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Protein language models (pLMs) have demonstrated success at generating functional proteins across vast sequence spaces but lack the ability to design high-fitness variants on demand. Here, we iteratively guide pLMs toward user-defined…

Biomolecules · Quantitative Biology 2025-12-01 Filippo Stocco , Maria Artigues-Lleixa , Andrea Hunklinger , Talal Widatalla , Marc Guell , Noelia Ferruz

Recent work using auxiliary prediction task classifiers to investigate the properties of LSTM representations has begun to shed light on why pretrained representations, like ELMo (Peters et al., 2018) and CoVe (McCann et al., 2017), are so…

Computation and Language · Computer Science 2019-01-08 Kelly W. Zhang , Samuel R. Bowman

This work introduces an approach to assessing phrase break in ESL learners' speech with pre-trained language models (PLMs). Different with traditional methods, this proposal converts speech to token sequences, and then leverages the power…

Computation and Language · Computer Science 2022-10-31 Zhiyi Wang , Shaoguang Mao , Wenshan Wu , Yan Xia

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with…

Biomolecules · Quantitative Biology 2025-03-14 Jiarui Lu , Xiaoyin Chen , Stephen Zhewen Lu , Chence Shi , Hongyu Guo , Yoshua Bengio , Jian Tang

Pre-trained Language Models (PLMs) have been widely used in various natural language processing (NLP) tasks, owing to their powerful text representations trained on large-scale corpora. In this paper, we propose a new PLM called PERT for…

Computation and Language · Computer Science 2022-03-15 Yiming Cui , Ziqing Yang , Ting Liu

Neural Machine Translation (NMT) has become a significant technology in natural language processing through extensive research and development. However, the deficiency of high-quality bilingual language pair data still poses a major…

Computation and Language · Computer Science 2024-01-17 Soon-Jae Hwang , Chang-Sung Jeong

Vision-language models (VLMs) have made substantial progress across a wide range of visual question answering benchmarks, spanning visual reasoning, document understanding, and multimodal dialogue. These improvements are evident in a wide…

Computer Vision and Pattern Recognition · Computer Science 2026-02-23 Dhruba Ghosh , Yuhui Zhang , Ludwig Schmidt

Proteins are complex biomolecules that play a central role in various biological processes, making them critical targets for breakthroughs in molecular biology, medical research, and drug discovery. Deciphering their intricate, hierarchical…

Machine Learning · Computer Science 2025-05-09 Viet Thanh Duy Nguyen , Truong-Son Hy

Recently, decomposing complex problems into simple subtasks--a crucial part of human-like natural planning--to solve the given problem has significantly boosted the performance of large language models (LLMs). However, leveraging such…

Computation and Language · Computer Science 2025-07-11 Mihir Parmar , Palash Goyal , Xin Liu , Yiwen Song , Mingyang Ling , Chitta Baral , Hamid Palangi , Tomas Pfister

Pre-trained language models (PrLM) has been shown powerful in enhancing a broad range of downstream tasks including various dialogue related ones. However, PrLMs are usually trained on general plain text with common language model (LM)…

Computation and Language · Computer Science 2021-08-03 Yi Xu , Hai Zhao

Simile interpretation is a crucial task in natural language processing. Nowadays, pre-trained language models (PLMs) have achieved state-of-the-art performance on many tasks. However, it remains under-explored whether PLMs can interpret…

Computation and Language · Computer Science 2022-03-17 Qianyu He , Sijie Cheng , Zhixu Li , Rui Xie , Yanghua Xiao

Recently, Language Models (LMs) instruction-tuned on multiple tasks, also known as multitask-prompted fine-tuning (MT), have shown the capability to generalize to unseen tasks. Previous work has shown that scaling the number of training…

Computation and Language · Computer Science 2023-02-10 Joel Jang , Seungone Kim , Seonghyeon Ye , Doyoung Kim , Lajanugen Logeswaran , Moontae Lee , Kyungjae Lee , Minjoon Seo

Representation learning for proteins has primarily focused on the global understanding of protein sequences regardless of their length. However, shorter proteins (known as peptides) take on distinct structures and functions compared to…

Quantitative Methods · Quantitative Biology 2022-11-15 Gil Sadeh , Zichen Wang , Jasleen Grewal , Huzefa Rangwala , Layne Price

Keyphrase Generation (KPG) is a longstanding task in NLP with widespread applications. The advent of sequence-to-sequence (seq2seq) pre-trained language models (PLMs) has ushered in a transformative era for KPG, yielding promising…

Computation and Language · Computer Science 2023-10-24 Di Wu , Wasi Uddin Ahmad , Kai-Wei Chang

The recent prevalence of pretrained language models (PLMs) has dramatically shifted the paradigm of semantic parsing, where the mapping from natural language utterances to structured logical forms is now formulated as a Seq2Seq task.…

Computation and Language · Computer Science 2022-12-06 Lunyiu Nie , Jiuding Sun , Yanlin Wang , Lun Du , Lei Hou , Juanzi Li , Shi Han , Dongmei Zhang , Jidong Zhai

Recent Pre-trained Language Models (PLMs) usually only provide users with the inference APIs, namely the emerging Model-as-a-Service (MaaS) setting. To adapt MaaS PLMs to downstream tasks without accessing their parameters and gradients,…

Computation and Language · Computer Science 2025-06-03 Zifeng Cheng , Zhaoling Chen , Zhiwei Jiang , Yafeng Yin , Cong Wang , Shiping Ge , Qing Gu

Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language…

Machine Learning · Computer Science 2025-08-18 Sanket Jantre , Tianle Wang , Gilchan Park , Kriti Chopra , Nicholas Jeon , Xiaoning Qian , Nathan M. Urban , Byung-Jun Yoon

Parameter-efficient (PE) methods (like Prompts or Adapters) for adapting pre-trained language models (PLM) to downstream tasks have been popular recently. However, hindrances still prevent these methods from reaching their full potential.…

Computation and Language · Computer Science 2024-05-31 Shih-Cheng Huang , Shih-Heng Wang , Min-Han Shih , Saurav Sahay , Hung-yi Lee

Masked language modeling (MLM) plays a key role in pretraining large language models. But the MLM objective is often dominated by high-frequency words that are sub-optimal for learning factual knowledge. In this work, we propose an approach…

Computation and Language · Computer Science 2023-04-05 Nafis Sadeq , Byungkyu Kang , Prarit Lamba , Julian McAuley

The advance of Artificial Intelligence (AI) is continuously reshaping the future 6G wireless communications. Particularly, the development of Large Language Models (LLMs) offers a promising approach to effectively improve the performance…

Information Theory · Computer Science 2025-03-10 Tianyue Zheng , Linglong Dai