Related papers: A Comparative Review of RNA Language Models

The reasoning capabilities of Large Language Models (LLMs) play a critical role in many downstream tasks, yet depend strongly on the quality of training data. Despite various proposed data construction methods, their practical utility in…

The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…

RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…

Geometric deep learning has recently achieved great success in non-Euclidean domains, and learning on 3D structures of large biomolecules is emerging as a distinct research area. However, its efficacy is largely constrained due to the…

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of…

Reward models (RMs) play a critical role in enhancing the reasoning performance of LLMs. For example, they can provide training signals to finetune LLMs during reinforcement learning (RL) and help select the best answer from multiple…

Machine Learning-guided solutions for protein learning tasks have made significant headway in recent years. However, success in scientific discovery tasks is limited by the accessibility of well-defined and labeled in-domain data. To tackle…

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially…

An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…

Language models (LM) are very powerful in lipreading systems. Language models built upon the ground truth utterances of datasets learn grammar and structure rules of words and sentences (the latter in the case of continuous speech).…

Large Language Models (LLMs) are known for their expensive and time-consuming training. Thus, oftentimes, LLMs are fine-tuned to address a specific task, given the pretrained weights of a pre-trained LLM considered a foundation model. In…

Generative large language models (LLMs) are a promising alternative to pre-trained language models for entity matching due to their high zero-shot performance and ability to generalize to unseen entities. Existing research on using LLMs for…

In past work (Onokpasa, Wild, Wong, DCC 2023), we showed that (a) for joint compression of RNA sequence and structure, stochastic context-free grammars are the best known compressors and (b) that grammars which have better compression…

While Large Language Models (LLMs) have demonstrated exceptional multitasking abilities, fine-tuning these models on downstream, domain-specific datasets is often necessary to yield superior performance on test sets compared to their…

Vision-Language Models (VLMs) have rapidly advanced alongside Large Language Models (LLMs). This study evaluates the capabilities of prominent generative VLMs, such as GPT-4.1 and Gemini 2.5 Pro, accessed via APIs, for histopathology image…

Denoising language models (DLMs) have been proposed as a powerful alternative to traditional language models (LMs) for automatic speech recognition (ASR), motivated by their ability to use bidirectional context and adapt to a specific ASR…

Recent breakthroughs in language models (LMs) using neural networks have raised the question: how similar are these models' processing to human language processing? Results using a framework called Brain Score (BS) -- predicting fMRI…

Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from…

Large Language Models (LLMs) have the potential to accelerate small molecule drug design due to their ability to reason about information from diverse sources and formats. However, their practical utility remains unclear due to the lack of…

This study examines whether Low-Rank Adaptation (LoRA) fine-tuned Large Language Models (LLMs) can approximate the performance of fully fine-tuned models in generating human-interpretable decisions and explanations for malware…