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Pre-training a language model and then fine-tuning it for downstream tasks has demonstrated state-of-the-art results for various NLP tasks. Pre-training is usually independent of the downstream task, and previous works have shown that this…

Computation and Language · Computer Science 2022-11-28 Tanish Lad , Himanshu Maheshwari , Shreyas Kottukkal , Radhika Mamidi

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

Recent works show that learning contextualized embeddings for words is beneficial for downstream tasks. BERT is one successful example of this approach. It learns embeddings by solving two tasks, which are masked language model (masked LM)…

Computation and Language · Computer Science 2020-11-10 Çağla Aksoy , Alper Ahmetoğlu , Tunga Güngör

Masked language modelling (MLM) as a pretraining objective has been widely adopted in genomic sequence modelling. While pretrained models can successfully serve as encoders for various downstream tasks, the distribution shift between…

Machine Learning · Computer Science 2025-02-26 Monireh Safari , Pablo Millan Arias , Scott C. Lowe , Lila Kari , Angel X. Chang , Graham W. Taylor

Large-scale language models such as DNABert and LOGO aim to learn optimal gene representations and are trained on the entire Human Reference Genome. However, standard tokenization schemes involve a simple sliding window of tokens like…

Computation and Language · Computer Science 2023-10-16 Soumyadeep Roy , Jonas Wallat , Sowmya S Sundaram , Wolfgang Nejdl , Niloy Ganguly

Language model pre-training, such as BERT, has achieved remarkable results in many NLP tasks. However, it is unclear why the pre-training-then-fine-tuning paradigm can improve performance and generalization capability across different…

Computation and Language · Computer Science 2019-08-16 Yaru Hao , Li Dong , Furu Wei , Ke Xu

Transformer-based pre-trained language models, such as BERT, achieve great success in various natural language understanding tasks. Prior research found that BERT captures a rich hierarchy of linguistic information at different layers.…

Computation and Language · Computer Science 2023-07-17 Qian Chen , Wen Wang , Qinglin Zhang , Chong Deng , Ma Yukun , Siqi Zheng

For protein sequence datasets, unlabeled data has greatly outpaced labeled data due to the high cost of wet-lab characterization. Recent deep-learning approaches to protein prediction have shown that pre-training on unlabeled data can yield…

Machine Learning · Computer Science 2020-12-02 Pascal Sturmfels , Jesse Vig , Ali Madani , Nazneen Fatema Rajani

Contextual embedding-based language models trained on large data sets, such as BERT and RoBERTa, provide strong performance across a wide range of tasks and are ubiquitous in modern NLP. It has been observed that fine-tuning these models on…

Computation and Language · Computer Science 2021-09-16 Vin Sachidananda , Jason S. Kessler , Yi-an Lai

Transformer-based masked language models such as BERT, trained on general corpora, have shown impressive performance on downstream tasks. It has also been demonstrated that the downstream task performance of such models can be improved by…

Computation and Language · Computer Science 2023-05-04 Zhi Hong , Aswathy Ajith , Gregory Pauloski , Eamon Duede , Kyle Chard , Ian Foster

Recently, the development of pre-trained language models has brought natural language processing (NLP) tasks to the new state-of-the-art. In this paper we explore the efficiency of various pre-trained language models. We pre-train a list of…

Computation and Language · Computer Science 2023-07-27 Tong Guo

Pre-training large-scale neural language models on raw texts has made a significant contribution to improving transfer learning in natural language processing (NLP). With the introduction of transformer-based language models, such as…

Computation and Language · Computer Science 2024-05-08 Shoya Wada , Toshihiro Takeda , Shiro Manabe , Shozo Konishi , Jun Kamohara , Yasushi Matsumura

Motivated by the success of pre-trained language models such as BERT in a broad range of natural language processing (NLP) tasks, recent research efforts have been made for adapting these models for different application domains. Along this…

Computation and Language · Computer Science 2021-12-07 Denghui Zhang , Zixuan Yuan , Yanchi Liu , Hao Liu , Fuzhen Zhuang , Hui Xiong , Haifeng Chen

Pretraining NLP models with variants of Masked Language Model (MLM) objectives has recently led to a significant improvements on many tasks. This paper examines the benefits of pretrained models as a function of the number of training…

Computation and Language · Computer Science 2020-06-17 Sinong Wang , Madian Khabsa , Hao Ma

Deep learning associated with neurological signals is poised to drive major advancements in diverse fields such as medical diagnostics, neurorehabilitation, and brain-computer interfaces. The challenge in harnessing the full potential of…

Signal Processing · Electrical Eng. & Systems 2024-07-08 Di Wu , Siyuan Li , Jie Yang , Mohamad Sawan

Recent advances in natural language processing (NLP) can be largely attributed to the advent of pre-trained language models such as BERT and RoBERTa. While these models demonstrate remarkable performance on general datasets, they can…

The current era of natural language processing (NLP) has been defined by the prominence of pre-trained language models since the advent of BERT. A feature of BERT and models with similar architecture is the objective of masked language…

Computation and Language · Computer Science 2023-07-04 Ed S. Ma

In recent years, major advancements in natural language processing (NLP) have been driven by the emergence of large language models (LLMs), which have significantly revolutionized research and development within the field. Building upon…

Computation and Language · Computer Science 2023-05-09 Hazal Türkmen , Oğuz Dikenelli , Cenk Eraslan , Mehmet Cem Çallı , Süha Süreyya Özbek

Natural language understanding has recently seen a surge of progress with the use of sentence encoders like ELMo (Peters et al., 2018a) and BERT (Devlin et al., 2019) which are pretrained on variants of language modeling. We conduct the…

Large pre-trained language models help to achieve state of the art on a variety of natural language processing (NLP) tasks, nevertheless, they still suffer from forgetting when incrementally learning a sequence of tasks. To alleviate this…

Computation and Language · Computer Science 2023-03-03 Mingxu Tao , Yansong Feng , Dongyan Zhao
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