Related papers: RNACG: A Universal RNA Sequence Conditional Genera…

Retrieval-Augmented Generation (RAG) represents a major advancement in natural language processing (NLP), combining large language models (LLMs) with information retrieval systems to enhance factual grounding, accuracy, and contextual…

Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…

Retrieval-Augmented Generation (RAG) quality depends on many interacting choices across retrieval, ranking, augmentation, prompting, and generation, so optimizing modules in isolation is brittle. We introduce RAGSmith, a modular framework…

Retrieval-augmented code generation utilizes Large Language Models as the generator and significantly expands their code generation capabilities by providing relevant code, documentation, and more via the retriever. The current approach…

Reliable evaluation of anomaly detection methods in multivariate time series remains an open challenge, largely due to the limitations of existing benchmark datasets. Current resources often lack fine-grained anomaly annotations, do not…

We introduce Flux Matching, a new paradigm for generative modeling that generalizes existing score-based models to a broader family of vector fields that need not be conservative. Rather than requiring the model to equal the data score, the…

Clustering analysis is fundamental in single-cell RNA sequencing (scRNA-seq) data analysis for elucidating cellular heterogeneity and diversity. Recent graph-based scRNA-seq clustering methods, particularly graph neural networks (GNNs),…

Generative models have the potential to accelerate key steps in the discovery of novel molecular therapeutics and materials. Diffusion models have recently emerged as a powerful approach, excelling at unconditional sample generation and,…

Retrieval-Augmented Generation (RAG) has emerged as a fundamental paradigm for expanding Large Language Models beyond their static training limitations. However, a critical misalignment exists between current RAG capabilities and real-world…

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from…

In this paper, we introduce Random Path Generative Adversarial Network (RPGAN) -- an alternative design of GANs that can serve as a tool for generative model analysis. While the latent space of a typical GAN consists of input vectors,…

Conditional generative adversarial networks (cGAN) have led to large improvements in the task of conditional image generation, which lies at the heart of computer vision. The major focus so far has been on performance improvement, while…

We introduce FragFM, a novel hierarchical framework via fragment-level discrete flow matching for efficient molecular graph generation. FragFM generates molecules at the fragment level, leveraging a coarse-to-fine autoencoder to reconstruct…

RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially…

Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…

Diverse and controllable scenario generation (e.g., wind, solar, load, etc.) is critical for robust power system planning and operation. As AI-based scenario generation methods are becoming the mainstream, existing methods (e.g.,…

We introduce Generator Matching, a modality-agnostic framework for generative modeling using arbitrary Markov processes. Generators characterize the infinitesimal evolution of a Markov process, which we leverage for generative modeling in a…

RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…

Key objectives in conditional molecular generation include ensuring chemical validity, aligning generated molecules with target properties, promoting structural diversity, and enabling efficient sampling for discovery. Recent advances in…

Since sequential information plays an important role in modeling user behaviors, various sequential recommendation methods have been proposed. Methods based on Markov assumption are widely-used, but independently combine several most recent…