Related papers: A Comparative Review of RNA Language Models

Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA language model pretrained on influenza genomes with intact,…

Recent work by Hewitt et al. (2020) provides an interpretation of the empirical success of recurrent neural networks (RNNs) as language models (LMs). It shows that RNNs can efficiently represent bounded hierarchical structures that are…

Vision-language models (VLMs) have enabled strong zero-shot classification through image-text alignment. Yet, their purely visual inference capabilities remain under-explored. In this work, we conduct a comprehensive evaluation of both…

Recent Active Learning (AL) approaches in Natural Language Processing (NLP) proposed using off-the-shelf pretrained language models (LMs). In this paper, we argue that these LMs are not adapted effectively to the downstream task during AL…

Recently, large language models (LLMs) have shown significant progress, approaching human perception levels. In this work, we demonstrate that despite these advances, LLMs still struggle to reason using molecular structural information.…

Large Language Models (LLMs), such as ChatGPT, have taken the world by storm and have passed certain forms of the Turing test. However, LLMs are not limited to human language and analyze sequential data, such as DNA, protein, and gene…

The rapid spread of multilingual misinformation requires robust automated fact verification systems capable of handling fine-grained veracity assessments across diverse languages. While large language models have shown remarkable…

Despite the widespread availability of LLMs, there remains a substantial gap in their capabilities and availability across diverse languages. One approach to address these issues has been to take an existing pre-trained LLM and continue to…

Multilingual large language models (LLMs) seem to generalize somewhat across languages. We hypothesize this is a result of implicit vector space alignment. Evaluating such alignment, we see that larger models exhibit very high-quality…

Less than 1% of protein sequences are structurally and functionally annotated. Natural Language Processing (NLP) community has recently embraced self-supervised learning as a powerful approach to learn representations from unlabeled text,…

While Language Models (LMs) are the workhorses of NLP, their interplay with structured knowledge graphs (KGs) is still actively researched. Current methods for encoding such graphs typically either (i) linearize them for embedding with LMs…

RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…

Large language models (LLMs) are the result of a massive experiment in bottom-up, data-driven reverse engineering of language at scale. Despite their utility in a number of downstream NLP tasks, ample research has shown that LLMs are…

Large Language Models (LLMs) have been evaluated using diverse question types, e.g., multiple-choice, true/false, and short/long answers. This study answers an unexplored question about the impact of different question types on LLM accuracy…

Multilingual Large Language Models (LLMs) have recently shown great capabilities in a wide range of tasks, exhibiting state-of-the-art performance through zero-shot or few-shot prompting methods. While there have been extensive studies on…

RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…

Enhancing the complex reasoning capabilities of Large Language Models (LLMs) attracts widespread attention. While reinforcement learning (RL) has shown superior performance for improving complex reasoning, its impact on cross-lingual…

Transformer-based language models (LMs) continue to advance state-of-the-art performance on NLP benchmark tasks, including tasks designed to mimic human-inspired "commonsense" competencies. To better understand the degree to which LMs can…

Recent advancements in large language models (LLMs) have shown promise in feature engineering for tabular data, but concerns about their reliability persist, especially due to variability in generated outputs. We introduce a multi-level…

Large Language Models (LLMs) have demonstrated remarkable abilities in text comprehension and logical reasoning, indicating that the text representations learned by LLMs can facilitate their language processing capabilities. In…