Explore the Frontier of Global Academia

01.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2606.16974

The embrace of open science: An analysis of a decade of AI research and 56 800 conference papers

Authors:

Kevin L Coakley↗Thijs Snelleman↗Holger Hoos↗Odd Erik Gundersen↗

arXiv:2606.16974v1 Announce Type: new Abstract: The reproducibility crisis has directed the AI research community toward improving documentation practices. Several studies have identified methodological issues, and in response, the most impactful venues in the field have introduced reproducibility checklists. We seek to understand whether documentation practices have changed over time by assessing all published papers at five leading AI conferences over the past decade. Seven reproducibility variables were identified, quality-assured and used to analyse 56 800 publications. Our analysis reveals that in the period 2014 to 2024, documentation practices have improved; papers sharing both code and data increased nearly sixfold, from 11% to 64% Building on empirical reproducibility rates from a prior study, we estimate - inferred from documentation practices, not direct testing - that reproducibility increased from 28% in 2014 to 64% in 2024. Improvements in documentation practices predate the introduction of reproducibility checklists, suggesting these changes reflect a broader movement toward open science rather than a direct response to formal requirements.

Read & Discuss → View Source →

02.

arXiv (CS.CV) 2026-06-11 DOI: arXiv:2606.10804

SCAIL-2: Unifying Controlled Character Animation with End-to-end In-Context Conditioning

Authors:

Wenhao Yan↗Fengjia Guo↗Zhuoyi Yang↗Jie Tang↗

Controlled character animation requires transferring motion from a driving sequence to a reference character. Prior works heavily rely on intermediate representations, including pose skeletons to represent motion or masked background to represent environment, which inevitably leads to information loss. To address this, we present SCAIL-2, a framework that bypasses those intermediates and achieves end-to-end character animation. By directly concatenating driving videos to the sequence, the model can obtain all the required visual information from the input video. To address the lack of end-to-end data, we unify sub-tasks of character animation with decoupled conditions and then curate a pipeline to synthesize MotionPair-60K, an end-to-end motion transfer dataset containing heterogeneous tasks of character animation. To achieve the unification, we utilize in-context mask conditioning and mode-specific RoPE as soft guidance beyond textual instructions and raw visual information. To address synthetic discrepancy in detailed regions, we propose Bias-Aware DPO to construct preference items to mitigate the errors. Extensive experiments demonstrate that our method substantially outperforms existing state-of-the-art approaches in various character animation tasks. A large subset of synthetic data as well as model weights will be released at our project page: https://teal024.github.io/SCAIL-2/.

Read & Discuss → View Source →

03.

arXiv (CS.AI) 2026-06-19 DOI: arXiv:2606.19538

ITNet: A Learnable Integral Transform That Subsumes Convolution, Attention, and Recurrence

Authors:

Ashim Dhor↗Rasel Mondal↗Pin Yu Chen↗

arXiv:2606.19538v1 Announce Type: new Abstract: Convolutional networks, recurrent networks, and transformers each encode different inductive biases – locality, sequential memory, and content-dependent pairwise interaction – and have remained mathematically distinct since their inception. We show that this fragmentation reflects not a fundamental diversity in how signals should be processed, but rather incomplete views of a single underlying mathematical object: a learnable integral transform. We introduce the Integral Transform Network (ITNet), a unified architecture built around a learnable kernel that depends jointly on positions and features. This kernel is implemented as a small neural network, specifically an MLP, that models pairwise interactions, enabling the model to adapt its behavior from data. We show that convolution, self-attention (including multi-head), and autoregressive recurrence (including LSTM, GRU, S4, and Mamba) arise as special cases under appropriate parameterizations, and that ITNet is a universal approximator of continuous operators. To make this practical, we develop tiled kernel fusion, importance-weighted Monte Carlo integration, and learned low-rank factorization, enabling efficient and scalable computation. A single ITNet architecture with a shared operator and lightweight modality-specific encoders matches or exceeds specialized baselines on ImageNet-1K , GLUE, ModelNet40, VQA\,v2 and NLVR2. The results demonstrate that a single learned interaction mechanism can recover the behavior of all three architectural families from data.

Read & Discuss → View Source →

04.

arXiv (CS.AI) 2026-06-19 DOI: arXiv:2605.07821

Mitigating Simplicity Bias in OOD Detection through Object Co-occurrence Analysis

Authors:

Boyang Dai↗Chaoqi Chen↗Yizhou Yu↗

arXiv:2605.07821v2 Announce Type: replace-cross Abstract: Out-of-distribution (OOD) detection is crucial for ensuring the reliability of deep learning models. Existing methods mostly focus on regular entangled representations to discriminate in-distribution (ID) and OOD data, neglecting the rich contextual information within images. This issue is particularly challenging for detecting near-OOD, as models with simplicity bias struggle to learn discriminative features in disentangled representations. The human visual system can use the co-occurrence of objects in the natural environment to facilitate scene understanding. Inspired by this, we propose an Object-Centric OOD detection framework that learns to capture Object CO-occurrence (OCO) patterns within images. The proposed method introduces a new OOD detection paradigm that understands object co-occurrence within an image by predicting disentangled representations for the test sample, then adaptively divides patterns into three scenarios based on object co-occurrence patterns observed in ID training data, and finally performs OOD detection in a divide-and-conquer manner. By doing so, OCO can distinguish near-OOD by considering the semantic contextual relationships present in their images, avoiding the tendency to focus solely on simple, easily learnable regions. We evaluate OCO through experiments across challenging and full-spectrum OOD settings, demonstrating competitive results and confirming its ability to address both semantic and covariate shifts. Code is released at https://github.com/Michael-McQueen/OCO.

Read & Discuss → View Source →

05.

arXiv (CS.CL) 2026-06-19 DOI: arXiv:2606.20527

StylisticBias: A Few Human Visual Cues Drive Most Social Biases in MLLMs

Authors:

Shaghayegh Kolli↗Timo Cavelius↗Nafiseh Nikeghbal↗Samantha Dalal↗Jana Diesner↗

Multimodal large language models (MLLMs) are increasingly deployed in personally and societally consequential settings, yet the visual cues that shape how these models judge people remain poorly understood. Prior work often compares different (groups of) individuals, making it difficult to separate appearance effects from identity differences. We introduce StylisticBias, a controlled benchmark for evaluating attribute-level social bias in MLLMs. We generate 500 photorealistic base faces and create about 50 single-attribute variations per face, producing about 25K images. This design keeps identity fixed and changes one visual attribute at a time. It lets us measure how specific cues shift model judgments. We evaluate six MLLMs across 25 binary social judgment scenarios. We find that age and body type dominate identity-level effects, while fashion style and other visual cues drive the largest attribute-level shifts. We further find that about 15 attributes account for nearly 80\% of the total variation, showing that bias is concentrated in a small set of visual cues. Sensitivity is strongest in judgments that are semantically aligned with appearance, especially socioeconomic and style-related judgments. We release StylisticBias as a benchmark for fine-grained bias evaluation in multimodal models. Code and dataset: https://github.com/timo-cavelius/StylisticBias and https://hf.co/datasets/shaghayegh/stylistic-bias-dataset.

Read & Discuss → View Source →

06.

arXiv (CS.AI) 2026-06-18 DOI: arXiv:2606.18897

SAERec: Constructing Fine-grained Interpretable Intents Priors via Sparse Autoencoders for Recommendation

Authors:

Jiangnan Xia↗Xuansheng Wu↗Yu Yang↗Xin Wang↗Ninghao Liu↗

arXiv:2606.18897v1 Announce Type: cross Abstract: Intent-based recommender systems have gained significant attention for improving accuracy and interpretability by modeling the underlying motivations behind user behaviors. Most existing models derive intents directly from user sequences via clustering or prototype learning. However, they are sensitive to sequence quality, require presetting the number of intents, and lack explicit semantic grounding. These issues lead to an incomplete and coarse intent set and limit the effectiveness of recommendation. In this paper, we propose the Sparse Autoencoder for intent-based recommendation (SAERec), a novel recommender that automatically constructs a fine-grained and interpretable intent space from a textual corpus to guide recommendation. Rather than treating texts as side signals, SAERec leverages them as high information density evidence for intent construction. Specifically, we first extract a comprehensive set of fine-grained interpretable intents from the latent space of large language models (LLMs) by using a sparse autoencoder (SAE) to disentangle and interpret text embeddings, which isolates intent-related semantics from textual noise. Then, for each user, we retrieve relevant intents from this set as priors to guide recommendation. It contains personal intents matching a user's current interests and public intents capturing general item patterns shared across users (e.g., quality, price). Finally, to integrate retrieved intents into sequence modeling, we propose a multi-branch attention mechanism that captures temporal dependencies and injects both personal and public intent signals, followed by an adaptive fusion layer to construct the final user representation for recommendation. Extensive experiments on public datasets demonstrate the superiority of SAERec, consistently outperforming state-of-the-art baselines while providing human-understandable explanations.

Read & Discuss → View Source →

07.

arXiv (CS.AI) 2026-06-15 DOI: arXiv:2606.14350

Design Methodology and Performance Trade-offs Management for Distributed and Compound AI Systems

Authors:

Milos Gravara↗Andrija Stanisic↗Stefan Nastic↗

arXiv:2606.14350v1 Announce Type: cross Abstract: Artificial Intelligence (AI) systems must typically satisfy service-level objectives including accuracy, latency, and cost. The prevailing model-centric approaches select a monolithic model at design time and apply identical computation regardless of input difficulty, cannot decompose tasks across specialized components, and have knowledge that is fixed at training time. During runtime, this can lead to performance degradation and increasing costs. Because the model is the main design variable, it determines the majority of system behavior, coupling operational objectives to a single design-time choice. Addressing these limitations requires shifting from model-centric to system-centric design. Compound AI systems realize this shift by orchestrating multiple models, algorithms, and tools as distributed AI systems through explicit control logic. The performance of such systems depends on their workflow topology, the models assigned to each task, and the parameters governing runtime behavior. We present a design methodology that organizes this space along two dimensions, workflow topology and configuration selection, and identifies eight design patterns, each consolidating techniques to address a specific limitation of monolithic deployment. We validate our methodology through three case studies. Across our case studies, Compound AI configurations approach accuracy of monolithic models within 2.5 to 4 percentage points while reducing latency by up to 60% and cost by up to 71%. We show that model selection and parameter configuration jointly determine system performance, but the resulting design space grows combinatorially, as workflows compose more patterns and components. Thus, we identify five open challenges that define a roadmap from manually configured prototypes towards systems that automatically discover and maintain SLO-compliance in Compound and Distributed AI systems.

Read & Discuss → View Source →

08.

arXiv (CS.CV) 2026-06-15 DOI: arXiv:2606.13723

Morphology-Aware Sample Assignment: Overcoming IoU Insensitivity for Surface Defect Detection

Authors:

Pengfei Liu↗Yuhan Guo↗

Intersection-over-Union (IoU), as a pivotal metric for evaluating the spatial alignment between candidate proposals and ground-truth annotations, directly determines the quality of positive sample sets and the training efficacy of visual detection models. Through theoretical modeling and analysis, we uncover a non-sensitive region on the IoU response curve, within which samples yield nearly identical IoU scores despite distinct geometric overlaps. To overcome this limitation, we introduce a set of morphological similarity metrics covering area, shape, and aspect ratio, to refine the positive sample assignment process, thereby ensuring more discriminative and reliable matching. A supplementary matching score is derived via mean-based aggregation of these multidimensional similarities, compensating for the intrinsic limitation of IoU in representing structural correspondence. Theoretically, incorporating morphological similarity reshapes the response distribution of the matching function, yielding both effective directional gradients and polygon-like iso-response contours, which tightly confine high-response regions around each ground-truth instance and substantially enhance the precision of positive sample selection. Experiments based on the YOLOv9 framework demonstrate consistent performance gains on both NEUDET and GC10- DET datasets. Notably, the proposed approach is fully plug-and-play and incurs zero additional inference overhead, thereby ensuring deployment efficiency for industrial visual inspection.

Read & Discuss → View Source →

09.

arXiv (math.PR) 2026-06-11 DOI: arXiv:2411.19444

Capital Asset Pricing Model with Size Factor and Normalizing by Volatility Index

Authors:

Abraham Atsiwo↗Andrey Sarantsev↗

arXiv:2411.19444v5 Announce Type: replace-cross Abstract: The Capital Asset Pricing Model (CAPM) relates a well-diversified stock portfolio to a benchmark portfolio. We insert size effect in CAPM, capturing the observation that small stocks have higher risk and return than large stocks, on average. For some size-based stock portfolios, dividing their returns by the Volatility Index makes them closer to independent and normal. In this article, we combine these ideas to create a new discrete-time model, which includes volatility, relative size, and CAPM. We fit this model using real-world data, prove the long-term stability, and connect this research to Stochastic Portfolio Theory. We fill important gaps in our previous article on CAPM with the size factor.

Read & Discuss → View Source →

10.

arXiv (CS.LG) 2026-06-15 DOI: arXiv:2605.26759

Time Series Causal Discovery via Context-Conditioned and Causality-Augmented Pretraining

Authors:

Biao Ouyang↗Tengxue Zhang↗Zhihao Zhuang↗Yang Shu↗Chenjuan Guo↗Bin Yang↗

arXiv:2605.26759v2 Announce Type: replace Abstract: Causal discovery from time series is critical for many real-world applications, such as tracing the root causes of anomalies. Existing approaches typically rely on dataset-specific optimization, making it difficult to transfer their causal discovery capabilities to new time series governed by diverse causal mechanisms. In this paper, we propose PTCD, a novel Pretraining framework for Time-series Causal Discovery, which improves cross-task generalization through context-conditioned modeling and transferable causal augmentation. To model complex temporal causal dependencies, PTCD employs a dual-scale iterative attention mechanism to capture window-level causal relationships, and a Gaussian mixture with a context-level routing mechanism to handle heterogeneous exogenous distributions. To further address distribution shifts across causal graphs, PTCD adopts a pretraining paradigm on synthetic datasets that integrates intervention-based learning and a causal mixup strategy, promoting stable causal discovery and stronger generalization. Extensive experiments on multiple real-world out-of-distribution (OOD) datasets demonstrate that PTCD excels in both causal discovery and root cause identification.

Read & Discuss → View Source →

11.

bioRxiv (Bioinfo) 2026-06-17 DOI: HASH:54c7aca31ea1731e47f32ea93e76790e

Beyond phylogeny: Genome-wide DNA sequence patterns suggest DNA physical properties associated with thermal adaptation in extremophile microbes

Authors:

Safari↗Kari↗

Temperature is a fundamental constraint on biological systems, yet how it is reflected in genome sequence organization remains unclear. Here, we show that genome-wide distributions of short DNA sequences contain a robust signal of thermal adaptation that is largely independent of phylogeny. Using Structural Topic Modelling (STM), a machine-learning approach for identifying groups of co-occurring sequence motifs, we analyze canonical 6-mer and 9-mer frequency profiles of bacterial and archaeal genome proxies (randomly sampled genomic regions) and identify motif families systematically associated with thermophiles and psychrophiles. In bacterial thermophiles, the identified motif families are dominated by highly specific, overrepresented and co-occurring C- and G-stacked hexamers, and a distinct family of CG-periodic hexamers recurring across multiple temperature comparisons. In contrast, bacterial psychrophile-associated motifs are dominated by low-complexity A-, T-, and AT-run hexamers. Thermophilic archaea generally exhibit a distinct CTAG-centred hexamer family, suggesting that different domains may adapt to similar environmental constraints through different sequence-level solutions. However, this domain-level contrast is not absolute: in a targeted analysis of two thermophilic bacterium–archaeon pairs, we find unusually similar frequencies of all the STM-identified thermophile-associated hexamer families, suggesting that shared high-temperature environments can, in specific cases, partially override phylogenetic divergence. Notably, the identified motif families constitute only a small and highly selective subset of the vast space of possible G+C-rich or A+T-rich sequences. This indicates that thermal adaptation is associated with specific sequence architectures rather than broad shifts in nucleotide composition. Accordingly, the observed signal cannot be explained by overall base composition alone, but instead arises from structured combinations and positional arrangements of nucleotides within short sequence contexts. Related motif families are recovered at both k=6 and k=9, indicating that the signal reflects systematic shifts in genome-wide sequence organization rather than isolated sequence motifs. These patterns are consistent with known sequence-dependent DNA physical properties documented in biochemical and biophysical studies, including differences in base-stacking interactions and conformational flexibility. Together, our results suggest that genome-wide sequence organization reflects sequence-dependent DNA physical properties associated with thermal adaptation, revealing a previously underappreciated physical layer of genomic information beyond phylogenetic history.

Read & Discuss → View Source →

12.

arXiv (CS.AI) 2026-06-15 DOI: arXiv:2602.00845

Optimizing Agentic Reasoning with Retrieval via Synthetic Semantic Information Gain Reward

Authors:

Senkang Hu↗Yong Dai↗Yuzhi Zhao↗Yihang Tao↗Yu Guo↗Zhengru Fang↗Sam Tak Wu Kwong↗Yuguang Fang↗

arXiv:2602.00845v3 Announce Type: replace Abstract: Agentic reasoning enables large reasoning models (LRMs) to dynamically acquire external knowledge, but yet optimizing the retrieval process remains challenging due to the lack of dense, principled reward signals. In this paper, we introduce InfoReasoner, a unified framework that incentivizes effective information seeking via a synthetic semantic information gain reward. Theoretically, we redefine information gain as uncertainty reduction over the model's belief states, establishing guarantees, including non-negativity, telescoping additivity, and channel monotonicity. Practically, to enable scalable optimization without manual retrieval annotations, we propose an output-aware intrinsic estimator that computes information gain directly from the model's output distributions using semantic clustering via bidirectional textual entailment. This intrinsic reward guides the policy to maximize epistemic progress, enabling efficient training via Group Relative Policy Optimization (GRPO). Experiments across seven question-answering benchmarks demonstrate that InfoReasoner consistently outperforms strong retrieval-augmented baselines, achieving up to 5.4% average accuracy improvement. Our work provides a theoretically grounded and scalable path toward agentic reasoning with retrieval. The code is available at https://github.com/dl-m9/InfoReasoner

Read & Discuss → View Source →

13.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2410.21258

Provable quantum speedups for computing persistence in topological data analysis

Authors:

Casper Gyurik↗Alexander Schmidhuber↗Robbie King↗Vedran Dunjko↗Ryu Hayakawa↗

arXiv:2410.21258v2 Announce Type: replace-cross Abstract: Topological data analysis (TDA) aims to extract noise-robust features from a data set by examining the number and persistence of holes in its topology. We provide an efficient quantum algorithm for a computational problem closely related to a core task in TDA – determining whether a given hole persists across different length scales. Further, we prove the problem itself is $\mathsf{BQP}_1$-hard, implying that a classical solution is extremely unlikely; this stands in contrast to all previous quantum approaches to TDA, where the problems were also intractable for quantum computers, or where a rigorous proof of classical hardness still remains open. This result implies an {exponential} quantum speedup for this problem under standard complexity-theoretic assumptions. Our approach relies on encoding the persistence of a hole in a variant of the guided sparse Hamiltonian problem, where the guiding state is constructed from a harmonic representative of the hole.

Read & Discuss → View Source →

14.

arXiv (CS.CV) 2026-06-11 DOI: arXiv:2606.11682

Parameter-Efficient Adapter Tuning for Tabular-Image Multimodal Learning

Authors:

Jiaqi Luo↗

Tabular-image multimodal learning aims to improve predictive modeling by jointly using structured tabular attributes and visual data. Although pretrained encoders provide strong modality-specific representations, full fine-tuning can be computationally expensive, while keeping encoders frozen may limit task-specific adaptation. We propose the Tabular-Image Adapter (TI-Adapter), a modality-specific adapter-based fine-tuning framework for efficient multimodal adaptation. TI-Adapter freezes the pretrained tabular encoder and learns an adapter after the extracted tabular embedding, while adapting the image branch with embedding-level and bottleneck-level adapters instead of full fine-tuning. Experiments on 20 tabular-image datasets show that TI-Adapter achieves competitive or better predictive performance than full fine-tuning while using substantially fewer trainable parameters. Ablation studies further demonstrate the importance of adapter placement for balancing performance and practical efficiency.

Read & Discuss → View Source →

15.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2507.15584

We Need to Rethink Benchmarking in Anomaly Detection

Authors:

Philipp R\"ochner↗Simon Kl\"uttermann↗Kevin Kammler↗Franz Rothlauf↗Emmanuel M\"uller↗Daniel Schl\"or↗

arXiv:2507.15584v2 Announce Type: replace Abstract: Despite the continuous proposal of new anomaly detection algorithms and extensive benchmarking efforts, progress seems to stagnate, with only minor performance differences between established baselines and new algorithms. In this position paper, we argue that this stagnation is due to limitations in how we evaluate anomaly detection algorithms. In current benchmarks, a trivial algorithm that only checks for extreme values in individual features performs competitively with state-of-the-art deep learning methods, despite failing on simple cases such as anomalies within an annulus of normal points. Moreover, existing benchmarks do not adequately reflect the diversity of anomaly detection applications, making it difficult for practitioners to reliably select algorithms for their applications. Consequently, we need to rethink benchmarking in anomaly detection. In our opinion, anomaly detection should be studied using scenarios that group applications sharing relevant characteristics, defined through a common taxonomy. Benchmarking within scenarios enables scenario-specific choices for preprocessing, metrics, and model selection, clarifying which advances transfer across similar applications and providing practitioners with reliable guidance for their specific contexts.

Read & Discuss → View Source →

16.

arXiv (math.PR) 2026-06-12 DOI: arXiv:2603.07245

The Lov\'{a}sz Local Lemma: Foundations and Applications

Authors:

Igal Sason↗

arXiv:2603.07245v5 Announce Type: replace-cross Abstract: The Lov\'{a}sz Local Lemma (LLL) is a central tool in probabilistic combinatorics, providing a sufficient condition under which a finite collection of undesirable events with limited dependencies can be simultaneously avoided with positive probability. This paper offers a self-contained expository treatment of the lemma and its strengthened versions, emphasizing mathematical foundations, conceptual clarity, and applications. We begin with a pedagogically motivated proof of the LLL based entirely on unconditional probability inequalities. Particular attention is given to the symmetric form of the lemma and several subsequent strengthenings. The paper also discusses a variety of classical applications of both the symmetric and asymmetric forms of the LLL in combinatorics and graph theory, including bounds for the edge-disjoint paths problem, satisfiability of Boolean formulas in conjunctive normal form, lower bounds on diagonal and off-diagonal Ramsey numbers, hypergraph coloring results, structural properties of directed graphs, and acyclic graph colorings. Additional observations and refinements are provided throughout. We also introduce the algorithmic framework of Moser and Tardos, highlighting its constructive counterpart to the LLL, together with an introduction to the entropy-compression principle. The lopsided LLL, a refinement of the LLL, is presented along with an application to the Latin transversal problem. We further discuss the cluster-expansion lemma and its relation to the LLL, and present an alternative treatment of the Latin transversal problem from the cluster-expansion perspective that yields an improved result. The paper concludes with a high-level overview of the iterated LLL, also known as the semi-random method.

Read & Discuss → View Source →

17.

medRxiv (Medicine) 2026-06-15 DOI: HASH:ba165e3de45668bc79149bc896852894

VarEx: A Large Language Model Pipeline for Automated Extraction of Exposures, Outcomes, and Covariates from Epidemiologic Studies

Authors:

Malec↗S. A↗Pradhan↗Upadhayaya↗Metzger↗

Objective: Observational studies are essential for investigating risk factors for Alzheimer's disease and related dementias (ADRD), but inconsistent reporting and selection of covariates can contribute to residual confounding, omitted-variable bias, and reduced reproducibility. We developed and evaluated VAREX (Variable Extraction), a large language model (LLM)-based information extraction framework designed to automatically identify exposures, outcomes, and covariates from epidemiologic studies and populate structured evidence repositories. Materials and Methods: VAREX combines retrieval-augmented generation, biomedical language-model embeddings, semantic chunking, cross-encoder reranking, and prompt-engineered LLM workflows to extract epidemiologic variables from full-text biomedical articles. The framework was evaluated using a reference-standard corpus of observational studies examining blood pressure variability (BPV) and Alzheimer's disease-related dementias (ADRD), together with external validation datasets involving other exposure-outcome relationships. Extracted variables were compared with independently curated human reference standards using semantic matching and one-to-one assignment procedures. Covariates were additionally classified into ten epidemiologically relevant semantic categories. Results: In the primary BPV[->]ADRD corpus (10 studies), VAREX achieved a precision of 0.91, recall of 0.84, and F1-score of 0.87 for variable extraction. Covariate classification accuracy was 0.90, yielding a strict extraction-and-classification F1-score of 0.78. External validation datasets demonstrated comparable performance across diverse epidemiologic domains, with extraction F1-scores ranging from 0.73 to 0.85. Category-level performance was strongest for health behaviors (F1=0.96), sociodemographic variables (F1=0.90), and medication exposures (F1=0.89). Compared with published estimates of manual systematic-review effort, VAREX reduced processing time from approximately 61 minutes to 9 minutes per article, representing an 85.7% reduction in review time. Discussion: These findings demonstrate that LLM-based information extraction can accurately identify and classify epidemiologic variables across heterogeneous observational-study designs. Automated extraction enables scalable construction of structured repositories of exposures, outcomes, and covariates while substantially reducing the labor required for evidence synthesis and systematic reviews. Conclusion: VAREX provides an effective framework for automated extraction and classification of epidemiologic variables from the biomedical literature. By supporting large-scale evidence synthesis and structured knowledge resource development, VAREX may facilitate more rigorous observational research, improved confounder identification, and enhanced reproducibility in epidemiology.

Read & Discuss → View Source →

18.

PLOS Medicine 2026-05-15 DOI: HASH:48fbfe16e5e0277eedd419e3b41ee93e

Spatial transcriptomic-metabolic features of tumor foci and tumor capsule in microvascular invasion with hepatocellular carcinoma: A spatial multi-omics study

Authors:

Zhi-Hui Luo↗

by Zhi-Hui Luo, Na Wang, Jingwei Zhao, Fei Long, Si Wu, Wei Zhong, Wei-Ming Chen, Bicheng Wang, Kun Wang, Yufeng Yuan, Jingjiao Zhou, Chunhui Yuan, Fubing Wang Background Microvascular invasion (MVI) is closely related to the recurrence and metastasis of hepatocellular carcinoma (HCC), but the underlying cellular mechanism remains largely elusive. This study aims to elucidate the regional cellular discrepancy between MVI-positive (MVI+) and MVI-negative (MVI−) HCC by integrating Spatial transcriptomics (ST) and spatial metabolomics (SM). Methods and findings ST and SM were performed on six tissue samples from four patients (including 2 MVI+, 2 MVI−, and 2 paratumor tissues), with the integration of 79 public single-cell RNA sequencing datasets of HCC. Patient identity was used as a covariate in the linear equation for regional differentially expressed gene analysis with the ST data. Clinical validation was conducted through multiplex immunofluorescence staining in 79 patients, together with external validation in the cancer genome atlas (TCGA)-liver hepatocellular carcinoma (LIHC) cohort (n = 299) and an independent microarray dataset (n = 62). For cell-type-specific metabolic profiling, spatial transcriptomic-metabolic registration was performed. The functional roles of key metabolites were further validated in vitro using inflammatory cancer-associated fibroblasts (iCAFs) derived from hepatic stellate cells (HSCs) and primary CAFs through co-culture models and various functional assays assessing cell proliferation, migration, and invasion. In the tumor lesion, a malignant STMN1+HMGN2+GPC3+ cell subtype enriched in MVI+ HCC was identified, which exhibited enhanced proliferative activity and was associated with poor prognosis. This finding was further confirmed in a local cohort of 79 patients, where multiplex immunofluorescence staining for the three genes (STMN1, HMGN2, and GPC3) showed significantly higher expression in the MVI+ group than in the MVI− group (p = 0.046). Integrated SM analysis further revealed that this cell population underwent metabolic reprogramming characterized by suppressed glycerolipid metabolism. In the tumor capsule, iCAFs-related genes were downregulated in MVI+ cases, and iCAFs were located distally from the tumor boundary. Spatial metabolite mapping showed a strong correlation between taurine and iCAFs, and functional assays demonstrated that taurine promotes HCC proliferation and migration by suppressing iCAF activity. One limitation of this study is the small sample size of spatial omics data, which hinders a more complete molecular functional analysis of the STMN1+HMGN2+GPC3+ cell subtype and iCAFs in MVI+ HCC. Larger-scale ST cohorts are required to further validate and expand the findings of this study. Conclusions This integrative spatial atlas proposes a hypothesis that there exists a highly proliferative and metabolically reprogrammed malignant cell subtype in the tumor lesion of MVI+ HCC, and that taurine in the tumor capsule modulates iCAF activity to influence tumor progression. The exploratory results provide mechanistic insights into MVI-related HCC progression and offer potential avenues for targeted therapeutic intervention of MVI+ HCC.

Read & Discuss → View Source →

19.

arXiv (CS.CV) 2026-06-11 DOI: arXiv:2606.12171

Beyond Dark Knowledge: Mixup-Based Distillation for Reliable Predictions

Authors:

Jos\'e Medina↗Paul Honeine↗Abdelaziz Bensrhair↗Amnir Hadachi↗

Knowledge Distillation (KD) and mixup have proven effective at inducing smoothness in class boundaries; KD captures inherent class relationships in probability distributions, and mixup enforces them through convex combinations of inputs. Their interaction, however, remains poorly understood, particularly when mixup is applied only during student training. In this setting, the teacher is queried on inputs drawn from a vicinal distribution it never saw during training, a controlled mismatch whose effect on knowledge transfer has not been characterised. We show that this mismatch causes the teacher's supervisory signal to be dominated by distributional confusion rather than inter-class structure. Despite it, the student does not merely imitate the teacher: it independently acquires greater linearity in the vicinal region, a structural property that the teacher lacks, and goes beyond dark-knowledge transfer. KD with mixup consistently improves student accuracy and reduces overconfidence by an order of magnitude relative to the baseline, across CIFAR and ImageNet with varying-capacity teachers. Crucially, calibration propagates from teacher to student independently of accuracy transfer, and temperature scaling governs a measurable accuracy-calibration trade-off that becomes more pronounced under vicinal training. These results reframe mixup distillation not as a degraded version of standard KD, but as a richer transfer channel that simultaneously shapes discriminative performance, uncertainty estimation, and representational geometry.

Read & Discuss → View Source →

20.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2605.21312

Frontier: Towards Comprehensive and Accurate LLM Inference Simulation

Authors:

Yicheng Feng↗Xin Tan↗Yangtao Deng↗Yimin Jiang↗Yibo Zhu↗Hong Xu↗

arXiv:2605.21312v2 Announce Type: replace-cross Abstract: Modern LLM serving is no longer homogeneous or monolithic. Production systems now combine disaggregated execution, complex parallelism, runtime optimizations, and stateful workloads such as reasoning, agents, and RL rollouts. Simulation is attractive for exploring this growing design space, yet existing simulators lack the architectural completeness and decision-grade fidelity it demands. Their monolithic-replica abstractions are ill-suited to disaggregated serving, while average-case analytical proxies can distort SLA predictions and even reverse optimization conclusions. We present Frontier, a discrete-event simulator for modern LLM inference serving. Frontier features a disaggregated abstraction. It captures the structure and dynamics of modern serving systems by modeling co-location, Prefill-Decode Disaggregation (PDD), and Attention-FFN Disaggregation (AFD) with role-specific cluster workers, incorporating key runtime optimizations (e.g., CUDA Graphs, speculative decoding) within the scheduler-batch-engine loop, and supporting stateful requests for emerging workloads. It further provides accurate and generalizable predictions of computation, communication, and memory costs across diverse serving scenarios with complex workload compositions. On 16-H800 GPU testbed, Frontier achieves an average throughput error below 4%. Compared with state-of-the-art simulators, it reduces end-to-end latency error from 44.9% to 6.4% under co-location and from 51.7% to 2.6% under disaggregation. It scales to over 1K GPUs on commodity CPUs and enables new use cases such as SLA-dependent Pareto frontier exploration, heterogeneous disaggregated allocation, agentic reasoning scheduling validation, and RL post-training reconfiguration. We release Frontier at https://github.com/NetX-lab/Frontier.

Read & Discuss → View Source →

21.

arXiv (CS.CV) 2026-06-16 DOI: arXiv:2606.17048

Exact Posterior Score Estimation for Solving Linear Inverse Problems

Authors:

Abbas Mammadov↗Ozgur Kara↗Kaan Oktay↗Iskander Azangulov↗Adil Kaan Akan↗Hyungjin Chung↗James Matthew Rehg↗Yee Whye Teh↗

Diffusion and flow-based models learn powerful data priors by training a denoiser to reverse Gaussian corruption. To use this prior to solve a linear inverse problem, one needs to sample from the posterior, but the score that the prior provides is the unconditional score, not the posterior score. Existing methods either steer a fixed pretrained denoiser with approximate measurement-matching corrections, or train a conditional restoration model that abandons the denoising structure of the prior. We derive the exact posterior score in closed form for linear Gaussian inverse problems under general Gaussian interpolants, and show that posterior sampling reduces to a denoising problem at an operator-dependent shifted pivot under an anisotropic noise covariance. We turn this identity into Exact Posterior Score (EPS), a denoising training objective that preserves the input/output structure of standard pretraining and can therefore be trained from scratch or fine-tuned from a pretrained denoiser. At inference, EPS uses the same sampler as the underlying backbone, with no likelihood gradients or projections. We evaluate EPS on five linear inverse problems across FFHQ and ImageNet, where it outperforms training-free and training-based baselines on fidelity, perceptual, and distributional metrics, while using roughly an order of magnitude fewer denoiser evaluations than gradient-based posterior samplers.

Read & Discuss → View Source →

22.

arXiv (CS.LG) 2026-06-17 DOI: arXiv:2410.10137

Variational autoencoders with latent high-dimensional steady geometric flows for dynamics

Authors:

Andrew Gracyk↗

arXiv:2410.10137v5 Announce Type: replace Abstract: We develop Riemannian approaches to variational autoencoders (VAEs) for PDE-type ambient data with regularizing geometric latent dynamics, which we refer to as VAE-DLM, or VAEs with dynamical latent manifolds. We redevelop the VAE framework such that manifold geometries, subject to our geometric flow, embedded in Euclidean space are learned in the intermediary latent space developed by encoders and decoders. By tailoring the geometric flow in which the latent space evolves, we induce latent geometric properties of our choosing, which are reflected in empirical performance. We reformulate the traditional evidence lower bound (ELBO) loss with a considerate choice of prior. We develop a linear geometric flow with a steady-state regularizing term. This flow requires only automatic differentiation of one time derivative, and can be solved in moderately high dimensions in a physics-informed approach, allowing more expressive latent representations. We discuss how this flow can be formulated as a gradient flow, and maintains entropy away from metric singularity. This, along with an eigenvalue penalization condition, helps ensure the manifold is sufficiently large in measure, nondegenerate, and a canonical geometry, which contribute to a robust representation. Our methods focus on the modified multi-layer perceptron architecture with tanh activations for the manifold encoder-decoder. We demonstrate, on our datasets of interest, our methods perform at least as well as the traditional VAE, and oftentimes better. Our methods can outperform this and a VAE endowed with our proposed architecture, frequently reducing out-of-distribution (OOD) error between 15% to 35% on select datasets. We highlight our method on ambient PDEs whose solutions maintain minimal variation in late times. We provide empirical justification towards how we can improve robust learning for external dynamics with VAEs.

Read & Discuss → View Source →

23.

arXiv (CS.AI) 2026-06-11 DOI: arXiv:2606.11473

CRUMB: Efficient Prior Fitted Network Inference via Distributionally Matched Context Batching

Authors:

Jamie Heredge↗Mattia J. Villani↗Pranav Deshpande↗Akshay Seshadri↗Niraj Kumar↗

arXiv:2606.11473v1 Announce Type: cross Abstract: Prior-fitted networks (PFNs) are a promising class of tabular foundation models that perform in-context learning, whereby the entire labelled training set is supplied as context, and predictions for test queries are produced in a single forward pass. However, the quadratically scaling self-attention mechanism in many PFN architectures makes inference prohibitive for very large training datasets. We propose CRUMB (Clustered Retrieval Using Minimised-MMD Batching), a three-stage inference wrapper that (i) clusters the test queries, (ii) selects a small, distributionally matched training subset for each cluster by greedily minimising the maximum mean discrepancy (MMD), and (iii) runs exact PFN inference on each reduced-context batch. CRUMB is architecture-agnostic and requires no retraining. On the 51-dataset TabArena benchmark, evaluated across three PFN architectures (TabPFNv2, TabICLv1, TabICLv2), we show that CRUMB outperforms similar state-of-the-art context selection strategies. We also show that CRUMB is resilient to covariate drift, as the MMD-minimisation step naturally helps align the training context distribution to match the current test batch distributions.

Read & Discuss → View Source →

24.

bioRxiv (Bioinfo) 2026-06-10 DOI: HASH:8324f2a93f6e27d4edbb4424ac39830e

Promera: a unified model for biomolecular structure prediction, filtering, and design

Authors:

Jing↗Bafna↗Diaz↗D. J↗Klivans↗A. R↗Berger↗

Generative models have become staple tools for modeling and designing biomolecular structures. However, although these tools have improved in structural prediction accuracy, their ability to filter designed binders—an essential use case—remains insufficient; whereas design methods have focused more on unconstrained binder generation rather than capabilities enabled by controllable design. We introduce Promera, a unified generative model that combines all-atom structure prediction with improved filtering and controllable design. We find that Promera's confidence metrics are more accurate for filtering binders from non-binders for both miniproteins and nanobodies, while its co-folding performance surpasses popular open-source models (OpenFold3-p2, Boltz-2) on therapeutically relevant categories. As a design model, Promera generates binders by predicting masked protein sequences with optional epitope, paratope, and template constraints. Remarkably, our nanobody designs match the in silico success rates from backprop-based techniques (mBER) when evaluated under co-folding confidence filters. We further provide two in silico demonstrations of the the versatile capabilities of our design method: epitope targeting of the Andes hantavirus glycoprotein with VHHs and active state stabilization of the beta-2 andrenergic GPCR. We conclude by proposing a scaling law for co-folding models, suggesting a path for further performance improvement.

Read & Discuss → View Source →

25.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2601.19697

AlignCoder: Aligning Retrieval with Target Intent for Repository-Level Code Completion

Authors:

Tianyue Jiang↗Yanli Wang↗Yanlin Wang↗Daya Guo↗Ensheng Shi↗Yuchi Ma↗Jiachi Chen↗Zibin Zheng↗

arXiv:2601.19697v2 Announce Type: replace-cross Abstract: Repository-level code completion remains a challenging task for existing code large language models (code LLMs) due to their limited understanding of repository-specific context and domain knowledge. While retrieval-augmented generation (RAG) approaches have shown promise by retrieving relevant code snippets as cross-file context, they suffer from two fundamental problems: misalignment between the query and the target code in the retrieval process, and the inability of existing retrieval methods to effectively utilize the inference information. To address these challenges, we propose AlignCoder, a repository-level code completion framework that introduces a query enhancement mechanism and a reinforcement learning based retriever training method. Our approach generates multiple candidate completions to construct an enhanced query that bridges the semantic gap between the initial query and the target code. Additionally, we employ reinforcement learning to train an AlignRetriever that learns to leverage inference information in the enhanced query for more accurate retrieval. We evaluate AlignCoder on two widely-used benchmarks (CrossCodeEval and RepoEval) across five backbone code LLMs, demonstrating an 18.1% improvement in EM score compared to baselines on the CrossCodeEval benchmark. The results show that our framework achieves superior performance and exhibits high generalizability across various code LLMs and programming languages.

Read & Discuss → View Source →