Related papers: ProtSent: Protein Sentence Transformers

Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…

One of the challenges with finetuning pretrained language models (PLMs) is that their tokenizer is optimized for the language(s) it was pretrained on, but brittle when it comes to previously unseen variations in the data. This can for…

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…

Objective To develop soft prompt-based learning algorithms for large language models (LLMs), examine the shape of prompts, prompt-tuning using frozen/unfrozen LLMs, transfer learning, and few-shot learning abilities. Methods We developed a…

Soft Prompt Tuning (SPT) is a parameter-efficient method for adapting pre-trained language models (PLMs) to specific tasks by inserting learnable embeddings, or soft prompts, at the input layer of the PLM, without modifying its parameters.…

Sparse Autoencoder (SAE) has emerged as a powerful tool for mechanistic interpretability of large language models. Recent works apply SAE to protein language models (PLMs), aiming to extract and analyze biologically meaningful features from…

Contrastive learning has proven to be an effective method for pre-training models using weakly labeled data in the vision domain. Sentence transformers are the NLP counterparts to this architecture, and have been growing in popularity due…

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM…

For sequence transduction tasks like speech recognition, a strong structured prior model encodes rich information about the target space, implicitly ruling out invalid sequences by assigning them low probability. In this work, we propose…

The increasing number of protein sequences decoded from genomes is opening up new avenues of research on linking protein sequence to function with transformer neural networks. Recent research has shown that the number of known protein…

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…

We introduce a pioneering methodology for boosting large language models in the domain of protein representation learning. Our primary contribution lies in the refinement process for correlating the over-reliance on co-evolution knowledge,…

We present a joint Speech and Language Model (SLM), a multitask, multilingual, and dual-modal model that takes advantage of pretrained foundational speech and language models. SLM freezes the pretrained foundation models to maximally…

Sentence embeddings encode sentences in fixed dense vectors and have played an important role in various NLP tasks and systems. Methods for building sentence embeddings include unsupervised learning such as Quick-Thoughts and supervised…

Autoregressive language models (LMs) generate one token at a time, yet human reasoning operates over higher-level abstractions - sentences, propositions, and concepts. This contrast raises a central question- Can LMs likewise learn to…

Fine-tuning pre-trained language models (PLMs) has demonstrated its effectiveness on various downstream NLP tasks recently. However, in many low-resource scenarios, the conventional fine-tuning strategies cannot sufficiently capture the…

The conditional generation of proteins with desired functions is a key goal for generative models. Existing methods based on prompting of protein language models (PLMs) can generate proteins conditioned on a target functionality, such as a…

Pre-trained models (PTMs) have shown great promise in the speech and audio domain. Embeddings leveraged from these models serve as inputs for learning algorithms with applications in various downstream tasks. One such crucial task is Speech…

Although pre-trained language models (PLMs) have achieved state-of-the-art performance on various natural language processing (NLP) tasks, they are shown to be lacking in knowledge when dealing with knowledge driven tasks. Despite the many…

Large language models (LLMs) have shown strong ability in generating rich representations across domains such as natural language processing and generation, computer vision, and multimodal learning. However, their application in biomedical…