Related papers: Unlocking Efficiency: Adaptive Masking for Gene Tr…

Gene enhancers control when and where genes switch on, yet their sequence diversity and tissue specificity make them hard to pinpoint in colorectal cancer. We take a sequence-only route and fine-tune DNABERT-2, a transformer genomic…

We discover a robust self-supervised strategy tailored towards molecular representations for generative masked language models through a series of tailored, in-depth ablations. Using this pre-training strategy, we train BARTSmiles, a…

We design and evaluate a Bayesian optimization framework for resource efficient pre-training of Transformer-based language models (TLMs). TLM pre-training requires high computational resources and introduces many unresolved design choices,…

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…

Large scale self-supervised pre-training of Transformer language models has advanced the field of Natural Language Processing and shown promise in cross-application to the biological `languages' of proteins and DNA. Learning effective…

This paper presents a novel training method, Conditional Masked Language Modeling (CMLM), to effectively learn sentence representations on large scale unlabeled corpora. CMLM integrates sentence representation learning into MLM training by…

Pre-trained language models based on masked language modeling (MLM) excel in natural language understanding (NLU) tasks. While fine-tuned MLM-based encoders consistently outperform causal language modeling decoders of comparable size,…

Autoregressive language models are the currently dominant paradigm for text generation, but they have some fundamental limitations that cannot be remedied by scale-for example inherently sequential and unidirectional generation. While…

Pre-trained encoder-only and sequence-to-sequence (seq2seq) models each have advantages, however training both model types from scratch is computationally expensive. We explore recipes to improve pre-training efficiency by initializing one…

Curriculum learning-organizing training data from easy to hard-has improved efficiency across machine learning domains, yet remains underexplored for language model pretraining. We present the first systematic investigation of curriculum…

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…

Bidirectional Encoder Representations from Transformers (BERT) has shown marvelous improvements across various NLP tasks, and its consecutive variants have been proposed to further improve the performance of the pre-trained language models.…

Peptide sequencing-the process of identifying amino acid sequences from mass spectrometry data-is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional…

Causal Language Modeling (CLM) and Masked Language Modeling (MLM) are two mainstream learning paradigms based on Transformer networks, specifically the Decoder-only and Encoder-only architectures. The strengths of each paradigm in…

This paper presents Masked ELMo, a new RNN-based model for language model pre-training, evolved from the ELMo language model. Contrary to ELMo which only uses independent left-to-right and right-to-left contexts, Masked ELMo learns fully…

Recently, prompt tuning \cite{lester2021power} has gradually become a new paradigm for NLP, which only depends on the representation of the words by freezing the parameters of pre-trained language models (PLMs) to obtain remarkable…

In the rapidly evolving landscape of genomics, deep learning has emerged as a useful tool for tackling complex computational challenges. This review focuses on the transformative role of Large Language Models (LLMs), which are mostly based…

Designing de-novo molecules with desired property profiles requires efficient exploration of the vast chemical space ranging from $10^{23}$ to $10^{60}$ possible synthesizable candidates. While various deep generative models have been…

As the cost of pretraining large language models grows, there is continued interest in strategies to improve learning efficiency during this core training stage. Motivated by cognitive development, where humans gradually build knowledge as…

Designing functional transition metal complexes (TMCs) faces challenges due to the vast search space of metals and ligands, requiring efficient optimization strategies. Traditional genetic algorithms (GAs) are commonly used, employing…