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Pretraining DNA language models (DNALMs) on the full human genome is resource-intensive, yet often considered necessary for strong downstream performance. Inspired by recent findings in NLP and long-context modeling, we explore an…

Genomics · Quantitative Biology 2025-06-24 Sohan Mupparapu , Parameswari Krishnamurthy , Ratish Puduppully

Tokenization is a fundamental preprocessing step in Natural Language Processing (NLP), significantly impacting the capability of large language models (LLMs) to capture linguistic and semantic nuances. This study introduces a novel…

Computation and Language · Computer Science 2025-08-19 M. Ali Bayram , Ali Arda Fincan , Ahmet Semih Gümüş , Sercan Karakaş , Banu Diri , Savaş Yıldırım

Large language models pretrained on general-domain corpora often exhibit tokenization inefficiencies when applied to specialized domains. Although continual pretraining for domain adaptation partially alleviate performance degradation, it…

Computation and Language · Computer Science 2026-05-19 Gunjan Balde , Soumyadeep Roy , Mainack Mondal , Niloy Ganguly

Biomedical named entity recognition (NER) is a fundamental task in text mining of medical documents and has many applications. Deep learning based approaches to this task have been gaining increasing attention in recent years as their…

Computation and Language · Computer Science 2018-08-16 Devendra Singh Sachan , Pengtao Xie , Mrinmaya Sachan , Eric P Xing

Biomedical named entity recognition (NER) presents unique challenges due to specialized vocabularies, the sheer volume of entities, and the continuous emergence of novel entities. Traditional NER models, constrained by fixed taxonomies and…

Computation and Language · Computer Science 2025-05-22 Anthony Yazdani , Ihor Stepanov , Douglas Teodoro

Large language models (LLMs), endowed with exceptional reasoning capabilities, are adept at discerning profound user interests from historical behaviors, thereby presenting a promising avenue for the advancement of recommendation systems.…

Information Retrieval · Computer Science 2024-12-19 Guanghan Li , Xun Zhang , Yufei Zhang , Yifan Yin , Guojun Yin , Wei Lin

Biomedical queries have become increasingly prevalent in web searches, reflecting the growing interest in accessing biomedical literature. Despite recent research on large-language models (LLMs) motivated by endeavours to attain generalized…

Computation and Language · Computer Science 2024-08-06 Ankan Mullick , Mukur Gupta , Pawan Goyal

Tokenization is a fundamental component of large language models (LLMs), yet its influence on model scaling and performance is not fully explored. In this paper, we introduce Over-Tokenized Transformers, a novel framework that decouples…

Computation and Language · Computer Science 2025-05-26 Hongzhi Huang , Defa Zhu , Banggu Wu , Yutao Zeng , Ya Wang , Qiyang Min , Xun Zhou

Tokenization is a critical component of language model pretraining, yet standard tokenization methods often prioritize information-theoretical goals like high compression and low fertility rather than linguistic goals like morphological…

Computation and Language · Computer Science 2025-11-14 Marisa Hudspeth , Patrick J. Burns , Brendan O'Connor

Named entity recognition (NER) models generally perform poorly when large training datasets are unavailable for low-resource domains. Recently, pre-training a large-scale language model has become a promising direction for coping with the…

Computation and Language · Computer Science 2021-12-02 Zihan Liu , Feijun Jiang , Yuxiang Hu , Chen Shi , Pascale Fung

Tokenizing raw texts into word units is an essential pre-processing step for critical tasks in the NLP pipeline such as tagging, parsing, named entity recognition, and more. For most languages, this tokenization step straightforward.…

Computation and Language · Computer Science 2022-03-22 Idan Brusilovsky , Reut Tsarfaty

Large Language Models (LLMs) have shown impressive abilities in data annotation, opening the way for new approaches to solve classic NLP problems. In this paper, we show how to use LLMs to create NuNER, a compact language representation…

Computation and Language · Computer Science 2024-02-26 Sergei Bogdanov , Alexandre Constantin , Timothée Bernard , Benoit Crabbé , Etienne Bernard

While pre-trained language models (LMs) have brought great improvements in many NLP tasks, there is increasing attention to explore capabilities of LMs and interpret their predictions. However, existing works usually focus only on a certain…

Computation and Language · Computer Science 2022-07-29 Yaozong Shen , Lijie Wang , Ying Chen , Xinyan Xiao , Jing Liu , Hua Wu

Pre-trained language models (PLMs) have proven to be effective for document re-ranking task. However, they lack the ability to fully interpret the semantics of biomedical and health-care queries and often rely on simplistic patterns for…

Computation and Language · Computer Science 2023-05-09 Deepak Gupta , Dina Demner-Fushman

Large Language Models (LLMs) have revolutionised the field of Natural Language Processing (NLP) and have achieved state-of-the-art performance in practically every task in this field. However, the prevalent approach used in text generation,…

Computation and Language · Computer Science 2024-08-12 Nicolo Micheletti , Samuel Belkadi , Lifeng Han , Goran Nenadic

Large Language Models (LLMs) have shown promising results on machine translation for high resource language pairs and domains. However, in specialised domains (e.g. medical) LLMs have shown lower performance compared to standard neural…

Computation and Language · Computer Science 2025-07-31 Miguel Rios

Subword tokenization has become the de-facto standard for tokenization, although comparative evaluations of subword vocabulary quality across languages are scarce. Existing evaluation studies focus on the effect of a tokenization algorithm…

Computation and Language · Computer Science 2023-10-23 Lisa Beinborn , Yuval Pinter

Neural models that do not rely on pre-training have excelled in the keyphrase generation task with large annotated datasets. Meanwhile, new approaches have incorporated pre-trained language models (PLMs) for their data efficiency. However,…

Computation and Language · Computer Science 2024-02-26 Di Wu , Wasi Uddin Ahmad , Kai-Wei Chang

In this work, we show a fundamental limitation in vocabulary adaptation approaches that use Byte-Pair Encoding (BPE) tokenization scheme for fine-tuning pretrained language models (PLMs) to expert domains. Current approaches trivially…

Computation and Language · Computer Science 2025-04-29 Gunjan Balde , Soumyadeep Roy , Mainack Mondal , Niloy Ganguly

Bengali is an underrepresented language in NLP research. However, it remains a challenge due to its unique linguistic structure and computational constraints. In this work, we systematically investigate the challenges that hinder Bengali…

Computation and Language · Computer Science 2025-08-01 Shimanto Bhowmik , Tawsif Tashwar Dipto , Md Sazzad Islam , Sheryl Hsu , Tahsin Reasat