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01.
arXiv (CS.CV) 2026-06-12

Cross-Modal Masked Compositional Concept Modeling for Enhancing Visio-Linguistic Compositionality

Contrastively trained vision-language models like CLIP, have made remarkable progress in learning joint image-text representations, but still face challenges in compositional understanding. They often exhibit a "bag-of-words" behavior–struggling to capture the object relations, attribute-object bindings, and word order dependencies. This limitation arises not only from the reliance on global, single-vector representations for optimization, but also from the insufficient exploitation and modeling of the rich compositional information inherently present in paired image text data. In this work, we propose MACCO (MAsked Compositional Concept MOdeling), a framework that masks compositional concepts in one modality and reconstructs them conditioned on the full contextual information from the other, enabling the model to capture and align cross-modal compositional structures more effectively. To facilitate this process, we introduce two auxiliary objectives that jointly align and regularize masked features both inter-modally and intra-modally. Extensive experiments on five compositional benchmarks, along with in-depth analyses, demonstrate that our approach not only significantly enhances compositionality in VLMs but also improves their ability to capture syntactic structure and linguistic information. Additionally, the improved compositionality also benefits text-to-image generation and multimodal large language model. Code is available at https://github.com/hiker-lw/MACCO.

02.
arXiv (CS.LG) 2026-06-11

Neural ensemble Kalman filter: Data assimilation for compressible flows with shocks

arXiv:2602.23461v2 Announce Type: replace-cross Abstract: Data assimilation (DA) for compressible flows with shocks is challenging because many classical DA methods generate spurious oscillations and nonphysical features near uncertain shocks. We focus here on the ensemble Kalman filter (EnKF). We show that the poor performance of the EnKF may be attributed to the bimodal forecast distribution that can arise in the vicinity of an uncertain shock location; this violates the assumptions underpinning the EnKF, which assume a forecast which is close to Gaussian. To address this issue we introduce the new neural EnKF. The basic idea is to systematically embed neural function approximations within ensemble DA by mapping the forecast ensemble of shocked flows to the parameter space (weights and biases) of a deep neural network (NN) and to subsequently perform DA in that space. The nonlinear mapping encodes sharp and smooth flow features in an ensemble of NN parameters. Neural EnKF updates are therefore well-behaved only if the NN parameters vary smoothly within the neural representation of the forecast ensemble. We show that such a smooth variation of network parameters can be enforced via physics-informed transfer learning, and demonstrate that in so-doing the neural EnKF avoids the spurious oscillations and nonphysical features that plague the EnKF. The applicability of the neural EnKF is demonstrated through a series of systematic numerical experiments with the inviscid Burgers' equation, the Sod shock tube, and a two-dimensional blast wave.

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

TivTok: Broadcasting Time-Invariant Tokens for Scalable Video Tokenization

Video tokenization is fundamental to scalable video generation, as the number of tokens directly determines the computational cost and the length of videos that can be modeled. Existing tokenizers mainly improve scalability by compressing videos into fewer tokens, but they often continue to represent persistent content, such as static backgrounds and consistent object appearances, repeatedly across frames and chunks. In this paper, we propose TivTok (Time-Invariant Tokenizer), a reuse-aware video tokenizer that makes persistent information reusable across time. TivTok represents a clip with Time-Invariant (TIV) tokens that encode information shared across frames and Time-Variant (TV) tokens that encode frame-specific residuals. To obtain this factorization, we introduce Scope-Induced Factorization (SIF), which assigns different attention scopes to the two token groups: TIV tokens attend to the full clip, whereas each TV token only accesses its corresponding frame together with the TIV tokens. In the decoder, Invariant Broadcasting (IB) reuses the same TIV tokens across frames and chunks for parallel reconstruction and long-video tokenization. Experiments show that TivTok achieves an rFVD of 12.65 on the standard $16{\times}256{\times}256$ benchmark and improves compression efficiency by 2.91$\times$ for 128-frame videos compared with the evaluated baselines, while using only 1.1\% of the tokens required by downsample-based tokenizers in our evaluation.

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

InfoNCE Induces Gaussian Distribution

arXiv:2602.24012v2 Announce Type: replace Abstract: Contrastive learning has become a cornerstone of modern representation learning, allowing training with massive unlabeled data for both task-specific and general (foundation) models. A prototypical loss in contrastive training is InfoNCE and its variants. In this work, we show that the InfoNCE objective induces Gaussian structure in representations that emerge from contrastive training. We establish this result in two complementary regimes. First, we show that under certain alignment and concentration assumptions, projections of the high-dimensional representation asymptotically approach a multivariate Gaussian distribution. Next, under less strict assumptions, we show that adding a small asymptotically vanishing regularization term that promotes low feature norm and high feature entropy leads to similar asymptotic results. We support our analysis with experiments on synthetic and CIFAR-10 datasets across multiple encoder architectures and sizes, demonstrating consistent Gaussian behavior. This perspective provides a principled explanation for commonly observed Gaussianity in contrastive representations. The resulting Gaussian model enables principled analytical treatment of learned representations and is expected to support a wide range of applications in contrastive learning.

05.
bioRxiv (Bioinfo) 2026-06-11

AGZArank: Investigating epitope-conditioned antibody binder ranking with structure-derived synthetic supervision

Computational antibody design methods can generate large libraries of candidate binders for a target epitope, but prioritizing which candidates to test experimentally remains a major bottleneck. Existing scoring approaches, including physics-based affinity estimators, structure-prediction-derived confidence measures, and inverse-folding likelihood models, provide useful proxy signals but are not explicitly optimized for early enrichment of binders among many structurally similar candidates. Here we investigate epitope-conditioned antibody binder ranking as a dedicated learning problem and introduce AGZArank, a geometric deep learning framework trained with structure-derived synthetic supervision based on normalized pseudo-energy targets. On a benchmark of 45 experimentally validated antibody-antigen interfaces, AGZArank recovered the true binder within the top ten candidates in 44.4% of cases and showed stronger generalization on post-2021 structures than ProteinMPNN, ESM-IF, and PRODIGY. Ablation experiments indicate that ranking performance depends primarily on training scale and alignment between the optimization objective and retrieval-based evaluation, rather than architectural complexity alone. These results support candidate prioritization as a distinct and tractable problem in computational antibody design.

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

BrainWorld: A Structural-Prior-Conditioned Generative Model for Whole-Brain 4D fMRI Dynamics

Whole-brain 4D fMRI generation is valuable for modeling functional brain dynamics, yet existing fMRI foundation models mainly target representation learning and downstream prediction rather than conditional predictive generation. We introduce BrainWorld, a structural-prior-conditioned generative model for whole-brain 4D fMRI dynamics. BrainWorld uses sMRI as subject-level anatomical context to guide future fMRI generation, integrating structural information into the denoising process rather than treating it as a parallel modality. Evaluated on 22 datasets spanning diverse cohorts and brain states, BrainWorld generates stable 4D fMRI trajectories up to 400 frames, improves downstream performance through generated-example augmentation, and learns transferable multimodal representations that outperform baselines. Together, these results establish BrainWorld as a condition-aware generative framework for long-horizon brain dynamics modeling and multimodal representation learning.

07.
arXiv (CS.LG) 2026-06-16

A polarity-aware multi-relational model for the signed interaction prediction in biological networks

arXiv:2407.07357v3 Announce Type: replace Abstract: Predicting signed interactions in biological networks is crucial for understanding drug mechanisms and facilitating drug repurposing. While deep graph models have demonstrated success in modeling complex biological systems, existing approaches often fail to distinguish between positive and negative interactions, limiting their utility for precise pharmacological predictions. In this study, we propose a novel deep graph model, PAMR (polarity-aware multi-relational model), designed to predict both polar (e.g., activation, inhibition) and non-polar (e.g., binding, affect) chemical-gene interactions. Our model integrates graph convolutional networks with tensor decomposition to enhance feature representation and incorporates a conflict-aware sampling strategy to resolve polarity ambiguities. We introduce new evaluation metrics, polarity discrimination score (PDS) and CP@100, to assess the model's ability to differentiate interaction types. Experimental results demonstrate that PAMR outperforms baseline models, achieving superior classification accuracy and improved discrimination of polar edges. Specifically, PAMR-CL attains a Macro AUROC of 0.9072 and CP@100 of 0.974, surpassing RGCN, GraphSAGE, TransE, and BioNet baselines. A case study on nicotine further identifies two novel chemical-gene suppression links, S100A6 and SPP1, that are corroborated by independent experimental literature. Furthermore, we analyze the impact of subgraph components on predictive performance, revealing that additional network structures do not always enhance accuracy. These findings highlight the importance of polarity-aware modeling in drug discovery and network pharmacology, providing a scalable computational framework for polarity-aware chemical-gene interaction prediction and network pharmacology analysis.

08.
arXiv (CS.CV) 2026-06-19

GH-ESD: Grounded Hypothesis-Driven Error Slice Discovery for Instance-Level Vision Tasks

Systematic failures of vision models on semantically coherent subsets, known as error slices, reveal limitations in robustness and evaluation. Existing slice discovery approaches largely model slices as clusters in representation space or combinations of predefined attributes. While effective for image-level classification, such formulations are insufficient for instance-level tasks such as object detection and segmentation, where failures often arise from contextual relational and spatially grounded visual patterns. We propose GH-ESD (Grounded Hypothesis-Driven Error Slice Discovery), a generate and verify framework that reformulates slice discovery as grounded hypothesis generation and statistical verification. GH-ESD constructs relational failure hypotheses using LLM priors and grounded visual evidence, discovers hypothesis slices at the instance level via Vision Language Models, and verifies them through statistical trend analysis over instance-level errors. We also introduce GESD (Grounded Error Slice Dataset), a new benchmark for instance-level error slice discovery, providing expert-defined and spatially grounded slices derived from detection and segmentation failures. Extensive experiments demonstrate that GH-ESD consistently outperforms baselines, improving Precision@10 by 0.10 (0.73 vs. 0.63) on the GESD benchmark for detection tasks, while also supporting segmentation scenarios. GH-ESD identifies interpretable slices that facilitate actionable model improvements. The GESD dataset will be made publicly available upon acceptance.

09.
arXiv (quant-ph) 2026-06-16

Achieving High-Quality Portfolio Optimization with the Variational Quantum Eigensolver

arXiv:2508.18625v2 Announce Type: replace Abstract: Portfolio optimization lies at the core of quantitative finance and aims to determine how assets should be allocated to balance expected returns against risk. It can be formulated as a Quadratic Unconstrained Binary Optimization (QUBO) problem, which is NP-hard. Quantum computing offers the potential to solve such problems more efficiently than classical methods. In this work, we employ the Variational Quantum Eigensolver (VQE) to address the portfolio optimization problem. To increase the likelihood of converging to high-quality solutions, we propose using the Weighted Conditional Value-at-Risk (WCVaR) as the cost function and the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) as the optimizer. Our experiments are conducted using both classical simulations and quantum hardware on the Wuyue QuantumAI platform. Together, these results demonstrate that the combination of WCVaR and CMA-ES improves the performance of VQE for portfolio optimization and provides a practical route for applications on NISQ devices.

10.
medRxiv (Medicine) 2026-06-15

Iron deficiency testing among people with incident heart failure in primary care

Background: Given around 50% of people with heart failure have a degree of iron deficiency, guidelines recommend screening. It is uncertain to what extent this is done in primary care and whether testing is equitable. Aim: To report the proportion of people with incident heart failure who undergo a ferritin test within 12 months. Design and setting: Retrospective primary care cohort study using Clinical Practice Research Datalink Aurum data, between 2016 and 2021. Methods: We report the proportion of adults with an incident diagnosis of heart failure who received a ferritin test within 12 months. Multivariable logistic regression was used to examine the odds of testing based on key demographic covariates and co-morbidities. Results: Among 105,749 individuals with an incident diagnosis of heart failure (mean age 71.6 years, SD 14.3), only 35,688 (33.7%) received a ferritin test within the subsequent year. Increasing age (odds ratio 1.25 per 10-year increase, 95% CI: 1.24-1.27), female sex (male sex OR 0.86, 0.84-0.89) and Asian ethnicity (OR 1.70, 1.59-1.80) were all associated with increased odds of testing as were diagnoses of coeliac disease (OR 1.86, 1.58-2.21), type 1 diabetes (OR 1.82, 1.51-2.19) and cirrhosis (OR 1.64, 1.43-1.87). There was geographic variation in testing, even in adjusted analyses. Conclusion: In a large primary care dataset, two thirds of people with incident heart failure did not receive a ferritin test for iron deficiency within a year of diagnosis demonstrating a gap in current practice and an opportunity for improvements in service delivery.

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

When in Doubt, Plan It Out: Committed Small Language Model Deliberation for Reactive Reinforcement Learning

arXiv:2606.16995v1 Announce Type: new Abstract: Reinforcement Learning (RL) policies often degrade in unfamiliar environments because they lack explicit deliberation. We propose Plan, Align, Commit, Think (PACT), a hybrid architecture that combines a fast, reactive RL policy with a slow, deliberative Small Language Model (SLM) planner. PACT invokes the SLM asynchronously to generate and validate candidate action plans. Once a plan is verified through simulation as safe, feasible, and complete, it is executed directly, bypassing the RL policy without retraining or modifying it. Evaluated on three FrozenLake configurations of increasing difficulty, PACT outperforms all baselines while relying on a 2B-parameter SLM backbone, suggesting that deliberative planning and reactive execution are more powerful in concert than either is alone in these settings.

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

Improving Medical Communication using Rubric-Guided Counterfactual Recommendations

Text-based telemedicine increasingly relies on lightweight patient feedback, however, such feedback primarily reflects perceived communication quality rather than medical accuracy. We introduce an LM-guided counterfactual recommendation pipeline that discovers and refines interpretable communication features such as tone, personalization, actionability and completeness in addressing patient concerns, without interfering with the medical content. These features are used together with patient-doctor interaction metadata to estimate positive feedback. At inference time, the system searches over low-cost ordinal feature changes and recommends minimal communication changes predicted to increase the probability of positive feedback, while independent auditor models test whether these gains generalize beyond the selection model. Across interactions, recommendations yield a mean +6.41% gain in predicted positive feedback probability under independent auditors, and are non-negative for 93.31% of recommendations. These results suggest that small, interpretable communication changes can capture most predicted gains while preserving the doctor's control over medical reasoning and final wording.

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

The Third Challenge on Image Denoising at NTIRE 2026: Methods and Results

This paper reports on the NTIRE 2026 Challenge on Image Denoising, specifically focusing on the high-noise regime ($\sigma = 50$). The competition investigates advanced neural architectures designed to restore high-fidelity details from images corrupted by additive white Gaussian noise (AWGN). Unlike constrained benchmarks, this track emphasizes peak quantitative performance, measured by Peak Signal-to-Noise Ratio (PSNR), without limitations on parameter count or computational overhead. By synthesizing contributions from 20 finalist teams out of 116 registrants, this report benchmarks the latest technical innovations and provides a comprehensive snapshot of the current state-of-the-art in unconstrained image restoration.

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

GLARE: A Natural Language Interface for Querying Global Explanations

arXiv:2606.19735v1 Announce Type: new Abstract: While global explanations are crucial for understanding vision models across datasets, classes, and decision contexts, their complex and monolithic nature often hinders practical exploration. Because users typically seek targeted answers to specific questions rather than static artifacts, we present an LLM-based interactive interface that provides natural language access to global explanations for black-box image classifiers. The system's core LLM acts as a mediator, translating natural language questions into structured SQL queries over local explanation data. This enables flexible aggregation without exposing users to low-level representations. For each query, the interface outputs statistics-augmented natural language responses, supporting local explanations, and intent-aligned visualizations. We evaluate the system on intent interpretation, query mapping accuracy, generalization to novel queries and datasets, and robustness to linguistic errors. Our results demonstrate that LLM-mediated querying substantially improves the accessibility and usability of global explanations for human-centered XAI.

15.
arXiv (math.PR) 2026-06-16

BBP Phase Transition for a Doubly Sparse Deformed Model

arXiv:2603.04832v3 Announce Type: replace Abstract: We prove the equivalent of the Baik, Ben Arous, Péché (2004) phenomenon for a novel, doubly sparse model where both the Wigner noise matrix and signal vector(s) are sparse. Specifically, we consider a deformed sub-Gaussian sparse Wigner ensemble with a fixed number of sub-Gaussian spike vectors of the same-order sparsity added. We show that spike vectors with signals greater than one are correlated with the top eigenvectors of the deformed ensemble and that each spike vector of signal greater than one induces an outlier eigenvalue. Notably, our results hold in the supercritical sparsity regime for the Wigner matrix ($q \gg \frac{\log n}{n}$) and for any sparse spike vector with an unbounded number of entries ($np\to \infty$). No further relationship between the sparsities of the noise matrix ($q$) and spike vectors ($p$) is necessary. This generalizes the work of Benaych-Georges and Nadakuditi (2010) and Péché (2005).

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

The Weight Norm Sets the Grokking Timescale: A Causal Delay Law

arXiv:2606.13753v1 Announce Type: cross Abstract: Grokking is the delayed onset of generalization in neural networks, arising long after they fit the training data. Whether the weight norm causes this delay is disputed: some studies report a critical norm at the transition, others observe grokking with no fixed norm at all. We settle this by intervening on the norm during training rather than only observing it. Under free training with weight decay, networks grok when the weight norm reaches a value Wc that varies little across seeds and learning rates (CV 1 to 2 percent) and grows with the modular base as a power law. When we instead clamp the norm to a fixed multiple rho of Wc and hold it there, the network still groks, but the delay follows T_grok proportional to exp(alpha rho). One exponent, alpha near 7.5, fits this delay across four moduli (R^2 = 0.996). Over the swept ranges the held norm moves the delay by about 19x and the learning rate by only about 2x, and holding the norm above Wc slows grokking rather than preventing it. A final LayerNorm removes the dependence by decoupling weight scale from the network function; without it the exponential law returns. This pinned-norm delay is the exponential counterpart to the logarithmic delay predicted for a freely contracting norm.

17.
arXiv (math.PR) 2026-06-12

Exact Fourier dimensions of dyadic Mandelbrot cascades under minimal integrability

arXiv:2606.08683v2 Announce Type: replace Abstract: We determine the Fourier dimension of dyadic Mandelbrot cascades under the minimal Kahane-Peyriere integrability condition. The interval theorem is proved in a vector-valued dyadic cascade model in which sibling weights may have arbitrary dependence. For every balanced energy-admissible vector law, almost surely on non-extinction, dim_F(mu)=dim_E(mu)=dim_2(mu)=D_E(X). In the canonical scalar case, under W>=0, E W=1, E[W log_2^+ W]

18.
arXiv (quant-ph) 2026-06-11

Global vs. Local Discrimination of Locally Implementable Multipartite Unitaries

arXiv:2509.10430v2 Announce Type: replace Abstract: We study single-shot distinguishability of locally implementable multipartite unitaries under Local Operations and Classical Communication (LOCC) and global operations. As unitary discrimination depends on both the choice of probing states and the measurements on the evolved states, we classify LOCC and global distinguishability into two categories: adaptive strategies, where probing states are chosen based on measurement outcomes from other subsystems, and restricted strategies, where probing states remain fixed. Our findings uncover three surprising features in the bipartite setting and establish new structural limits for unitary discrimination: (i) Certain pairs of unitaries are globally distinguishable with restricted strategies but indistinguishable under LOCC, even with adaptive strategies. (ii) There exist sets of four unitaries that are distinguishable via LOCC, yet remain globally indistinguishable with restricted strategies. (iii) Some sets of unitaries are globally indistinguishable under adaptive strategies, when probed with separable states, but become distinguishable via LOCC.

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

High-Fidelity Two-Step Image Generation via Teacher-Aligned End-to-End Distillation

Few-step diffusion distillation has become increasingly mature for 4-8-step generation, yet pushing further to 2 steps remains challenging. In this work, we introduce Z-Image Turbo++, a high-quality 2-step image generation model distilled from the 8-step Z-Image Turbo teacher. Our method addresses the central bottlenecks of increased task difficulty and limited model capacity in 2-step generation through three simple but effective design choices tailored to this regime. First, we propose Distribution-Aligned Adversarial Learning, which uses teacher-generated images rather than external real images as real samples for GAN training, providing a more attainable and informative adversarial target. Second, we adopt Step-Decoupled Parameterization, assigning independent model parameters to the two denoising steps to better match their distinct capacity demands. Third, we perform End-to-End Training with Iterative Regularization, allowing the first step to receive gradients from final image quality while preserving a meaningful intermediate generation through an explicit step-1 loss. Together, these designs substantially narrow the quality gap between 2-step and 8-step generation in both qualitative and quantitative evaluations, highlighting the potential of carefully tailored distillation strategies for improving the quality-efficiency trade-off in few-step generation.

20.
arXiv (CS.CV) 2026-06-16

Revealing Artifacts via Noise Amplification: A Novel Perspective for AI-Generated Video Detection

With the rapid advancement of video generation models, distinguishing between AI-generated and authentic videos has emerged as a challenging endeavor. The majority of existing research endeavors concentrate on the development of detectors for identifying samples generated by generative adversarial networks. Nevertheless, the detection of AI-generated videos, particularly those produced by text-to-video models, still remains an uncharted territory. Although state-of-the-art text-to-video models can generate realistic visual content similar to real videos, they fall short of generating the details of the images and the changes in details within the videos. Inspired by this, we address AI-generated video detection from a novel perspective of bit-planes, which can effectively describe the details or noises in images or videos. To this end, we propose a simple yet effective approach called Noise Amplification. This approach first extracts noise signals based on bit-planes, then amplifies these noise signals, and finally feeds them into the discriminator networks for video fake classification. Noise amplification is comprehensively constructed by incorporating three aspects: pixel-level intensity enhancement, region-level spatial amplification, and frame-level temporal aggregation. To evaluate methods of AI-generated video detection in challenging scenarios, we also introduce a benchmark named HardGVD. Extensive experiments on both the large-scale dataset GenVidBench and HardGVD show that our simple approach significantly outperforms state-of-the-art methods.

21.
arXiv (CS.CV) 2026-06-19

Occ-VLM: Occupancy Grounded Vision Language Model for Indoor Scene Understanding

Recently, vision-language models (VLMs) have made significant progress in 3D scene understanding, driving advances in applications such as embodied intelligence and robotic vision. However, existing approaches typically either rely directly on explicit 3D inputs (e.g., point clouds or RGB-D sequences), or introduce an additional 3D geometry encoder to derive 3D-aware visual tokens from 2D images. Such designs structurally decouple 3D geometric perception from the rich 2D semantics learned via vision-language pre-training, hindering the development of a unified 3D vision-language representation. In this work, we propose Occ-VLM, a novel framework for 3D scene understanding that operates purely on posed RGB images and employs a single 2D vision encoder. Specifically, Occ-VLM reconstructs 3D scene occupancy as an auxiliary geometric prior, which is utilized to spatially associate foreground 2D tokens with 3D space. These tokens are then decoded by a Large Language Model (LLM) for unified scene understanding. Extensive experiments demonstrate that Occ-VLM achieves both accurate geometric perception and robust vision-language reasoning: it attains state-of-the-art performance on multi-view occupancy prediction, while performing on par with 3D-input VLMs on 3D Visual Question Answering (VQA) and 3D dense captioning benchmarks.

22.
arXiv (CS.LG) 2026-06-12

NetCause: Counterfactual Learning for Root Cause Analysis in Large-Scale Networks

arXiv:2606.13543v1 Announce Type: cross Abstract: Can a learned model capture how faults propagate through a large-scale network and use this knowledge to causally attribute customer impact to its underlying root cause? Existing root cause analysis techniques often rely on static rules, correlation heuristics, or topology-local reasoning, which struggle to generalize in dynamic environments where faults propagate across complex physical and logical dependencies. We present NetCause, a self-supervised learning-based framework that models network incidents as graph-temporal processes and uses counterfactual simulation to rank candidate root causes. This approach produces an interpretable ranking of root cause hypotheses and integrates naturally with operator-defined mitigation and remediation actions. We train the model on over 1,500 incidents collected over six months from a leading cloud provider's production network and evaluate it on 31 expert-labeled incidents. NetCause consistently improves root cause ranking quality in the regime most relevant to operational decision-making, achieving a 16.1% accuracy improvement over a rule-based heuristic baseline. While training is computationally intensive, inference is lightweight, requiring only seconds of GPU runtime per incident (well below typical telemetry collection latencies).

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

SCAR: Semantic Continuity-Aware Retrieval for Efficient Context Expansion in RAG

Fixed-length chunking in Retrieval-Augmented Generation (RAG) often leads to boundary fragmentation, where critical evidence is split across segments, degrading retrieval recall. While static windowing and parent retrieval improve recall, they introduce significant token overhead. We propose SCAR (Semantic Continuity-Aware Retrieval), an adaptive retrieval policy that selectively expands neighboring chunks by weighing query-neighbor relevance against a structural continuity penalty. SCAR uses a relative expansion threshold tied to each retrieved chunk's own query-relevance, yielding an approximately scale-invariant decision rule that transfers across embedding models without recalibration. Across four diverse corpora (RFC, GDPR, a 10-K report, and a Merger agreement; N=320 queries; 160 boundary-fragmented), SCAR achieves 92.8% recall on boundary-fragmented queries with only 7.84 chunks, a 22.9% reduction compared to static windowing (10.16 chunks). Paired bootstrap tests (B=10,000) confirm the chunk reduction is highly significant (p

24.
arXiv (CS.LG) 2026-06-19

MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

arXiv:2606.19624v1 Announce Type: new Abstract: Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery. Subtle issues in experimental design and model evaluation procedures can degrade the trustworthiness of such benchmarks and lead to erroneous conclusions. We conduct a thorough review of model evaluation issues in the recent MS/MS machine learning literature, using the standard MassSpecGym benchmark suite as a case study to illustrate the impact of these issues. We find evaluation issues in at least 17 of 26 papers reporting MassSpecGym benchmark results in the first year of its adoption. We isolate three classes of failures: (i) data leakage, (ii) shortcut learning, and (iii) implementation bugs and metric divergence. Through extensive experimentation and code replication, we quantify the impact of these issues and show how they corrupt the evaluation standards MassSpecGym was designed to enforce. We distill our findings into recommendations generalizable to MS/MS challenges, benchmarks, and custom evaluation setups. We also release MassSpecGym v1.5, an implementation of our recommendations in the MassSpecGym benchmarking suite which addresses the failure modes identified in this audit. MassSpecGym v1.5 is publicly available at https://github.com/pluskal-lab/MassSpecGym.

25.
arXiv (CS.CL) 2026-06-11

Cross-Layer Discrete Concept Discovery for Interpreting Language Models

Interpreting language models remains challenging due to the existence of residual stream, which linearly mixes and duplicates features across adjacent layers, causing single-layer analyses to miss this cross-layer structure. Cross-layer sparse autoencoders (SAEs) address layer mixing but operate in continuous space, where concepts split across many neurons without clear boundaries. We introduce Cross-Layer Vector Quantized-Variational Autoencoder (CLVQ-VAE), a novel framework which maps representations from a lower layer to a higher layer through a discrete vector-quantization bottleneck, collapsing duplicated residual-stream features into compact, interpretable concept vectors. Our approach combines top-k temperature-based sampling with exponential moving average (EMA) codebook updates, providing controlled exploration of the discrete latent space while maintaining codebook diversity. Across both encoder- and decoder-based models on ERASER-Movie, Jigsaw, and AGNews, CLVQ-VAE outperforms clustering, single-layer vector quantized-variational autoencoder (VQ-VAE), and sparse autoencoder (SAE) baselines across three evaluation axes: removing identified concepts drops model accuracy by up to 93%, LLM judges rank our concepts first in 66.7% of comparisons, and human annotators recover model predictions from our visualizations with 78% accuracy versus 54% for clustering.