Related papers: Long-range gene expression prediction with token a…

Large Language Models (LLMs), such as Generative Pre-trained Transformers (GPTs) are revolutionizing the generation of human-like text, producing contextually relevant and syntactically correct content. Despite challenges like biases and…

Purpose: Large Language Models (LLMs) like GPT (Generative Pre-trained Transformer) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI are increasingly recognized for their potential in the field of cheminformatics,…

We propose a novel convolutional architecture, named $gen$CNN, for word sequence prediction. Different from previous work on neural network-based language modeling and generation (e.g., RNN or LSTM), we choose not to greedily summarize the…

Speech-LLM models have demonstrated great performance in multi-modal and multi-task speech understanding. A typical speech-LLM paradigm is integrating speech modality with a large language model (LLM). While the Whisper encoder was…

In standard genetic programming (stdGP), solutions are varied by modifying their syntax, with uncertain effects on their semantics. Geometric-semantic genetic programming (GSGP), a popular variant of GP, effectively searches the semantic…

Generic generation and manipulation of text is challenging and has limited success compared to recent deep generative modeling in visual domain. This paper aims at generating plausible natural language sentences, whose attributes are…

In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…

Spatial transcriptomics (ST) has emerged as an advanced technology that provides spatial context to gene expression. Recently, deep learning-based methods have shown the capability to predict gene expression from WSI data using ST data.…

Prompt tuning, a recently emerging paradigm, enables the powerful vision-language pre-training models to adapt to downstream tasks in a parameter -- and data -- efficient way, by learning the ``soft prompts'' to condition frozen…

The gene set analysis (GSA) is a foundational approach for uncovering the molecular functions associated with a group of genes. Recently, LLM-powered methods have emerged to annotate gene sets with biological functions together with…

Automated Short Answer Scoring (ASAS) is a critical component in educational assessment. While traditional ASAS systems relied on rule-based algorithms or complex deep learning methods, recent advancements in Generative Language Models…

Temporal expressions in text play a significant role in language understanding and correctly identifying them is fundamental to various retrieval and natural language processing systems. Previous works have slowly shifted from rule-based to…

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how…

The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…

Large language models (LLMs) augmented with retrieval systems have significantly advanced natural language processing tasks by integrating external knowledge sources, enabling more accurate and contextually rich responses. To improve the…

We apply topological data analysis (TDA) to speech classification problems and to the introspection of a pretrained speech model, HuBERT. To this end, we introduce a number of topological and algebraic features derived from Transformer…

Training generative adversarial networks (GANs) with limited data is challenging because the discriminator is prone to overfitting. Previously proposed differentiable augmentation demonstrates improved data efficiency of training GANs.…

Predicting how cells respond to genetic perturbations is fundamental to understanding gene function, disease mechanisms, and therapeutic development. While recent deep learning approaches have shown promise in modeling single-cell…

Cross-modal alignment is one key challenge for Vision-and-Language Navigation (VLN). Most existing studies concentrate on mapping the global instruction or single sub-instruction to the corresponding trajectory. However, another critical…

Recent progress in the task of Grammatical Error Correction (GEC) has been driven by addressing data sparsity, both through new methods for generating large and noisy pretraining data and through the publication of small and higher-quality…