Annotation-Informed Block-Sparse Bayesian Modeling for cis-Expression Prediction

Genotype-based cis-expression prediction depends on accurately modeling local regulatory architecture. We present block-sparse Bayesian sparse linear mixed model (bsBSLMM), an extension of Bayesian sparse linear mixed model (BSLMM) that incorporates linkage disequilibrium (LD)-block spike-and-slab sparsity and a transcription start site (TSS)-informed SNP inclusion prior. Across 23,098 genes from GEUVADIS European-ancestry lymphoblastoid cell lines, bsBSLMM retained more predictable genes than BSLMM, LASSO, BLUP, TIGAR elastic net, and TIGAR Dirichlet-process regression under matched evaluation criteria. Compared with BSLMM, bsBSLMM improved held-out prediction performance for most shared genes, with gains driven primarily by LD-block sparsity and further enhanced by the TSS-informed prior. Variants selected by bsBSLMM showed stronger enrichment in GM12878 DNase and H3K27ac regulatory regions than variants selected by BSLMM. In transcriptome-wide association study (TWAS) analysis, bsBSLMM recovered established inflammatory bowel disease signals, including IL23R, and identified additional genome-wide significant genes not detected by BSLMM. Independent validation in the Louisiana Osteoporosis Study reproduced the increased prediction yield across ancestries and recovered biologically relevant bone mineral density pathways in downstream TWAS and gene set enrichment analyses. These results demonstrate that incorporating LD-block structure and biologically informed SNP priors improves cis-expression prediction and enhances downstream TWAS discovery.

Embodied3DBench: Benchmarking Low-Level Embodied Spatial Intelligence of Vision Language Models

Are current Vision Language Models (VLMs) ready to comprehend and reason about complex embodied interactions in 3D environments? We introduce Embodied3DBench, a robot-centric benchmark targeting low-level spatial intelligence in embodied 3D environments. To systematically evaluate these foundational perceptual capabilities, the benchmark includes 6 task categories divided into two core groups: Spatial Structural Understanding (Grounding, Spatial Relation Prediction, and Multi-view Correspondence) and Interaction-Oriented Perception (Affordance Prediction, Grasp Point Prediction, and Trajectory Prediction). The benchmark spans 12 subcategories and contains over 21k high-quality question-answer pairs. We evaluate 13 state-of-the-art models, and the results show that while current models exhibit relatively strong high-level spatial reasoning, such as understanding object-to-object positional relations, they remain fragile in interaction-oriented perception, highlighting a significant lack of robust 3D-aware interaction priors. To actively bridge this capability gap revealed by our benchmark, we further synthesize a large-scale training dataset comprising 1.3M QA pairs. Notably, fine-tuning on this dataset yields significant improvements in low-level spatial intelligence. Ultimately, Embodied3DBench fills a critical gap by providing both a systematic evaluation framework and a scalable data solution, setting a clear target for the development of interaction-aware multimodal systems.

SkillEvolBench: Benchmarking the Evolution from Episodic Experience to Procedural Skills

Large language model (LLM) agents accumulate rich episodic trajectories while solving real-world tasks, but it remains unclear whether such experience can be distilled into reusable procedural skills. We introduce SkillEvolBench, a diagnostic benchmark for evaluating this step from experience reuse to skill formation. It contains 180 tasks across six real-world agent environments, organized into role-conditioned task families with shared latent procedures. Agents learn from acquisition tasks, update an external skill library using compacted trajectories and verifier feedback, and then face frozen deployment tasks testing context shift, adversarial shortcuts, and composition. By comparing self-generated and curated-start skill evolution against no-skill and raw-trajectory controls, SkillEvolBench separates procedural abstraction from base capability, curated prior knowledge, and direct reuse of episodic traces. Across ten model configurations and three agent harnesses, we find that current agents often adapt locally but rarely form robust reusable skills. Skill-based conditions can improve acquisition or replay, and individual models sometimes gain on specific deployment axes, but these gains are unstable under frozen deployment. Raw-trajectory reuse frequently outperforms distilled skills, suggesting that current abstraction procedures discard contextual and procedural cues that remain useful for future tasks. Capacity and cost analyses further show that writing more skills or larger Tier-3 resource libraries is not sufficient: additional updates can improve coverage while introducing episode-specific drift and procedural clutter. These findings position SkillEvolBench as a testbed for measuring when one-off experience becomes durable procedural knowledge rather than task-local memory.

JoyAI-RA 0.1: A Foundation Model for Robotic Autonomy

Robotic autonomy in open-world environments is fundamentally limited by insufficient data diversity and poor cross-embodiment generalization. Existing robotic datasets are often limited in scale and task coverage, while relatively large differences across robot embodiments impede effective behavior knowledge transfer. To address these challenges, we propose JoyAI-RA, a vision-language-action (VLA) embodied foundation model tailored for generalizable robotic manipulation. JoyAI-RA presents a multi-source multi-level pretraining framework that integrates web data, large-scale egocentric human manipulation videos, simulation-generated trajectories, and real-robot data. Through training on heterogeneous multi-source data with explicit action-space unification, JoyAI-RA effectively bridges embodiment gaps, particularly between human manipulation and robotic control, thereby enhancing cross-embodiment behavior learning. JoyAI-RA outperforms state-of-the-art methods in both simulation and real-world benchmarks, especially on diverse tasks with generalization demands.

Streaming Structured Inference with Flash-SemiCRF

Semi-Markov Conditional Random Fields (semi-CRFs) assign labels to segments of a sequence rather than to individual positions, enabling exact inference over segment-level features and principled uncertainty estimates at their boundaries. However, existing implementations must materialize a large edge potential tensor whose size grows with sequence length, maximum segment length, and label count, becoming prohibitive for speech-scale state spaces and intractable at genomic scales where sequences can exceed 100,000 positions. This memory bottleneck has limited the adoption of exact segment-level inference for long sequences and large label sets. We identify that the core inefficiency is materializing edge potentials that can instead be evaluated on-the-fly from a compact prefix-sum array, and make several improvements. First, replacing the stored edge tensor with prefix-sum lookup reduces the memory footprint by a factor proportional to the product of segment length and label count. Second, a streaming forward-backward pass with checkpoint-boundary normalization keeps working memory sublinear in sequence length while preserving exact gradients. Third, zero-centered cumulative scores control numerical drift and induce an adaptive duration prior under label imbalance. We integrate these ideas into Flash-SemiCRF, a fused Triton kernel that enables exact semi-CRF inference on previously intractable problem sizes. Available at https://github.com/biobenkj/flash-semicrf.

Attention Sink in Transformers: A Survey on Utilization, Interpretation, and Mitigation

As the foundational architecture of modern machine learning, Transformers have driven remarkable progress across diverse AI domains. Despite their transformative impact, a persistent challenge across various Transformers is Attention Sink (AS), in which a disproportionate amount of attention is focused on a small subset of specific yet uninformative tokens. AS complicates interpretability, significantly affecting the training and inference dynamics, and exacerbates issues such as hallucinations. In recent years, substantial research has been dedicated to understanding and harnessing AS. However, a comprehensive survey that systematically consolidates AS-related research and offers guidance for future advancements remains lacking. To address this gap, we present the first survey on AS, structured around three key dimensions that define the current research landscape: Fundamental Utilization, Mechanistic Interpretation, and Strategic Mitigation. Our work provides a pivotal contribution by clarifying key concepts and guiding researchers through the evolution and trends of the field. We envision this survey as a definitive resource, empowering researchers and practitioners to effectively manage AS within the current Transformer paradigm, while simultaneously inspiring innovative advancements for the next generation of Transformers. The paper list of this work is available at https://github.com/ZunhaiSu/Awesome-Attention-Sink.

GESS: Multi-cue Guided Local Feature Learning via Geometric and Semantic Synergy

Robust local feature detection and description are foundational tasks in computer vision. Existing methods primarily rely on single appearance cues for modeling, leading to unstable keypoints and insufficient descriptor discriminability. In this paper, we propose a multi-cue guided local feature learning framework that leverages semantic and geometric cues to synergistically enhance detection robustness and descriptor discriminability. Specifically, we construct a joint semantic-normal prediction head and a depth stability prediction head atop a lightweight backbone. The former leverages a shared 3D vector field to deeply couple semantic and normal cues, thereby resolving optimization interference from heterogeneous inconsistencies. The latter quantifies the reliability of local regions from a geometric consistency perspective, providing deterministic guidance for robust keypoint selection. Based on these predictions, we introduce the Semantic-Depth Aware Keypoint (SDAK) mechanism for feature detection. By coupling semantic reliability with depth stability, SDAK reweights keypoint responses to suppress spurious features in unreliable regions. For descriptor construction, we design a Unified Triple-Cue Fusion (UTCF) module, which employs a semantic-scheduled gating mechanism to adaptively inject multi-attribute features, improving descriptor discriminability. Extensive experiments on four benchmarks validate the effectiveness of the proposed framework. The source code and pre-trained model will be available at: https://github.com/yiyscut/GESS.git.

GenoBERT: A Language Model for Accurate Genotype Imputation

Genotype imputation enables dense variant coverage for genome-wide association and risk-prediction studies, yet conventional reference-panel methods remain limited by ancestry bias and reduced rare-variant accuracy. We present Genotype Bidirectional Encoder Representations from Transformers (GenoBERT), a transformer-based, reference-free framework that tokenizes phased genotypes and uses a self-attention mechanism to capture both short- and long-range linkage disequilibrium (LD) dependencies. Benchmarking on two independent datasets including the Louisiana Osteoporosis Study (LOS) and the 1000 Genomes Project (1KGP) across ancestry groups and multiple genotype missingness levels (5-50%) shows that GenoBERT achieves the highest overall accuracy compared to four baseline methods (Beagle5.4, SCDA, BiU-Net, and STICI). At practical sparsity levels (up to 25% missing), GenoBERT attains high overall imputation accuracy ($r^2 approx 0.98$) across datasets, and maintains robust performance ($r^2 > 0.90$) even at 50% missingness. Experimental results across different ancestries confirm consistent gains across datasets, with resilience to small sample sizes and weak LD. A 128-SNP (single-nucleotide polymorphism) context window (approximately 100 Kb) is validated through LD-decay analyses as sufficient to capture local correlation structures. By eliminating reference-panel dependence while preserving high accuracy, GenoBERT provides a scalable and robust solution for genotype imputation and a foundation for downstream genomic modeling.

MathGen: Revealing the Illusion of Mathematical Competence through Text-to-Image Generation

Modern generative models have demonstrated the ability to solve challenging mathematical problems. In many real-world settings, however, mathematical solutions must be expressed visually through diagrams, plots, geometric constructions, and structured symbolic layouts, where correctness depends on precise visual composition. This naturally raises the question of whether generative models can still do so when the answer must be rendered visually rather than written in text? To study this problem, we introduce MathGen, a rigorous benchmark of 900 problems spanning seven core domains, each paired with an executable verifier under a Script-as-a-Judge protocol for deterministic and objective evaluation. Experiments on representative open-source and proprietary text-to-image models show that mathematical fidelity remains a major bottleneck: even the best closed-source model reaches only 42.0% overall accuracy, while open-source models achieve just ~ 1-11%, often near 0% on structured tasks. Overall, current T2I models remain far from competent at even elementary mathematical visual generation.

MMSpec: Benchmarking Speculative Decoding for Vision-Language Models

Vision-language models (VLMs) achieve strong performance on multimodal tasks but suffer from high inference latency due to large model sizes and long multimodal contexts. Speculative decoding has recently emerged as an effective acceleration technique, yet its behavior in VLMs remains insufficiently understood. We introduce MMSpec, the first benchmark for evaluating speculative decoding in vision-language models. MMSpec contains 600 multimodal samples across six task categories and integrates ten representative speculative decoding algorithms under a unified evaluation framework. Our study reveals three key findings: (1) methods designed for text-only LLMs degrade in multimodal scenarios, (2) vision awareness becomes increasingly important at larger batch sizes, and (3) throughput speedup alone does not reliably reflect latency performance. Motivated by these findings, we propose ViSkip, a plug-and-play speculative decoding method that dynamically adapts speculation to vision tokens and achieves state-of-the-art performance.