Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored.

Predicting disease risk from DNA presents an unprecedented emerging challenge as biobanks approach population scale sizes ($N> 10^6$ individuals) with ultra-high-dimensional features ($L> 10^5$ genotypes). Current methods, often linear and reliant on summary statistics, fail to capture complex genetic interactions and discard valuable individual-level information. We introduce **PRSformer**, a scalable deep learning architecture designed for end-to-end, multitask disease prediction directly from million-scale individual genotypes. PRSformer employs neighborhood attention, achieving linear $O(L)$ complexity per layer, making Transformers tractable for genome-scale inputs. Crucially, PRSformer utilizes a stacking of these efficient attention layers, progressively increasing the effective receptive field to model local dependencies (e.g., within linkage disequilibrium blocks) before integrating information across wider genomic regions. This design, tailored for genomics, allows PRSformer to learn complex, potentially non-linear and long-range interactions directly from raw genotypes. We demonstrate PRSformer's effectiveness using a unique large private cohort ($N \approx 5$M) for predicting 18 autoimmune and inflammatory conditions using $L \approx 140$k variants. PRSformer significantly outperforms highly optimized linear models trained on the *same individual-level data* and state-of-the-art summary-statistic-based methods (LDPred2) derived from the *same cohort*, quantifying the benefits of non-linear modeling and multitask learning at scale. Furthermore, experiments reveal that the advantage of non-linearity emerges primarily at large sample sizes ($N > 1$M), and that a multi-ancestry trained model improves generalization, establishing PRSformer as a new framework for deep learning in population-scale genomics.

Recently, deep learning-based pan-sharpening algorithms have achieved notable advancements over traditional methods. However, deep learning-based methods incur substantial computational overhead during inference, especially with large images. This excessive computational demand limits the applicability of these methods in real-world scenarios, particularly in the absence of dedicated computing devices such as GPUs and TPUs. To address these challenges, we propose Pan-LUT, a novel learnable look-up table (LUT) framework for pan-sharpening that strikes a balance between performance and computational efficiency for large remote sensing images. Our method makes it possible to process 15K$\times$15K remote sensing images on a 24GB GPU. To finely control the spectral transformation, we devise the PAN-guided look-up table (PGLUT) for channel-wise spectral mapping. To effectively capture fine-grained spatial details, we introduce the spatial details look-up table (SDLUT).

Training multi-modal large language models (MLLMs) that align with human intentions is a long-term challenge. Traditional score-only reward models for alignment suffer from low accuracy, weak generalization, and poor interpretability, blocking the progress of alignment methods, \textit{e.g.,} reinforcement learning from human feedback (RLHF). Generative reward models (GRMs) leverage MLLMs' intrinsic reasoning capabilities to discriminate pair-wise responses, but their pair-wise paradigm makes it hard to generalize to learnable rewards. We introduce Generative RLHF-V, a novel alignment framework that integrates GRMs with multi-modal RLHF. We propose a two-stage pipeline: \textbf{multi-modal generative reward modeling from RL}, where RL guides GRMs to actively capture human intention, then predict the correct pair-wise scores; and \textbf{RL optimization from grouped comparison}, which enhances multi-modal RL scoring precision by grouped responses comparison. Experimental results demonstrate that, besides out-of-distribution generalization of RM discrimination, our framework improves 4 MLLMs' performance across 7 benchmarks by 18.1\%, while the baseline RLHF is only 5.3\%. We further validate that Generative RLHF-V achieves a near-linear improvement with an increasing number of candidate responses.

This position paper argues that real-time generative AI has the potential to become the next wave of addictive digital media, creating a new class of digital content akin to ``digital heroin'' with severe implications for mental health and youth development. By shortening the content-generation feedback loop to mere seconds, these advanced models will soon be able to hyper-personalize outputs on the fly. When paired with misaligned incentives (e.g., maximizing user engagement), this will fuel unprecedented compulsive consumption patterns with far-reaching consequences for mental health, cognitive development, and social stability. Drawing on interdisciplinary research, from clinical observations of social media addiction to neuroscientific studies of dopamine-driven feedback, we illustrate how real-time tailored content generation may erode user autonomy, foment emotional distress, and disproportionately endanger vulnerable groups, such as adolescents. Due to the rapid advancement of generative AI and its potential to induce severe addiction-like effects, we call for strong government oversight akin to existing controls on addictive substances, particularly for minors. We further urge the machine learning community to act proactively by establishing robust design guidelines, collaborating with public health experts, and supporting targeted policy measures to ensure responsible and ethical deployment, rather than paving the way for another wave of unregulated digital dependence.

Sequential deep learning models excel in domains with temporal or sequential dependencies, but their complexity necessitates post-hoc feature attribution methods for understanding their predictions. While existing techniques quantify feature importance, they inherently assume fixed feature ordering -- conflating the effects of (1) feature values and (2) their positions within input sequences. To address this gap, we introduce OrdShap, a novel attribution method that disentangles these effects by quantifying how a model's predictions change in response to permuting feature position. We establish a game-theoretic connection between OrdShap and Sanchez-Bergantiños values, providing a theoretically grounded approach to position-sensitive attribution. Empirical results from health, natural language, and synthetic datasets highlight OrdShap's effectiveness in capturing feature value and feature position attributions, and provide deeper insight into model behavior.

Large reasoning models (LRMs), such as OpenAI-o1 and DeepSeek-R1, demonstrate impressive long-horizon reasoning capabilities. However, their reliance on static internal knowledge limits their performance on complex, knowledge-intensive tasks and hinders their ability to produce comprehensive research reports requiring synthesis of diverse web information. To address this, we propose WebThinker, a deep research agent that empowers LRMs to autonomously search the web, navigate among web pages, and draft reports during the reasoning process. WebThinker integrates a Deep Web Explorer module, enabling LRMs to dynamically search, navigate, and extract information from the web when encountering knowledge gaps. It also employs an Autonomous Think-Search-and-Draft strategy, allowing the model to seamlessly interleave reasoning, information gathering, and report writing in real time. To further enhance research tool utilization, we introduce an RL-based training strategy via iterative online Direct Preference Optimization (DPO). Extensive experiments on complex reasoning benchmarks (GPQA, GAIA, WebWalkerQA, HLE) and scientific report generation tasks (Glaive) demonstrate that WebThinker significantly outperforms existing methods and strong proprietary systems. Our approach enhances LRM reliability and applicability in complex scenarios, paving the way for more capable and versatile deep research systems.

Recent works have introduced new equivariant neural networks, motivated by their improved generalization compared to traditional deep neural networks. While experiments support this advantage, the theoretical understanding of their generalization properties remains limited. In this paper, we analyze the generalization capabilities of Group Convolutional Neural Networks (GCNNs) with the ReLU activation function through the lens of Vapnik-Chervonenkis (VC) dimension theory. We investigate how architectural factors--such as the number of layers, weights, and input dimensions--affect the VC dimension. A key challenge in our analysis is proving a lower bound on the VC dimension, for which we introduce new techniques, establishing a novel connection between GCNNs and standard deep neural networks. Additionally, we compare our derived bounds to those known for fully connected neural networks. Our results extend previous findings on the VC dimension of continuous GCNNs with two layers, offering new insights into their generalization behavior, particularly their dependence on input resolution.

Uncertainty quantification (UQ) is crucial for deploying machine learning models in high-stakes applications, where overconfident predictions can lead to serious consequences. An effective UQ method must balance computational efficiency with the ability to generalize across diverse scenarios. Evidential deep learning (EDL) achieves efficiency by modeling uncertainty through the prediction of a Dirichlet distribution over class probabilities. However, the restrictive assumption of Dirichlet-distributed class probabilities limits EDL's robustness, particularly in complex or unforeseen situations. To address this, we propose *flexible evidential deep learning* ($\mathcal{F}$-EDL), which extends EDL by predicting a flexible Dirichlet distribution--a generalization of the Dirichlet distribution--over class probabilities. This approach provides a more expressive and adaptive representation of uncertainty, significantly enhancing UQ generalization and reliability under challenging scenarios. We theoretically establish several advantages of $\mathcal{F}$-EDL and empirically demonstrate its state-of-the-art UQ performance across diverse evaluation settings, including classical, long-tailed, and noisy in-distribution scenarios.

Generating diverse responses from large language models (LLMs) is crucial for applications such as adversarial testing, search, and synthetic data generation, where diversity provides distinct answers across generations. Previous approaches rely solely on increasing the temperature, sacrificing quality. Furthermore, the model's next-token probabilities may not be representative of the true answer distribution. To combat these challenges, we propose SimpleStrat, an alternative that uses the language model itself to partition the solution space into strata from which to sample. To measure resampling diversity, we introduce CoverageQA, a dataset of underspecified questions with multiple equally plausible answers. We propose measuring resampling diversity as the KL Divergence between the response distribution and the uniform distribution over valid ground truth answers and use recall as an alternative when assessing proprietary models. On CoverageQA, SimpleStrat improves diversity across all temperatures, showing orthogonal benefits. Quantifiably, we achieve as much as 4X better recall when applied to GPT-4o, and an average reduction in KL divergence by 0.36 when applied to Llama 3. Furthermore, we show that SimpleStrat achieves more resampling diversity at temperature T=0 than scaling temperature to T=1 on creative writing, an open-ended domain.