Gene regulatory network (GRN) inference serves as a cornerstone for deciphering cellular decision-making processes. Early approaches rely exclusively on gene expression data, thus their predictive power remain fundamentally constrained by the vast combinatorial space of potential gene-gene interactions. Subsequent methods integrate prior knowledge to mitigate this challenge by restricting the solution space to biologically plausible interactions. However, we argue that the effectiveness of these approaches is contingent upon the precision of prior information and the reduction in the search space will circumscribe the models' potential for novel biological discoveries. To address these limitations, we introduce KINDLE, a three-stage framework that decouples GRN inference from prior knowledge dependencies.

Text-to-Visualization (Text2VIS) enables users to create visualizations from natural language queries, making data insights more accessible. However, Text2VIS faces challenges in interpreting ambiguous queries, as users often express their visualization needs in imprecise language. To address this challenge, we introduce nBench 2.0, a new benchmark designed to evaluate Text2VIS systems in scenarios involving ambiguous queries.

Efficient LLM pre-training requires well-tuned hyperparameters (HPs), including learning rate η and weight decay λ. We study scaling laws for HPs: formulas for how to scale HPs as we scale model size N, dataset size D, and batch size B. Recent work suggests the AdamW timescale, τ = B/(ηλD), should remain constant across training settings, and we verify the implication that optimal λ scales linearly with B, for a fixed N and D. However, as N and D scale, we show optimal τ obeys a precise power law in the tokens-per-parameter ratio, D/N. This law thus provides a method to accurately predict λopt in advance of large-scale training. We also study scaling laws for optimal batch size Bopt (the B enabling lowest loss at a given N,D) and critical batch size Bcrit (the B beyond which further data parallelism becomes ineffective). In contrast to prior work, we find both Bopt and Bcrit scale as power laws in D, independent of model size, N. Finally, we analyze how these findings inform the real-world selection of Pareto-optimal N and D under dual training time and compute objectives.

Model fingerprinting has emerged as a powerful tool for model owners to identify their shared model given API access. In order to lower false discovery rate, fight fingerprint leakage, and defend against coalitions of model users attempting to bypass detection, we argue that scaling up the number of fingerprints one can embed into a model, i.e. of fingerprints, is critical. Hence, we pose scalability as a crucial requirement for fingerprinting schemes. We experiment with fingerprint design at a scale significantly larger than previously considered, and introduce a new method, dubbed Perinucleus sampling, to generate scalable, persistent, and harmless fingerprints. We demonstrate that this scheme can add 24,576 fingerprints to a Llama-3.1-8B

Enhancing large vision-language models (LVLMs) with visual slow-thinking reasoning is crucial for solving complex multimodal tasks. However, since LVLMs are mainly trained with vision-language alignment, it is difficult to adopt on-policy reinforcement learning (RL) to develop the slow thinking ability because the rollout space is restricted by its initial abilities. Off-policy RL offers a way to go beyond the current policy, but directly distilling trajectories from external models may cause visual hallucinations due to mismatched visual perception abilities across models.

Realistic 3D indoor scene synthesis is vital for embodied AI and digital content creation. It can be naturally divided into two subtasks: object generation and layout generation. While recent generative models have significantly advanced object-level quality and controllability, layout generation remains challenging due to limited datasets. Existing methods either overfit to these datasets or rely on predefined constraints to optimize numerical layout that sacrifice flexibility. As a result, they fail to generate scenes that are both open-vocabulary and aligned with fine-grained user instructions.

Test-time adaptation (TTA) methods have gained significant attention for enhancing the performance of vision-language models (VLMs) such as CLIP during inference, without requiring additional labeled data. However, current TTA researches generally suffer from major limitations such as duplication of baseline results, limited evaluation metrics, inconsistent experimental settings, and insufficient analysis. These problems hinder fair comparisons between TTA methods and make it difficult to assess their practical strengths and weaknesses. To address these challenges, we introduce TTA-VLM, a comprehensive benchmark for evaluating TTA methods on VLMs. Our benchmark implements 8 episodic TTA and 7 online TTA methods within a unified and reproducible framework, and evaluates them across 15 widely used datasets. Unlike prior studies focused solely on CLIP, we extend the evaluation to SigLIP--a model trained with a Sigmoid loss--and include training-time tuning methods such as CoOp, MaPLe, and TeCoA to assess generality. Beyond classification accuracy, TTA-VLM incorporates various evaluation metrics, including robustness, calibration, out-of-distribution detection, and stability, enabling a more holistic assessment of TTA methods. Through extensive experiments, we find that 1) existing TTA methods produce limited gains compared to the previous pioneering work; 2) current TTA methods exhibit poor collaboration with training-time fine-tuning methods; 3) accuracy gains frequently come at the cost of reduced model trustworthiness. We release TTA-VLM to provide fair comparison and comprehensive evaluation of TTA methods for VLMs, and we hope it encourages the community to develop more reliable and generalizable TTA strategies.

Reinforcement learning (RL) using foundation models for policy approximations in multi-turn tasks remains challenging. We identify two main limitations related to sparse reward settings and policy gradient updates, based on which we formulate a key insight: updates from positive samples with high returns typically do not require policy regularisation, whereas updates from negative samples, reflecting undesirable behaviour, can harm model performance. This paper introduces Succeed or Learn Slowly (SoLS), a novel off-policy RL algorithm evaluated on mobile app control tasks. SoLS improves sample efficiency when fine-tuning foundation models for user interface navigation via a modified off-policy actor-critic approach, applying direct policy updates for positive samples and conservative, regularised updates for negative ones to prevent model degradation. We augment SoLS with Successful Transition Replay (STR), which prioritises learning from successful interactions, further improving sample efficiency. We evaluate SoLS on the AndroidWorld benchmark, where it significantly outperforms existing methods (at least 17\% relative increase), including prompt-engineering and RL approaches, while requiring substantially fewer computational resources than GPT-4o-based methods with 5-60x faster inference.

Classifier-Free Guidance (CFG) is an essential component of text-to-image diffusion models, and understanding and advancing its operational mechanisms remains a central focus of research. Existing approaches stem from divergent theoretical interpretations, thereby limiting the design space and obscuring key design choices. To address this, we propose a unified perspective that reframes conditional guidance as fixed point iterations, seeking to identify a golden path where latents produce consistent outputs under both conditional and unconditional generation. We demonstrate that CFG and its variants constitute a special case of single-step short-interval iteration, which is theoretically proven to exhibit inefficiency. To this end, we introduce Foresight Guidance (FSG), which prioritizes solving longer-interval subproblems in early diffusion stages with increased iterations.

Causal mediation analysis is crucial for deconstructing complex mechanisms of action. However, in current mediation analysis, complex structures derived from causal discovery lack direct interpretation of mediation pathways, while traditional mediation analysis and effect estimation are limited by the reliance on pre-specified pathways, leading to a disconnection between structure discovery and causal mechanism understanding. Therefore, a unified framework integrating structure discovery, pathway identification, and effect estimation systematically quantifies mediation pathways under structural uncertainty, enabling automated identification and inference of mediation pathways. To this end, we propose Structure-Informed Guided Mediation Analysis (SIGMA), which guides automated mediation pathway identification through probabilistic causal structure discovery and uncertainty quantification, enabling end-to-end propagation of structural uncertainty from structure learning to effect estimation. Specifically, SIGMA employs differentiable Flow-Structural Equation Models to learn structural posteriors, generating diverse Directed Acyclic Graphs (DAGs) to quantify structural uncertainty. Based on these DAGs, we introduce the Path Stability Score to evaluate the marginal probability of pathways, identifying high-confidence mediation paths. For identified mediation pathways, we integrate Efficient Influence Functions with Bayesian model averaging to fuse within-structure estimation uncertainty and between-structure effect variation, propagating uncertainty to the final effect estimates. In synthetic data experiments, SIGMA achieves state-of-the-art performance in pathway identification accuracy and effect quantification precision under structures uncertainty, concurrent multiple pathways, and nonlinear scenarios. In real-world applications using Human Phenotype Project data, SIGMA identifies mediation effects of sleep quality on cardiovascular health through inflammatory and metabolic pathways, uncovering previously unspecified multiple mediation paths.