGEC

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

Greedy Coordinate Diffusion: Effective and Semantically Coherent Adversarial Attacks via Diffusion Guidance

arXiv:2606.15531v1 Announce Type: new Abstract: Fine-tuning aligned language models on benign tasks (e.g. math tutoring) systematically breaks safety guardrails, even when training data contains no harmful content. While mechanistic approaches have shed light on where alignment resides in model weights, they do not by provide a general formal framework for deriving guarantees about when fine-tuning degrades it – leaving the field without principled tools for predicting or preventing alignment collapse. We develop a local geometric framework through geometric analysis of parameter-space trajectories and apply it to understand the fragility of alignment in fine-tuning. While first-order analysis suggests orthogonal updates are safe, we prove this is illusory: the curvature of the fine-tuning loss induces second-order acceleration that can induce second-order drift into alignment-sensitive regions. We formalize a construct of our framework as the Alignment Instability Condition (AIC), three geometric properties that, when present, are sufficient to guarantee degradation. Our main result proves quartic onset of alignment degradation along gradient-flow trajectories, determined by how sharply alignment depends on specific parameters and how strongly tasks couple to these parameters. These findings yield formal sufficient conditions under which static first-order protection can fail under gradient descent. We further empirically validate the framework's foundations, showing that the Fisher Information Matrix provides a proxy for the degree of safety degradation across diverse fine-tuning.

25.
arXiv (quant-ph) 2026-06-15

Quantum gates with parametrically driven multi-qubit couplers

arXiv:2606.14522v1 Announce Type: new Abstract: Superconducting quantum processors could significantly profit from enhanced connectivity together with precise control of interactions and gates between qubits. Here we investigate plaquettes of four qubits that are coupled via a central tunable coupling circuit, so that not only gates between qubits connected by an edge of the plaquette can be executed but also between qubits across the diagonal. By numerically and analytically analyzing parametrically driven processes, we explore $\sqrt{iSWAP}$-gates between any pair of qubits, also across the diagonal, as well as three-qubit interactions and gates. For experimentally available circuit parameters, we for example find $\sqrt{iSWAP}$-gates with a gate time of 50 ns and 99.9\% fidelity, which is decreased to 99.4\% if two such gates are executed in parallel on disjoint qubit pairs in the plaquette. For three-qubit gates we find fidelities of 95\% fidelity at a gate time of 200 ns.