Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction

DNA cis-regulatory elements (CREs) such as enhancers control gene expression levels. Accurately predicting regulatory activity from DNA sequences is valuable but challenging, as it requires understanding complex biological regulatory processes. Existing methods typically regress activity scores from sequences in a black-box manner, limiting both interpretability and regression performance. Meanwhile, large language models (LLMs) benefit from explicit reasoning processes, yet directly applying LLMs to raw DNA sequences performs poorly. In this paper, we bridge this gap by introducing R3LM, a framework that teaches LLMs reasoning-informed regression on regulatory DNA through structured biological knowledge. Specifically, we design a biologically grounded data format that structures DNA's regulatory information for improved LLM understanding, and construct CRE-ReasonBench, the first dataset that associates DNA sequences and activity scores with mechanistic reasoning traces. Through two-stage training that first teaches LLMs reasoning over structured biological information then performs regression, R3LM achieves state-of-the-art performance on enhancer prediction across three cell types, outperforming both LLMs with raw sequence input and specialized DNA models while providing interpretable mechanistic explanations. We expect R3LM as an interpretable reward model that can effectively assist biologists in CRE design. Code is available at https://github.com/DuanYi516/R3LM.

Reinforcement Learning from Cross-domain Videos with Video Prediction Model

Reinforcement learning from expert videos across visually distinct domains is challenging due to the absence of reward signals and the presence of domain gaps. We introduce XIPER (Cross-domain Video Prediction Reward), a reward model for learning from expert videos collected in a visually different domain, where the agent's appearance differs due to factors such as color, morphology, or the sim-to-real gap. More specifically, XIPER trains a cross-domain video prediction model that maps agent observations into the expert domain and uses the prediction likelihood as a reward signal. Experiments on the DMC Color Suite (8 tasks) and DMC Body Suite (3 tasks) show that XIPER consistently outperforms baselines despite domain gaps such as differences in agent color and morphology. We further analyze XIPER on a sim-to-real transfer dataset, demonstrating that it produces meaningful reward signals for real-robot observations given only simulated expert videos. Code, pretrained models, datasets and video demonstrations can be found on our project webpage: https://sites.google.com/view/xiper

CityGen: Structure-Guided City-Style Synthesis for Cross-City Autonomous Driving

Autonomous driving systems are commonly trained and evaluated within limited geographic regions, which hinders their scalability when deployed in new cities. However, significant domain shifts in appearance, road topology, and traffic patterns often cause severe performance degradation under cross-city deployment. Existing approaches based on domain adaptation, data augmentation, or synthetic data generation typically rely on labeled target data, city-specific annotations, or task-specific designs, limiting their scalability and effectiveness for holistic evaluation. In this paper, we introduce CityTransfer-Bench, a geographically disjoint benchmark for evaluating cross-city generalization across perception, segmentation, and planning, and propose CityGen, a diffusion-based generative framework that performs zero-label city adaptation via HD-map-conditioned synthesis guided by city-level visual prompts. Extensive experiments demonstrate that CityGen consistently improves cross-city robustness across multiple tasks, establishing a scalable and label-efficient foundation for generalizable autonomous driving.

A Heterogeneous Temporal Memory Governance Framework for Long-Term LLM Persona Consistency

Large language models often suffer from fact loss, timeline confusion, persona drift, and reduced stability during long-range interaction, especially under high-noise knowledge bases, context clearing, and cross-model transfer. To address these issues, we introduce ARPM, an external temporal memory governance framework for long-term dialogue. ARPM separates static knowledge memory from dynamic dialogue experience memory and combines vector retrieval, BM25, RRF fusion, dual-temporal reranking, chronological evidence reading, and a controlled analysis protocol for evidence verification and answer binding. Unlike approaches that encode persona consistency into model weights or rely only on long context, ARPM treats continuity as a traceable, auditable, and transferable governance problem. Using engineering logs, we conduct three experiments. First, in a 50-round question-answering setting, we compare signal-to-noise ratios of 1:5 and 1:200+, and distinguish CSV auto-judgment from manual review. Under 1:5, CSV recall accuracy is 54.0%, while manual review raises it to 100.0%. Under 1:200+, the values are 44.0% and 80.0%. These results show that automatic rules can underestimate recall after supporting evidence enters the prompt. Second, ablation results show that dialogue history retrieval is necessary for recent continuity: disabling it reduces strict accuracy from 100% to 66.7%, and disabling BM25 reduces it to 80.0%, indicating that pure semantic retrieval is insufficient for correction and tracing. Third, under a 5.1-million-character noise substrate, periodic context clearing, and multi-model handoff, ARPM maintains semantic continuity, boundary continuity, and persona consistency, while exposing limits caused by weak protocol compliance. These findings show that long-term persona consistency can be decomposed into governable components and evaluated in a white-box manner.

Cornerstones or Stumbling Blocks? Deciphering the Rock Tokens in On-Policy Distillation

While recent work in Reinforcement Learning with Verifiable Rewards (RLVR) has shown that a small subset of critical tokens disproportionately drives reasoning gains, an analogous token-level understanding of On-Policy Distillation (OPD) remains largely unexplored. In this work, we investigate high-loss tokens, a token type that--as the most direct signal of student-teacher mismatch under OPD's per-token KL objective--should progressively diminish as training converges according to existing studies; however, our empirical analysis shows otherwise. Even after OPD training reaches apparent saturation, a substantial subset of tokens continues to exhibit persistently high loss; these tokens, which we term Rock Tokens, can account for up to 18\% of the tokens in generated outputs. Our investigation reveals two startling paradoxes. First, despite their high occurrence frequency providing a disproportionately large share of total gradient norms, Rock Tokens themselves remain stagnant throughout training, resisting teacher-driven corrections. Second, through causal intervention, we find that these tokens provide negligible functional contribution to the model's actual reasoning performance. These findings suggest that a vast amount of optimization bandwidth is spent on structural and discourse residuals that the student model cannot or need not internalize. By deconstructing these dynamics, we demonstrate that strategically bypassing these ``stumbling blocks'' can significantly streamline the alignment process, challenging the necessity of uniform token weighting and offering a more efficient paradigm for large-scale model distillation.

GroundVTS: Visual Token Sampling in Multimodal Large Language Models for Video Temporal Grounding

Video temporal grounding (VTG) is a critical task in video understanding and a key capability for extending video large language models (Vid-LLMs) to broader applications. However, existing Vid-LLMs rely on uniform frame sampling to extract video information, resulting in a sparse distribution of key frames and the loss of crucial temporal cues. To address this limitation, we propose Grounded Visual Token Sampling (GroundVTS), a Vid-LLM architecture that focuses on the most informative temporal segments. GroundVTS employs a fine-grained, query-guided mechanism to filter visual tokens before feeding them into the LLM, thereby preserving essential spatio-temporal information and maintaining temporal coherence. Futhermore, we introduce a progressive optimization strategy that enables the LLM to effectively adapt to the non-uniform distribution of visual features, enhancing its ability to model temporal dependencies and achieve precise video localization. We comprehensively evaluate GroundVTS on three standard VTG benchmarks, where it outperforms existing methods, achieving a 7.7-point improvement in mIoU for moment retrieval and 12.0-point improvement in mAP for highlight detection. Code is available at https://github.com/Florence365/GroundVTS.

D3LM: A Discrete DNA Diffusion Language Model for Bidirectional DNA Understanding and Generation

Early DNA foundation models adopted BERT-style training, achieving good performance on DNA understanding tasks but lacking generative capabilities. Recent autoregressive models enable DNA generation, but employ left-to-right causal modeling that is suboptimal for DNA where regulatory relationships are inherently bidirectional. We present D3LM (\textbf{D}iscrete \textbf{D}NA \textbf{D}iffusion \textbf{L}anguage \textbf{M}odel), which unifies bidirectional representation learning and DNA generation through masked diffusion. D3LM directly adopts the Nucleotide Transformer (NT) v2 architecture but reformulates the training objective as masked diffusion in discrete DNA space, enabling both bidirectional understanding and generation capabilities within a single model. Compared to NT v2 of the same size, D3LM achieves improved performance on understanding tasks. Notably, on regulatory element generation, D3LM achieves an SFID of 10.92, closely approaching real DNA sequences (7.85) and substantially outperforming the previous best result of 29.16 from autoregressive models. Our work suggests diffusion language models as a promising paradigm for unified DNA foundation models. We further present the first systematic study of masked diffusion models in the DNA domain, investigating practical design choices such as tokenization schemes and sampling strategies, thereby providing empirical insights and a solid foundation for future research. D3LM has been released at https://huggingface.co/collections/Hengchang-Liu/d3lm.

Unifying Language-Action Understanding and Generation for Autonomous Driving

Vision-Language-Action (VLA) models are emerging as a promising paradigm for end-to-end autonomous driving, valued for their potential to leverage world knowledge and reason about complex driving scenes. However, existing methods suffer from two critical limitations: a persistent misalignment between language instructions and action outputs, and the inherent inefficiency of typical auto-regressive action generation. In this paper, we introduce LinkVLA, a novel architecture that directly addresses these challenges to enhance both alignment and efficiency. First, we establish a structural link by unifying language and action tokens into a shared discrete codebook, processed within a single multi-modal model. This structurally enforces cross-modal consistency from the ground up. Second, to create a deep semantic link, we introduce an auxiliary action understanding objective that trains the model to generate descriptive captions from trajectories, fostering a bidirectional language-action mapping. Finally, we replace the slow, step-by-step generation with a two-step coarse-to-fine generation method C2F that efficiently decodes the action sequence, saving 86% inference time. Experiments on closed-loop driving benchmarks show consistent gains in instruction following accuracy and driving performance, alongside reduced inference latency.

Extending Sequence Length is Not All You Need: Effective Integration of Multimodal Signals for Gene Expression Prediction

Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length to locate distal enhancers, which may influence target genes from hundreds of kilobases away. Our work first reveals that for current models, long sequence modeling can decrease performance. Even carefully designed algorithms only mitigate the performance degradation caused by long sequences. Instead, we find that proximal multimodal epigenomic signals near target genes prove more essential. Hence we focus on how to better integrate these signals, which has been overlooked. We find that different signal types serve distinct biological roles, with some directly marking active regulatory elements while others reflect background chromatin patterns that may introduce confounding effects. Simple concatenation may lead models to develop spurious associations with these background patterns. To address this challenge, we propose Prism, a framework that learns multiple combinations of high-dimensional epigenomic features to represent distinct background chromatin states and uses backdoor adjustment to mitigate confounding effects. Our experimental results demonstrate that proper modeling of multimodal epigenomic signals achieves state-of-the-art performance using only short sequences for gene expression prediction.

Diffusion LMs Can Approximate Optimal Infilling Lengths Implicitly

Diffusion language models (DLMs) provide a bidirectional generation framework naturally suited for infilling, yet their performance is constrained by the pre-specified infilling length. In this paper, we reveal that DLMs possess an inherent ability to discover the correct infilling length. We identify two key statistical phenomena in the first-step denoising confidence: a local \textit{Oracle Peak} that emerges near the ground-truth length and a systematic \textit{Length Bias} that often obscures this signal. By leveraging this signal and calibrating the bias, our training-free method \textbf{CAL} (\textbf{C}alibrated \textbf{A}daptive \textbf{L}ength) enables DLMs to approximate the optimal length through an efficient search before formal decoding. Empirical evaluations demonstrate that CAL improves Pass@1 by up to 47.7\% over fixed-length baselines and 40.5\% over chat-based adaptive methods in code infilling, while boosting BLEU-2 and ROUGE-L by up to 8.5\% and 9.9\% in text infilling. These results demonstrate that CAL paves the way for robust DLM infilling without requiring any specialized training. Code is available at https://github.com/NiuHechang/Calibrated_Adaptive_Length.