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.

TAPFormer: Robust Arbitrary Point Tracking via Transient Asynchronous Fusion of Frames and Events

Tracking any point (TAP) is a fundamental yet challenging task in computer vision, requiring high precision and long-term motion reasoning. Recent attempts to combine RGB frames and event streams have shown promise, yet they typically rely on synchronous or non-adaptive fusion, leading to temporal misalignment and severe degradation when one modality fails. We introduce TAPFormer, a transformer-based framework that performs asynchronous temporal-consistent fusion of frames and events for robust and high-frequency arbitrary point tracking. Our key innovation is a Transient Asynchronous Fusion (TAF) mechanism, which explicitly models the temporal evolution between discrete frames through continuous event updates, bridging the gap between low-rate frames and high-rate events. In addition, a Cross-modal Locally Weighted Fusion (CLWF) module adaptively adjusts spatial attention according to modality reliability, yielding stable and discriminative features even under blur or low light. To evaluate our approach under realistic conditions, we construct a novel real-world frame-event TAP dataset under diverse illumination and motion conditions. Our method outperforms existing point trackers, achieving a 28.2% improvement in average pixel error within threshold. Moreover, on standard point tracking benchmarks, our tracker consistently achieves the best performance. Project website: tapformer.github.io

DSDR: Dual-Scale Diversity Regularization for Exploration in LLM Reasoning

Reinforcement learning with verifiers (RLVR) is a central paradigm for improving large language model (LLM) reasoning, yet existing methods often suffer from limited exploration. Policies tend to collapse onto a few reasoning patterns and prematurely stop deep exploration, while conventional entropy regularization introduces only local stochasticity and fails to induce meaningful path-level diversity, leading to weak and unstable learning signals in group-based policy optimization. We propose DSDR, a Dual-Scale Diversity Regularization reinforcement learning framework that decomposes diversity in LLM reasoning into global and coupling components. Globally, DSDR promotes diversity among correct reasoning trajectories to explore distinct solution modes. Locally, it applies a length-invariant, token-level entropy regularization restricted to correct trajectories, preventing entropy collapse within each mode while preserving correctness. The two scales are coupled through a global-to-local allocation mechanism that emphasizes local regularization for more distinctive correct trajectories. We provide theoretical support showing that DSDR preserves optimal correctness under bounded regularization, sustains informative learning signals in group-based optimization, and yields a principled global-to-local coupling rule. Experiments on multiple reasoning benchmarks demonstrate consistent improvements in accuracy and pass@k, highlighting the importance of dual-scale diversity for deep exploration in RLVR. Code is available at https://github.com/SUSTechBruce/DSDR.

OVD: On-policy Verbal Distillation

Knowledge distillation offers a promising path to transfer reasoning capabilities from large teacher models to efficient student models; however, existing token-level on-policy distillation methods require token-level alignment between the student and teacher models, which restricts the student model's exploration ability, prevent effective use of interactive environment feedback, and suffer from severe memory bottlenecks in reinforcement learning. We introduce On-policy Verbal Distillation (OVD), a memory-efficient framework that replaces token-level probability matching with trajectory matching using discrete verbal scores (0--9) from teacher models. OVD dramatically reduces memory consumption while enabling on-policy distillation from teacher models with verbal feedback, and avoids token-level alignment, allowing the student model to freely explore the output space. Extensive experiments on Web question answering and mathematical reasoning tasks show that OVD substantially outperforms existing methods, delivering up to +12.9% absolute improvement in average EM on Web Q&A tasks and a up to +25.7% gain on math benchmarks (when trained with only one random samples), while also exhibiting superior training efficiency. Our project page is available at https://OVD.github.io

Locate, Steer, and Improve: A Practical Survey of Actionable Mechanistic Interpretability in Large Language Models

Mechanistic Interpretability (MI) has emerged as a vital approach to demystify the opaque decision-making of Large Language Models (LLMs). However, existing reviews primarily treat MI as an observational science, summarizing analytical insights while lacking a systematic framework for actionable intervention. To bridge this gap, we present a practical survey structured around the pipeline: "Locate, Steer, and Improve." We formally categorize Localizing (diagnosis) and Steering (intervention) methods based on specific Interpretable Objects to establish a rigorous intervention protocol. Furthermore, we demonstrate how this framework enables tangible improvements in Alignment, Capability, and Efficiency, effectively operationalizing MI as an actionable methodology for model optimization. The curated paper list of this work is available at https://github.com/rattlesnakey/Awesome-Actionable-MI-Survey.

MMFormalizer: Multimodal Autoformalization in the Wild

Autoformalization, which translates natural language mathematics into formal statements to enable machine reasoning, faces fundamental challenges in the wild due to the multimodal nature of the physical world, where physics requires inferring hidden constraints (e.g., mass or energy) from visual elements. To address this, we propose MMFormalizer, which extends autoformalization beyond text by integrating adaptive grounding with entities from real-world mathematical and physical domains. MMFormalizer recursively constructs formal propositions from perceptually grounded primitives through recursive grounding and axiom composition, with adaptive recursive termination ensuring that every abstraction is supported by visual evidence and anchored in dimensional or axiomatic grounding. We evaluate MMFormalizer on a new benchmark, PhyX-AF, comprising 115 curated samples from MathVerse, PhyX, Synthetic Geometry, and Analytic Geometry, covering diverse multimodal autoformalization tasks. Results show that frontier models such as GPT-5 and Gemini-3-Pro achieve the highest compile and semantic accuracy, with GPT-5 excelling in physical reasoning, while geometry remains the most challenging domain. Overall, MMFormalizer provides a scalable framework for unified multimodal autoformalization, bridging perception and formal reasoning. To the best of our knowledge, this is the first multimodal autoformalization method capable of handling classical mechanics (derived from the Hamiltonian), as well as relativity, quantum mechanics, and thermodynamics. More details are available on our project page: MMFormalizer.github.io

DoPE: Denoising Rotary Position Embedding

Rotary Position Embedding (RoPE) in Transformer models has inherent limits that weaken length extrapolation. We reinterpret the attention map with positional encoding as a noisy feature map, and propose Denoising Positional Encoding (DoPE), a training-free method based on truncated matrix entropy to detect outlier frequency bands in the feature map. Leveraging the noise characteristics of the feature map, we further reparameterize it with a parameter-free Gaussian distribution to achieve robust extrapolation. Our method theoretically reveals the underlying cause of the attention sink phenomenon and its connection to truncated matrix entropy. Experiments on needle-in-a-haystack and many-shot in-context learning tasks demonstrate that DoPE significantly improves retrieval accuracy and reasoning stability across extended contexts (up to 64K tokens). The results show that the denoising strategy for positional embeddings effectively mitigates attention sinks and restores balanced attention patterns, providing a simple yet powerful solution for improving length generalization. Our project page is Project: https://The-physical-picture-of-LLMs.github.io

PF-DAformer: Proximal Femur Segmentation via Domain Adaptive Transformer for Dual-Center QCT

Quantitative computed tomography (QCT) plays a crucial role in assessing bone strength and fracture risk by enabling volumetric analysis of bone density distribution in the proximal femur. However, deploying automated segmentation models in practice remains difficult because deep networks trained on one dataset often fail when applied to another. This failure stems from domain shift, where scanners, reconstruction settings, and patient demographics vary across institutions, leading to unstable predictions and unreliable quantitative metrics. Overcoming this barrier is essential for multi-center osteoporosis research and for ensuring that radiomics and structural finite element analysis results remain reproducible across sites. In this work, we developed a domain-adaptive transformer segmentation framework tailored for multi-institutional QCT. Our model is trained and validated on one of the largest hip fracture related research cohorts to date, comprising 1,024 QCT images scans from Tulane University and 384 scans from Rochester, Minnesota for proximal femur segmentation. To address domain shift, we integrate two complementary strategies within a 3D TransUNet backbone: adversarial alignment via Gradient Reversal Layer (GRL), which discourages the network from encoding site-specific cues, and statistical alignment via Maximum Mean Discrepancy (MMD), which explicitly reduces distributional mismatches between institutions. This dual mechanism balances invariance and fine-grained alignment, enabling scanner-agnostic feature learning while preserving anatomical detail.