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Natural Language Processing (NLP) has transformed various fields beyond linguistics by applying techniques originally developed for human language to the analysis of biological sequences. This review explores the application of NLP methods…

Computation and Language · Computer Science 2025-06-04 Ella Rannon , David Burstein

We present a comparison of word-based and character-based sequence-to-sequence models for data-to-text natural language generation, which generate natural language descriptions for structured inputs. On the datasets of two recent generation…

Computation and Language · Computer Science 2018-10-12 Glorianna Jagfeld , Sabrina Jenne , Ngoc Thang Vu

We present a framework for generating natural language description from structured data such as tables; the problem comes under the category of data-to-text natural language generation (NLG). Modern data-to-text NLG systems typically employ…

Computation and Language · Computer Science 2019-10-08 Anirban Laha , Parag Jain , Abhijit Mishra , Karthik Sankaranarayanan

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…

Genomics · Quantitative Biology 2024-09-24 Gonzalo Benegas , Chengzhong Ye , Carlos Albors , Jianan Canal Li , Yun S. Song

Natural Language Processing (NLP) has become one of the leading application areas in the current Artificial Intelligence boom. Transfer learning has enabled large deep learning neural networks trained on the language modeling task to vastly…

Computation and Language · Computer Science 2022-06-16 Csaba Veres

In recent times, Transformer-based language models are making quite an impact in the field of natural language processing. As relevant parallels can be drawn between biological sequences and natural languages, the models used in NLP can be…

Computation and Language · Computer Science 2025-12-25 Nimisha Ghosh , Daniele Santoni , Indrajit Saha , Giovanni Felici

Language models, especially transformer-based ones, have achieved colossal success in NLP. To be precise, studies like BERT for NLU and works like GPT-3 for NLG are very important. If we consider DNA sequences as a text written with an…

Genomics · Quantitative Biology 2026-01-21 Musa Nuri Ihtiyar , Arzucan Ozgur

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in…

Computation and Language · Computer Science 2022-11-18 Tianyu Liu , Yuchen Jiang , Nicholas Monath , Ryan Cotterell , Mrinmaya Sachan

Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…

Other Quantitative Biology · Quantitative Biology 2025-01-29 Wang Liang

We present a natural language generator based on the sequence-to-sequence approach that can be trained to produce natural language strings as well as deep syntax dependency trees from input dialogue acts, and we use it to directly compare…

Computation and Language · Computer Science 2017-09-18 Ondřej Dušek , Filip Jurčíček

Recent advances in machine learning have made revolutionary breakthroughs in computer games, image and natural language understanding, and scientific discovery. Foundation models and large-scale language models (LLMs) have recently achieved…

Neurons and Cognition · Quantitative Biology 2023-10-31 Ran Wang , Zhe Sage Chen

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…

Quantitative Methods · Quantitative Biology 2025-02-04 Jiajia Liu , Mengyuan Yang , Yankai Yu , Haixia Xu , Tiangang Wang , Kang Li , Xiaobo Zhou

Language models for biological and chemical sequences enable crucial applications such as drug discovery, protein engineering, and precision medicine. Currently, these language models are predominantly based on Transformer architectures.…

Generative models reliant on sequential autoregression have been at the forefront of language generation for an extensive period, particularly following the introduction of widely acclaimed transformers. Despite its excellent performance,…

Computation and Language · Computer Science 2024-06-21 Yaguang Li , Xin Chen

Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis…

Computation and Language · Computer Science 2025-03-07 Jiyue Jiang , Zikang Wang , Yuheng Shan , Heyan Chai , Jiayi Li , Zixian Ma , Xinrui Zhang , Yu Li

Large Language Models (LLMs) have become capable of generating highly fluent text in certain languages, without modules specially designed to capture grammar or semantic coherence. What does this mean for the future of linguistic expertise…

Computation and Language · Computer Science 2025-10-17 Juri Opitz , Shira Wein , Nathan Schneider

Recent breakthroughs in Natural Language Processing (NLP) have been driven by language models trained on a massive amount of plain text. While powerful, deriving supervision from textual resources is still an open question. For example,…

Computation and Language · Computer Science 2022-07-22 Mingda Chen

Natural Language Processing (NLP) is a key technique for developing Medical Artificial Intelligence (AI) systems that leverage Electronic Health Record (EHR) data to build diagnostic and prognostic models. NLP enables the conversion of…

Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4…

Biomolecules · Quantitative Biology 2023-05-04 Sergio Romero-Romero , Sebastian Lindner , Noelia Ferruz

Human languages have evolved to be structured through repeated language learning and use. These processes introduce biases that operate during language acquisition and shape linguistic systems toward communicative efficiency. In this paper,…

Computation and Language · Computer Science 2024-12-16 Tom Kouwenhoven , Max Peeperkorn , Tessa Verhoef
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