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Gene regulation is a dynamic process that connects genotype and phenotype. Given the difficulty of physically mapping mammalian gene circuitry, we require new computational methods to learn regulatory rules. Natural language is a valuable…

In recent times, Vision-Language Models (VLMs) have been trained under two predominant paradigms. Generative training has enabled Multimodal Large Language Models (MLLMs) to tackle various complex tasks, yet issues such as hallucinations…

The performance of Neural Network (NN)-based language models is steadily improving due to the emergence of new architectures, which are able to learn different natural language characteristics. This paper presents a novel framework, which…

Recent advances in applying deep learning in genomics include DNA-language and single-cell foundation models. However, these models take only one data type as input. We introduce dynamic token adaptation and demonstrate how it combines…

Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language…

Various machine-learning models, including deep neural network models, have already been developed to predict deleteriousness of missense (non-synonymous) mutations. Potential improvements to the current state of the art, however, may still…

We report a mixture of expert strategy to create fine-tuned large language models using a deep layer-wise token-level approach based on low-rank adaptation (LoRA). Starting with a set of pre-trained LoRA adapters, our gating strategy uses…

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…

Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize…

Despite the well-developed cut-edge representation learning for language, most language representation models usually focus on specific levels of linguistic units. This work introduces universal language representation learning, i.e.,…

Domain Generalization (DG) seeks to develop a versatile model capable of performing effectively on unseen target domains. Notably, recent advances in pre-trained Visual Foundation Models (VFMs), such as CLIP, have demonstrated considerable…

Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of Natural Language Processing is to understand sequences of words, a major…

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently…

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that…

The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types.…

Efficient exploration is essential for intelligent systems interacting with their environment, but existing language models often fall short in scenarios that require strategic information gathering. In this paper, we present Paprika, a…

State-of-the-art large language and vision models are trained over trillions of tokens that are aggregated from a large variety of sources. As training data collections grow, manually managing the samples becomes time-consuming, tedious,…

We present a deep neural network based singing voice synthesizer, inspired by the Deep Convolutions Generative Adversarial Networks (DCGAN) architecture and optimized using the Wasserstein-GAN algorithm. We use vocoder parameters for…

Generative information retrieval, encompassing two major tasks of Generative Document Retrieval (GDR) and Grounded Answer Generation (GAR), has gained significant attention in the area of information retrieval and natural language…

We propose a novel spectral generative modeling framework for natural language processing that jointly learns a global time varying Fourier dictionary and per token mixing coefficients, replacing the ubiquitous self attention mechanism in…