The rapid advancement of single-cell ATAC sequencing (scATAC-seq) technologies holds great promise for investigating the heterogeneity of epigenetic landscapes at the cellular level. The amplification process in scATAC-seq experiments often introduces noise due to dropout events, which results in extreme sparsity that hinders accurate analysis. Consequently, there is a significant demand for the generation of high-quality scATAC-seq data in silico. Furthermore, current methodologies are typically task-specific, lacking a versatile framework capable of handling multiple tasks within a single model. In this work, we propose ATAC-Diff, a versatile framework, which is based on a diffusion model conditioned on the latent auxiliary variables to adapt for various tasks. ATAC-Diff is the first diffusion model for the scATAC-seq data generation and analysis, composed of auxiliary modules encoding the latent high-level variables to enable the model to learn the semantic information to sample high-quality data. Gaussian Mixture Model (GMM) as the latent prior and auxiliary decoder, the yield variables reserve the refined genomic information beneficial for downstream analyses. Another innovation is the incorporation of mutual information between observed and hidden variables as a regularization term to prevent the model from decoupling from latent variables. Through extensive experiments, we demonstrate that ATAC-Diff achieves high performance in both generation and analysis tasks, outperforming state-of-the-art models.

The stochastic compositional optimization (SCO) is popular in many real-world applications, including risk management, reinforcement learning, and meta-learning. However, most of the previous methods for SCO require the smoothness assumption on both the outer and inner functions, which limits their applications to a wider range of problems. In this paper, we study the SCO problem in that both the outer and inner functions are Lipschitz continuous but possibly nonconvex and nonsmooth. In particular, we propose gradient-free stochastic methods for finding the $(\delta, \epsilon)$-Goldstein stationary points of such problems with non-asymptotic convergence rates. Our results also lead to an improved convergence rate for the convex nonsmooth SCO problem. Furthermore, we conduct numerical experiments to demonstrate the effectiveness of the proposed methods.

Plus: OpenAI is also creating a super app. OpenAI has a new grand challenge: building an AI researcher--a fully automated agent-based system capable of tackling large, complex problems by itself. The San Francisco firm said the new goal will be its "north star" for the next few years. By September, the company plans to build "an autonomous AI research intern" that can take on a small number of specific research problems. The intern will be the precursor to the fully automated multi-agent system, which is slated to debut in 2028. In an exclusive interview this week, OpenAI's chief scientist, Jakub Pachocki, talked me through the plans.

Photographer Tom Murphy has documented the park's wildlife for decades. Now, one of his photos will be on a Forever Stamp. The new stamp features one of Yellowstone's signature bison and will be out later in 2026. Breakthroughs, discoveries, and DIY tips sent six days a week. It's a warm July day in Yellowstone National Park's grassy Hayden Valley and wildlife photographer Tom Murphy is tracking herds of chocolate-colored bison gathered for the annual breeding season.

Graph-structured data is integral to many applications, prompting the development of various graph representation methods. Graph autoencoders (GAEs), in particular, reconstruct graph structures from node embeddings. Current GAE models primarily utilize self-correlation to represent graph structures and focus on node-level tasks, often overlooking multi-graph scenarios. Our theoretical analysis indicates that self-correlation generally falls short in accurately representing specific graph features such as islands, symmetrical structures, and directional edges, particularly in smaller or multiple graph contexts.To address these limitations, we introduce a cross-correlation mechanism that significantly enhances the GAE representational capabilities. Additionally, we propose the GraphCroc, a new GAE that supports flexible encoder architectures tailored for various downstream tasks and ensures robust structural reconstruction, through a mirrored encoding-decoding process. This model also tackles the challenge of representation bias during optimization by implementing a loss-balancing strategy. Both theoretical analysis and numerical evaluations demonstrate that our methodology significantly outperforms existing self-correlation-based GAEs in graph structure reconstruction.

We study the problem of PAC learning $\gamma$-margin halfspaces with Massart noise. We propose a simple proper learning algorithm, the Perspectron, that has sample complexity $\widetilde{O}((\epsilon\gamma)^{-2})$ and achieves classification error at most $\eta+\epsilon$ where $\eta$ is the Massart noise rate. Prior works (DGT19, CKMY20) came with worse sample complexity guarantees (in both $\epsilon$ and $\gamma$) or could only handle random classification noise (DDKWZ23,KITBMV23)--- a much milder noise assumption. We also show that our results extend to the more challenging setting of learning generalized linear models with a known link function under Massart noise, achieving a similar sample complexity to the halfspace case. This significantly improves upon the prior state-of-the-art in this setting due to CKMY20, who introduced this model.

Trained on vast corpora of human language, language models demonstrate emergent human-like reasoning abilities. Yet they are still far from true intelligence, which opens up intriguing opportunities to explore the parallels of humans and model behaviors. In this work, we study the ability to skip steps in reasoning--a hallmark of human expertise developed through practice. Unlike humans, who may skip steps to enhance efficiency or to reduce cognitive load, models do not inherently possess such motivations to minimize reasoning steps. To address this, we introduce a controlled framework that stimulates step-skipping behavior by iteratively refining models to generate shorter and accurate reasoning paths. Empirical results indicate that models can develop the step skipping ability under our guidance. Moreover, after fine-tuning on expanded datasets that include both complete and skipped reasoning sequences, the models can not only resolve tasks with increased efficiency without sacrificing accuracy, but also exhibit comparable and even enhanced generalization capabilities in out-of-domain scenarios. Our work presents the first exploration into human-like step-skipping ability and provides fresh perspectives on how such cognitive abilities can benefit AI models.

As part of the effort to understand how the brain learns, ongoing research seeks to combine biological knowledge with current artificial intelligence (AI) modeling in an attempt to find an efficient biologically plausible learning scheme. Current models often use a cortical-like combination of bottom-up (BU) and top-down (TD) processing, where the TD part carries feedback signals for learning. However, in the visual cortex, the TD pathway plays a second major role in visual attention, by guiding the visual process toward locations and tasks of interest. A biological model should therefore integrate both learning and visual guidance. We introduce a model that uses a cortical-like combination of BU and TD processing that naturally integrates the two major functions of the TD stream. This integration is achieved through an appropriate connectivity pattern between the BU and TD streams, a novel processing cycle that uses the TD stream twice, and a'Counter-Hebb' learning mechanism that operates across both streams. We show that the'Counter-Hebb' mechanism can provide an exact backpropagation synaptic modification. Additionally, our model can effectively guide the visual stream to perform a task of interest, achieving competitive performance on standard multi-task learning benchmarks compared to AI models. The successful combination of learning and visual guidance could provide a new view on combining BU and TD processing in human vision and suggests possible directions for both biologically plausible models and artificial instructed models, such as vision-language models (VLMs).

The generation of equilibrium samples of molecular systems has been a long-standing problem in statistical physics. Boltzmann Generators are a generative machine learning method that addresses this issue by learning a transformation via a normalizing flow from a simple prior distribution to the target Boltzmann distribution of interest. Recently, flow matching has been employed to train Boltzmann Generators for small molecular systems in Cartesian coordinates. We extend this work and propose a first framework for Boltzmann Generators that are transferable across chemical space, such that they predict zero-shot Boltzmann distributions for test molecules without being retraining for these systems. These transferable Boltzmann Generators allow approximate sampling from the target distribution of unseen systems, as well as efficient reweighting to the target Boltzmann distribution. The transferability of the proposed framework is evaluated on dipeptides, where we show that it generalizes efficiently to unseen systems.Furthermore, we demonstrate that our proposed architecture enhances the efficiency of Boltzmann Generators trained on single molecular systems.

Existing dynamic scene generation methods mostly rely on distilling knowledge from pre-trained 3D generative models, which are typically fine-tuned on synthetic object datasets.As a result, the generated scenes are often object-centric and lack photorealism. To address these limitations, we introduce a novel pipeline designed for photorealistic text-to-4D scene generation, discarding the dependency on multi-view generative models and instead fully utilizing video generative models trained on diverse real-world datasets. Our method begins by generating a reference video using the video generation model.We then learn the canonical 3D representation of the video using a freeze-time video, delicately generated from the reference video.To handle inconsistencies in the freeze-time video, we jointly learn a per-frame deformation to model these imperfections.We then learn the temporal deformation based on the canonical representation to capture dynamic interactions in the reference video.