相关论文: Enhancing DNA Foundation Models to Address Masking…

Various types of social biases have been reported with pretrained Masked Language Models (MLMs) in prior work. However, multiple underlying factors are associated with an MLM such as its model size, size of the training data, training…

Machine Learning-guided solutions for protein learning tasks have made significant headway in recent years. However, success in scientific discovery tasks is limited by the accessibility of well-defined and labeled in-domain data. To tackle…

Masked language model (MLM) has been widely used for understanding tasks, e.g. BERT. Recently, MLM has also been used for generation tasks. The most popular one in speech is using Mask-CTC for non-autoregressive speech recognition. In this…

We explore a framework for protein sequence representation learning that decomposes the task between manifold learning and distributional modelling. Specifically we present a Latent Space Diffusion architecture which combines a protein…

We propose a novel task-agnostic in-domain pre-training method that sits between generic pre-training and fine-tuning. Our approach selectively masks in-domain keywords, i.e., words that provide a compact representation of the target…

Computational biology and bioinformatics provide vast data gold-mines from protein sequences, ideal for Language Models taken from NLP. These LMs reach for new prediction frontiers at low inference costs. Here, we trained two…

Machine reading comprehension (MRC) is a challenging natural language processing (NLP) task. Recently, the emergence of pre-trained models (PTM) has brought this research field into a new era, in which the training objective plays a key…

In recent years, language models have drastically grown in size, and the abilities of these models have been shown to improve with scale. The majority of recent scaling laws studies focused on high-compute high-parameter count settings,…

Recently multi-lingual pre-trained language models (PLM) such as mBERT and XLM-R have achieved impressive strides in cross-lingual dense retrieval. Despite its successes, they are general-purpose PLM while the multilingual PLM tailored for…

Large Language Models (LLMs) have demonstrated remarkable performance across various domains, including healthcare. However, their ability to effectively represent structured non-textual data, such as the alphanumeric medical codes used in…

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently…

Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA language model pretrained on influenza genomes with intact,…

Masked diffusion models (MDMs) have emerged as a promising alternative to autoregressive models for language modeling, yet the effective design of transformer architectures for MDMs remains underexplored. In this paper, we show that…

Most works on transformers trained with the Masked Language Modeling (MLM) objective use the original BERT model's fixed masking rate of 15%. We propose to instead dynamically schedule the masking rate throughout training. We find that…

Masked diffusion models (MDMs) have emerged as a promising alternative to autoregressive models (ARMs) for language modeling. However, MDMs are known to learn substantially more slowly than ARMs, which may become problematic when scaling…

State-of-the-art neural models typically encode document-query pairs using cross-attention for re-ranking. To this end, models generally utilize an encoder-only (like BERT) paradigm or an encoder-decoder (like T5) approach. These paradigms,…

Multi-modal Large Language Model (MLLM) refers to a model expanded from a Large Language Model (LLM) that possesses the capability to handle and infer multi-modal data. Current MLLMs typically begin by using LLMs to decompose tasks into…

Multilingual Large Language Models (LLMs) can process many languages, yet how they internally represent this diversity remains unclear. Do they form shared multilingual representations with language-specific decoding, and if so, why does…

Pre-training has shown success in different areas of machine learning, such as Computer Vision, Natural Language Processing (NLP), and medical imaging. However, it has not been fully explored for clinical data analysis. An immense amount of…

Due to the huge amount of parameters, fine-tuning of pretrained language models (PLMs) is prone to overfitting in the low resource scenarios. In this work, we present a novel method that operates on the hidden representations of a PLM to…