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01.
arXiv (CS.LG) 2026-06-16

A Biased Nonnegative Block Term Tensor Decomposition Model for Dynamic QoS Prediction

arXiv:2605.04813v2 Announce Type: replace Abstract: With the rapid development of cloud computing and Web services, Quality of Service (QoS) has become a key criterion for service selection and recommendation. Tensor latent feature analysis provides an effective way to model multidimensional QoS data, and most existing QoS prediction methods are mainly based on Canonical Polyadic (CP) decomposition or Tucker decomposition. However, constrained by their inherent structural properties, these methods cannot accurately capture the complex and dynamic dependencies in user-service interactions, which limits their prediction performance. To address this issue, this paper proposes a dynamic QoS prediction framework based on the Biased Nonnegative Block Term Tensor Decomposition Model, termed BNBT. Specifically, the proposed framework is developed from three aspects: (1) block term tensor decomposition is employed to enhance the representation capability of latent feature learning; (2) linear bias terms are incorporated to further improve prediction accuracy; and (3) a tensor-oriented single-element-dependent nonnegative multiplicative update algorithm, called SLF-NMUT, is designed for efficient parameter estimation. Extensive experiments on real-world QoS datasets demonstrate that the proposed BNBT framework consistently outperforms several state-of-the-art QoS prediction methods in terms of prediction accuracy.

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

Structuring and Tokenizing Distributed User Interest Context for Generative Recommendation

arXiv:2606.20554v1 Announce Type: cross Abstract: Generative recommendation is an emerging paradigm that has shown promise in industrial recommendation systems, aiming to predict users' next interactions from their historical behaviors. At the core of generative recommendation lies item tokenization, which bridges item semantics and recommendation models. However, existing methods often struggle to effectively organize and inject complex user-behavioral and item-semantic contexts into recommendation models simultaneously. On the one hand, existing graph-based integration methods, such as graph serialization and graph neural networks, either suffer from scalability issues or exploit only local graph information. On the other hand, existing semantic tokenization methods typically rely on heuristics and lack explicit supervision signals, which may lead to inaccurate or suboptimal semantic representations. To address these limitations in user interest context modeling, we propose G2Rec, a scalable framework that unifies holistic graph-based user co-engagement modeling with semantic tokenization for industrial-scale generative recommendation. Overall, G2Rec enables recommendation models to capture holistic and semantically grounded user interest prototypes without requiring ground-truth user interests, thereby providing more comprehensive and accurate modeling of user behavior contexts in industrial sequential recommendation. Online deployment across product surfaces and extensive experiments on public datasets demonstrate the superiority of G2Rec over existing methods.

03.
arXiv (CS.CV) 2026-06-17

SierpinskiCam: Camera-Controlled Video Retaking with Sierpinski Triangle Pattern Cues

Generating novel renderings of a scene along user-defined camera trajectories from a single monocular video, dubbed video retaking, is a compelling but difficult problem in content creation and visual effects. Existing geometry-guided approaches reconstruct a 4D representation from the source video and render it along the target trajectory to condition video diffusion models. However, this guidance degrades as the target camera departs from the source trajectory, leaving newly revealed regions sparse or entirely missing. We propose SierpinskiCam, which addresses this limitation by augmenting geometry-based guidance with Sierpinski dome texture cues that contains rich trackable features even under large viewpoint changes. We further introduce a reference video conditioning mechanism that appends source-video tokens to the target-token sequence and separates the two streams with negative RoPE indices, enabling appearance grounding without architectural modification or per-video adaptation. Extensive experiments show that SierpinskiCam achieves significant gains in camera controllability, geometric consistency, and video quality across diverse and challenging retaking scenarios. Project page: https://hyelinnam.github.io/SierpinskiCam/.

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

When Confidence Lacks Concepts: Interpretable OOD Detection via Representation Perturbations

Deep neural networks have achieved remarkable performance across medical imaging tasks, yet their tendency to overgeneralize under distributional shifts poses a major obstacle to safe clinical deployment. Out-of-Distribution (OOD) detection methods aim to mitigate this risk, but most existing approaches rely on opaque internal signals with poorly understood semantic meaning, limiting trust in safety-critical settings. In this work, we propose an interpretable OOD detection framework that probes the stability of model predictions under class-conditioned semantic perturbations. Leveraging sparse autoencoders (SAEs), we learn class-specific concept vectors from in-distribution data that disentangle dense intermediate representations into sparse, semantically meaningful components. At inference, we perturb deeper-layer representations using the concept vectors associated with the model's predicted class and measure the class logits stability. We hypothesize that in-distribution samples exhibit low sensitivity to such perturbations, as their representations align with class-specific semantic directions, whereas OOD samples show amplified deviations due to representational misalignment. By framing OOD detection as a concept conditioned stability analysis, our approach provides both a discriminative OOD signal and an interpretable lens into the internal mechanisms driving model uncertainty, making it particularly suitable for high stakes medical applications.

05.
arXiv (CS.LG) 2026-06-12

To GAN or Not To GAN: Segmentation Analysis on Mars DEM

arXiv:2606.13252v1 Announce Type: new Abstract: To better understand Martian Surface, which is needed to enable Rovers navigate Mars with ease, it is necessary to be able to determine the location of mounds. Detecting and studying these morphologies can also help us find evidence of extraterrestrial life, in this case, more specifically, water or signs of life conducive environments. Detection of mounds was done by manually mapping morphological parameters onto Digital Elevation Models. This paper solves the problem by automatically detecting and or predicting mounds on Mars using Neural Network based Semantic Segmentation methodologies. This is done by using supervised semantic segmentation model and generative adversarial approach. A comparison of the approaches shows that adding extra artificially generated data did not improve the result.

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

On Subquadratic Architectures: From Applications to Principles

arXiv:2606.12364v1 Announce Type: new Abstract: Transformers dominate modern sequence modeling, but their quadratic attention incurs substantial computational cost. Subquadratic architectures offer a scalable alternative. However, it remains unclear which designs yield the most effective sequence models. We compare three leading approaches: xLSTM, Mamba-2, and Gated DeltaNet. We evaluate these models on tasks with complex dependencies: (1) code-model pre-training, (2) distillation of code models from large language models, and (3) pre-training of time-series foundation models. Across these settings, xLSTM delivers the strongest overall performance. To explain xLSTM's advantage, we present a unified formulation and analyze the underlying architectural mechanisms, focusing on state tracking and memory dynamics. Our results show that xLSTM enables more flexible and stable memory correction via its gating scheme. We corroborate these findings on controlled synthetic length-generalization tasks. Overall, our findings indicate that xLSTM's gains on complex tasks stem from robust state tracking and accumulation.

07.
arXiv (CS.LG) 2026-06-17

Credibility-Weighted Pricing of Autonomous Vehicle Liability Under Operational Design Domain Shift

作者:

arXiv:2606.17451v1 Announce Type: new Abstract: Automated Driving System deployments create a foundational ratemaking challenge: sparse experience, shifting operational design domains, and non-stationary risk across software releases. We propose a hierarchical Bayesian credibility framework pooling across cities, software versions, and territories via a learned ODD-similarity kernel, nesting Buhlmann-Straub as a limiting case. Demonstrated on 648 verified-engaged Waymo crashes across four U.S. metros from the NHTSA Standing General Order database against 116 million matched miles, city-aggregate credibility weights are moderate (0.12-0.46), partial pooling decisively outperforms no pooling, and a power analysis shows the learned kernel's advantage becomes detectable at approximately twelve deployed cities.

08.
arXiv (math.PR) 2026-06-11

Matrix Discrepancy for Representations of Finite Groups

arXiv:2606.12181v1 Announce Type: new Abstract: Given a finite group $G$, we prove that there exist signs $\varepsilon\in\{\pm1\}^G$ such that $$\left\| \sum_{g\in G} \varepsilon_g\rho(g) \right\|\leq C\, \sqrt{|G|},$$ where $\rho$ is the left regular representation of $G$, and $C$ is a universal constant. This special case of the Matrix Spencer conjecture was posed in [BKMZ24], where it was established for simple groups.

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

Beyond Scalar Rewards by Internalizing Reasoning into Score Distributions

Reward models are central to text-to-image post-training, but visual preference is subjective and better represented as a distribution over rubric scores than as a deterministic scalar. Existing scalar, score-token, and pairwise reward models over-compress uncertainty and fine-grained score differences, while reasoning-based generative rewards provide stronger judgments but are costly to deploy and difficult to use as direct optimization signals. We propose Z-Reward, a teacher-student reward modeling framework that decouples reasoning-heavy judgment from efficient reward deployment. The teacher is a large VLM that uses reasoning to infer rubric-aligned score distributions, and is trained with Group-wise Direct Score Optimization (GDSO), which combines policy-gradient rewards from distribution expectations with direct pointwise and pairwise supervision on score distributions and score gaps. The student is trained with Reasoning-Internalized Score Distillation (RISD), which transfers the teacher's reasoning-conditioned score distribution into a compact VLM without requiring explicit reasoning chains at inference time. On our internally annotated evaluation set, the 27B GDSO teacher reaches 89.6% human preference accuracy, outperforming SFT, RewardDance, and GRPO, while the 9B RISD student reaches 88.6%, outperforming the OPD baseline and closely matching the larger teacher. We further show that Z-Reward can serve as a differentiable reward signal for text-to-image optimization, yielding a 41.3% net human-preference improvement over the SFT baseline.

10.
arXiv (CS.LG) 2026-06-15

Implicit Variational Rejection Sampling

arXiv:2606.14235v1 Announce Type: new Abstract: Variational Inference (VI) is a fundamental inference technique in Bayesian machine learning for approximating complex posterior distributions. Traditional VI often relies on the mean-field factorization, which can inadequately capture true posterior complexity. Recent advancements have leveraged neural networks to model implicit distributions, offering increased flexibility. However, the practical constraints of neural network architectures still produces inaccuracies. In this paper, we propose a method called Implicit Variational Rejection Sampling (IVRS), which integrates implicit distributions with rejection sampling to improve the posterior approximation. Our method uses neural networks to construct implicit proposal distributions, and rejection sampling with a discriminator network that estimates the density ratio between the implicit proposal and the true posterior for refining the approximation. Towards this end, we introduce the Implicit Resampling Evidence Lower Bound (IR-ELBO) as a metric to characterize the resampled distribution's quality and derive a tighter variational lower bound. Experimental results demonstrate that our method outperforms traditional variational inference techniques.

11.
bioRxiv (Bioinfo) 2026-06-16

FlowBench: separating planning, fault recovery and interpretation in agentic bioinformatics

Agentic large language model (LLM) systems are being deployed in bioinformatics faster than they are understood, and single-metric evaluations conflate capabilities that fail independently. We introduce FlowBench, a benchmark that decomposes agentic bioinformatics performance into planning, fault recovery, biological interpretation, and end-to-end output-fidelity. Existing systems achieve high plan completeness, but their closed, single-provider designs prevent attribution of performance to scaffolding versus the underlying model. We therefore built FlowAgent, a modular, provider-agnostic framework whose components can be selectively disabled and whose backbone model can be swapped across providers on a shared harness, and used it to evaluate 23 models from three main providers. Three findings emerge. First, generating a valid workflow plan from a named toolchain is largely solved, whereas inferring an appropriate toolchain from biological intent alone is uniformly difficult regardless of model tier, compressing all models into a narrow 44-57% pass-rate band. Second, ablation shows that the dependency-structured plan and a completeness-reflection step drive performance, while adding a same-context validator-driven retry makes structural quality worse. Third, fault recovery and data-grounded interpretation remain unsolved. Models frequently propose fixes that force a clean exit while leaving the underlying data invalid, and data-grounded interpretation lags internal-knowledge recall by a consistent margin. Safety does not emerge from capability, and reasoning-tier models were among the least reliable at recognising unrecoverable faults. Once planning saturates, agent architecture and refusal calibration, not model scale, are the productive frontier.

12.
arXiv (CS.LG) 2026-06-18

A Streaming Sparse Cholesky Method for Derivative-Informed Gaussian Process Surrogates Within Digital Twin Applications

arXiv:2511.00366v2 Announce Type: replace-cross Abstract: Digital twins are developed to model the behavior of a specific physical asset (or twin), and they can consist of high-fidelity physics-based models or surrogates. A highly accurate surrogate is often preferred over multi-physics models as they enable forecasting the physical twin future state in real-time. To adapt to a specific physical twin, the digital twin model must be updated using in-service data from that physical twin. In this paper, we combine and extend several previous surrogate-related advancements with the goal of demonstrating an end-to-end digital twin (DT) solution for predicting performance of an aircraft structure (the physical asset). To this end, we extend Gaussian process (GP) models to include derivative data, for improved accuracy, with dynamic updating to ingest physical twin data during service. Including derivative data, however, comes at a prohibitive cost of increased covariance matrix dimension. We circumvent this issue through our modified dynamic sparse Cholesky linear system solver. Numerical experiments demonstrate that the prediction accuracy of the derivative-enhanced sparse Cholesky GP method produces improved models upon dynamic data additions. Lastly, we demonstrate the developed algorithm within a DT framework to model fatigue crack growth in an aerospace vehicle, thereby exhibiting through our assembled engineered system how digital twin technologies can be combined in practice.

13.
arXiv (math.PR) 2026-06-11

Marked random graphs with given degree sequence: large deviations on the local topology

arXiv:2401.00351v2 Announce Type: replace Abstract: We investigate the behavior of the empirical neighborhood distribution of marked graphs in the framework of local weak convergence. Here we extend known results by considering uniform random graphs with given degree sequences and i.i.d. marks on half-edges and vertices. We establish a large deviation principle for such families of empirical measures. The proof builds on Bordenave and Caputo's seminal 2015 paper, and Delgosha and Anantharam's 2019 introduction of BC entropy, relying on combinatorial lemmas that allow one to construct suitable approximations of measures supported on marked trees. Possible applications of these results are in the study of interacting diffusions on top of random graphs.

14.
arXiv (CS.CV) 2026-06-15

MUSE: Agentic 3D Scene Authoring via Memory-Grounded Incremental Requirement Satisfaction

Text-driven 3D scene generation is a promising technique for digital content creation, embodied AI simulation, and interactive design, yet practical workflows often require refining, extending, or correcting existing scenes while preserving non-target content. Existing methods can produce realistic and structurally plausible scenes, but they generally lack editability with requirement-level state tracking, so part-level failures often lead to full-scene regeneration or manual intervention. To tackle this challenge, we formulate controllable 3D scene authoring as incremental requirement satisfaction, unifying construction and editing. In this paper, we present MUSE, a memory-grounded multi-agent framework in which an Architect compiles instructions into structured requirements, a Sculptor executes local scene operations, and an Inspector verifies each step while updating Working, Scene, and Skill Memory. To evaluate requirement-level controllability and preservation-aware editing, we introduce AuthorBench, offering 145 constrained construction cases and a 1,584-case preservation-aware editing pool paired with external structured checks. On full construction cases, MUSE improves All-Goal success from 37.9 to 80.7 and surface-constraint fulfillment from 35.0 to 92.6 over the strongest baseline. On a stratified 240-case editing test split, MUSE achieves 49.6 All-Goal success, 99.9 preservation rate, and only 0.6 unintended change rate. Beyond automated metrics, human evaluations on compared local-editing baselines support stronger alignment with user intent, and downstream navigation-proxy tests indicate stronger spatial stability. Combined with ablations validating our memory designs, these results establish MUSE as an effective framework for controllable 3D scene authoring.

15.
medRxiv (Medicine) 2026-06-23

Multivariate Echocardiographic Phenotyping of Hypertensive Heart Failure Using Unsupervised Machine Learning: A Pilot Study

Background Heart failure in hypertensive patients is heterogeneous and poorly captured by traditional left ventricular ejection fraction (LVEF) based classification. Multivariate echocardiographic data combined with unsupervised machine learning may provide a more precise phenotypic characterization. This pilot study evaluated the feasibility of unsupervised clustering of routine transthoracic echocardiographic data to identify phenotypic subgroups of hypertensive heart failure. Methods This retrospective pilot study analyzed transthoracic echocardiography reports from hypertensive patients with clinical heart failure. After data cleaning and exclusion of incomplete records, 102 patients with 11 echocardiographic variables were included. Variables describing left ventricular geometry, systolic function, and diastolic performance were standardized and subjected to K-means clustering. Optimal cluster number was determined using the elbow method and silhouette analysis. Cluster characteristics were assessed using descriptive statistics and Kruskal Wallis testing. Concordance with LVEF based heart failure categories was evaluated. Results Three distinct echocardiographic phenotypes were identified. Cluster 0 (n = 50) demonstrated preserved LVEF with concentric remodeling, consistent with heart failure with preserved ejection fraction (HFpEF) phenotype. Cluster 1 (n = 37) showed marked ventricular dilation and reduced systolic function, consistent with heart failure with reduced ejection fraction (HFrEF). Cluster 2 (n = 15) exhibited concentric hypertrophy with intermediate LVEF, consistent with heart failure with mildly reduced ejection fraction (HFmrEF) like phenotype. All echocardiographic variables differed significantly across clusters (p < 0.001). While Cluster 0 showed strong concordance with HFpEF (96%), Clusters 1 and 2 demonstrated substantial overlap across LVEF categories, indicating partial discordance between structural phenotypes and LVEF based classification. Conclusion Application of unsupervised machine learning to routine echocardiographic data identifies distinct heart failure phenotypes in hypertensive patients. These phenotypes demonstrate significant structural heterogeneity beyond LVEF based classification, supporting the utility of data-driven approaches for refined cardiac phenotyping. This pilot study provides a foundation for larger prospective studies.

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

MVEB: Massive Video Embedding Benchmark

We introduce the Massive Video Embedding Benchmark (MVEB), a 23-task benchmark for video embeddings spanning classification, zero-shot classification, clustering, pair classification, retrieval, and video-centric question answering. We evaluate 33 models and find that no single model dominates: MLLM-based embeddings lead on classification, clustering, pair classification, and QA; multimodal binding leads on retrieval and zero-shot classification; generative MLLMs without contrastive adaptation collapse on cross-modal tasks. Paired video-only vs. audio+video evaluations show that audio's contribution depends on dataset annotation provenance: audio helps when labels were produced from both modalities and hurts when they were produced from visuals alone, a six-point gap consistent across model families. MVEB is derived from MVEB+, a 184-task pool, and is designed to maintain task diversity while reducing evaluation cost. It integrates into the MTEB ecosystem for unified evaluation across text, image, audio, and video. We release MVEB and all 184 tasks along with code and a leaderboard at https://github.com/embeddings-benchmark/mteb.

17.
PLOS Computational Biology 2026-06-08

Statistics of cortical representational drift can enable robust readout

by Charles Micou, Timothy O’Leary Representational drift of fixed stimuli, learned tasks and familiar environments is observed in many brain areas, leading to reconfiguration of population codes over days to weeks. This raises the question of whether downstream brain regions employ mechanisms to track changes in population activity and thus preserve the fidelity of the information they extract. We show that the statistical properties of drift have a significant impact on such mechanisms. Over an extended period, a net change in population tuning due to drift can arise from an accumulation of small changes distributed across the population, or via abrupt jumps that affect smaller subsets of cells at each time point. We demonstrate that an adaptive readout can exploit the heavy-tailed statistics of abrupt jumps to maintain a more stable readout using a simple inference mechanism. Using experimental data, we investigate the extent to which heavy-tailed drift statistics are observed during representational drift in the posterior parietal cortex and visual cortex. We find that experimentally measured drift does not conform to a Gaussian random walk. Instead, we find sudden jumps in neural tuning that would be advantageous for a downstream observer adapting to changes in representation. These observations motivate future study to determine whether adaptive decoding mechanisms exist in the brain and to determine the physiological mechanisms that shape the statistics of representational drift.

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

Teaching Diffusion to Speculate Left-to-Right

Large language models (LLMs) achieve remarkable performance across a wide range of tasks, but their autoregressive decoding process incurs substantial inference costs due to inherently sequential token generation. Speculative decoding addresses this bottleneck by employing a lightweight draft model to propose multiple future tokens that are subsequently verified in parallel by a larger target model. Recent work has demonstrated that diffusion language models are well suited for this setting, as they can generate entire blocks of draft tokens in parallel and thereby alleviate the sequential constraints of autoregressive drafting. A subtlety of this regime is that block-diffusion drafters generate tokens bidirectionally within a block, whereas verification is performed by an autoregressive target model that evaluates tokens in a strictly left-to-right manner, leaving a gap between the symmetric training-time objective and the asymmetric verification-time reward. In this work, we offer an empirical analysis of three training-time interventions that narrow this gap: token positional weighting, a first-error focal loss that targets the position that breaks the accepted prefix within each block, and a chain loss term that substitutes a differentiable surrogate for the expected accepted length. The three interventions act along orthogonal axes (position, block-conditional first error, joint prefix) and compose additively; they are likewise orthogonal to test-time alignment mechanisms such as multi-draft self-selection, with which they can in principle be combined. Across four target models and six reasoning, code, and dialogue benchmarks, the three interventions raise accepted draft length by 21-76% per benchmark over a position-uniform baseline, without adding additional forward passes and without changing the inference pipeline or the rejection-sampling exactness contract.

19.
arXiv (quant-ph) 2026-06-16

Synthesizing Arbitrary Non-Hermitian Hamiltonian with Stochastic Floquet Engineering

arXiv:2606.15664v1 Announce Type: new Abstract: The conventional Floquet engineering scheme synthesizes a given target Hamiltonian with a deterministic temporal periodic driving field. In this work, we introduce the stochastic Floquet engineering scheme that can synthesize an arbitrary non-Hermitian target Hamiltonian using a time-periodic driving field with noisy amplitude. Our method is rooted in the Hermitian dynamics taking noise as a valuable quantum resource with no need for loss or gain in prior. We apply our method to engineer a cavity Hamiltonian with dissipative coupling between Fock states, and to prepare a given quantum state from a generally arbitrary quantum state. The stochastic Floqut engineering also provides a way to generate non-unitary quantum gates, which take advantage in certain tasks compared to unitary quantum computing, without the need for ancillae or state-dependent updating.

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

KCSAT-ML: Probing Reasoning Models with Nationwide-Cohort Human Difficulty

Math reasoning benchmarks have proliferated, yet most lack a per-item difficulty signal grounded in actual human performance. We introduce KCSAT-ML, a decade (2014-2025) of Korean College Scholastic Ability Test (KCSAT; Suneung) mathematics: 664 problems with a 339-item core set carrying official per-item error rates from nationwide cohorts of hundreds of thousands of examinees. We pair the benchmark with Difficulty-aligned Reasoning Gain (DRG): a score-orthogonal metric that asks whether a model's mistakes concentrate on the items humans found hard, or on items humans found easy. Together they expose, across a wide range of VLMs (and LLMs via OCR), three patterns: (i) low-budget accuracy collapses on the high-human-error tail at every model size; (ii) test-time scaling (TTS) raises token use roughly linearly with cohort error rate, while accuracy gains follow a non-monotonic curve; (iii) within a single family, TTS flips between anti-scaling on the hardest items and overthinking on easier ones – two faces of the same alignment failure. On DRG, models with near-identical accuracy can sit at near-opposite values: one model gets wrong what humans also find hard, while another solves the hardest items yet fails on items humans find easy – a contrast that aggregate accuracy hides. Our code and dataset builder will be open-sourced at https://github.com/naver-ai/KCSAT-ML.

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

RT-VLA: Real-Time Vision-Language-Action Models via Knowledge Distillation

Vision-Language-Action (VLA) models have shown strong potential for end-to-end autonomous driving by jointly modeling visual perception, language reasoning, explainability and action prediction. However, their large vision-language backbones and reasoning modules introduce substantial inference latency and thereby prevent their deployment in the unforgiving reality of the road networks. We propose RT-VLA, a lightweight, distilled VLA model that transfers the driving and reasoning capabilities of the state-of-the-art SimLingo model into a compact student through multi-level supervised distillation. RT-VLA preserves language-based reasoning and supports post-hoc explanation through offline language analysis of safety-critical driving moments without adding latency to real-time control. Compared to the SimLingo teacher, RT-VLA maintains competitive closed-loop driving and language reasoning performance while reducing inference time by 44.8X in vision-only mode and 7.9X in vision+language mode. These results suggest that supervised distillation is a practical approach for building real-time, explainable VLA-style autonomous driving models.

22.
arXiv (CS.CL) 2026-06-16

The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models

High-grade gliomas integrate into neural circuits through functional synapses with neurons, raising the question of which noncoding elements shape synaptogenic gene expression in tumor cells. The regulatory program written across the dark genome, what we call the $dark regulome$, is the natural substrate to probe, and sequence foundation models offer a zero-shot route through in-silico mutagenesis (ISM); yet likelihood-based scoring is tautologically coupled to local sequence predictability, leaving the regulatory interpretation underdetermined. Across three architecturally distinct foundation models (Caduceus-Ph, HyenaDNA, Enformer) and 30,448 dark genome elements at 92 glioma-relevant loci, we introduce a residualization-and-permutation diagnostic that separates predictability-driven from regulation-driven RIS variance. A sharp 10kb proximal-regulatory horizon survives every control we apply, but the LM-derived element-class hierarchy does not: a six-feature linear baseline matches Caduceus top-decile membership at AUC $= 0.985$. Cross-architecture decomposition cleanly separates a sequence-predictability layer (the two language models co-rank long well-predicted transposable elements) from a regulatory-output layer (Enformer alone retains residual cCRE-discriminative signal), with literally zero overlap between the two top-100 lists. Conservation, brain cis-eQTL, and STRING-PPI cross-checks then anchor what biology survives: top-100 elements across all three models are $3.3\times$ enriched per model for matching brain eQTLs ($p_\mathrm{emp} < 5\times 10^{-3}$), while a tempting transposable-element regulatory layer and a striking NRXN1+NLGN1 protein-pair convergence both fail proper permutation tests once those tests are constructed. We deliver the diagnostic as a general methodological tool for any ISM-based regulatory study.

23.
arXiv (CS.CL) 2026-06-11

Judging Against the Reference: Uncovering Knowledge-Driven Failures in LLM-Judges on QA Evaluation

While large language models (LLMs) are increasingly used as automatic judges for question answering (QA) and other reference-conditioned evaluation tasks, little is known about their ability to adhere to a provided reference. We identify a critical failure mode of such reference-based LLM QA evaluation: when the provided reference conflicts with the judge model's parametric knowledge, the resulting scores become unreliable, substantially degrading evaluation fidelity. To study this phenomenon systematically, we introduce a controlled swapped-reference QA framework that induces reference-belief conflicts. Specifically, we replace the reference answer with an incorrect entity and construct diverse pairings of original and swapped references with correspondingly aligned candidate answers. Surprisingly, grading reliability drops sharply under swapped references across a broad set of judge models. We empirically show that this vulnerability is driven by judges' over-reliance on parametric knowledge, leading judges to disregard the given reference under conflict. Finally, we find that this failure persists under common prompt-based mitigation strategies, highlighting a fundamental limitation of LLM-as-a-judge evaluation and motivating reference-based protocols that enforce stronger adherence to the provided reference.

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

FORGE: Foundational Optimization Representations from Graph Embeddings

arXiv:2508.20330v5 Announce Type: replace Abstract: Combinatorial optimization problems are ubiquitous in science and engineering. Still, learning-based approaches to accelerate combinatorial optimization often require solving a large number of difficult instances to collect training data, incurring significant computational cost. Existing learning-based methods require training dedicated models for each problem distribution, for each downstream task, severely limiting their scalability and generalization. We introduce Forge: Foundational Optimization Representations from Graph Embeddings, a framework that pre-trains a vector-quantized graph autoencoder on a large, diverse collection of mixed-integer programming (MIP) instances in an unsupervised manner, without relying on optimization solvers or optimal solutions. Vector quantization produces discrete code assignments that serve as a vocabulary for representing optimization instances. We evaluate Forge in both unsupervised and supervised settings. In the unsupervised setting, Forge embeddings effectively cluster unseen instances across problem domains and sizes. In the supervised setting, we fine-tune Forge embeddings and show that a single pre-trained model helps predicting both the integrality gap for cut-generation and variable hints for search guidance across multiple problem and size distributions. In both tasks, we improve the performance of a commercial optimization solver and outperform state-of-the-art learning-based methods. Finally, we open-source our training code, pre-trained Forge weights, and embeddings for multiple MIP distributions to foster further research in representation learning for optimization problems https://skadio.github.io/forge/

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

Proto-LeakNet: Towards Signal-Leak Aware Attribution in Synthetic Human Face Imagery

The growing sophistication of synthetic image and deepfake generation models has turned source attribution and authenticity verification into a critical challenge for modern computer vision systems. Recent studies suggest that diffusion pipelines unintentionally imprint persistent statistical traces, known as signal-leaks, within their outputs, particularly in latent representations. Building on this observation, we propose Proto-LeakNet, a signal-leak-aware and interpretable attribution framework that integrates Closed-set classification with a density-based Open-set evaluation on the learned embeddings, enabling analysis of unseen generators without retraining. Acting in the latent domain of diffusion models, our method re-simulates partial forward diffusion to expose residual generator-specific cues. A temporal attention encoder aggregates multi-step latent features, while a feature-weighted prototype head structures the embedding space and enables transparent attribution. Trained solely on closed data and achieving a Macro AUC of 98.13\%, Proto-LeakNet learns a latent geometry that remains robust under post-processing, surpassing state-of-the-art methods, and achieves strong separability both between real images and known generators, and between known and unseen ones. The codebase is available at the following link: https://github.com/claudiunderthehood/Proto-LeakNet .