Related papers: EvoLen: Evolution-Guided Tokenization for DNA Lang…

DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…

Commonly-used transformer language models depend on a tokenization schema which sets an unchangeable subword vocabulary prior to pre-training, destined to be applied to all downstream tasks regardless of domain shift, novel word formations,…

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D)…

Diffusion Language Models (DLMs) offer a promising alternative for language modeling by enabling parallel decoding through iterative refinement. However, most DLMs rely on hard binary masking and discrete token assignments, which hinder the…

This paper presents a novel hybrid tokenization strategy that enhances the performance of DNA Language Models (DLMs) by combining 6-mer tokenization with Byte Pair Encoding (BPE-600). Traditional k-mer tokenization is effective at capturing…

Extending pre-trained text Large Language Models (LLMs)'s speech understanding or generation abilities by introducing various effective speech tokens has attracted great attention in the speech community. However, building a unified speech…

Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of the labeled data due…

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the…

There are already many DNA large language models, but most of them still follow traditional uses, such as extracting sequence features for classification tasks. More innovative applications of large language models, such as prompt…

Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…

The prevalent use of Byte Pair Encoding (BPE) in Large Language Models (LLMs) facilitates robust handling of subword units and avoids issues of out-of-vocabulary words. Despite its success, a critical challenge persists: long tokens, rich…

How to best develop foundational models for time series forecasting remains an important open question. Tokenization is a crucial consideration in this effort: what is an effective discrete vocabulary for a real-valued sequential input? To…

Modern tokenizers employ deterministic algorithms to map text into a single "canonical" token sequence, yet the same string can be encoded as many non-canonical tokenizations using the tokenizer vocabulary. In this work, we investigate the…

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged…

Currently, many studies view DNA sequences as a special type of language and utilize Transformers to model them. These studies use fixed-length k-mer segmentation and BPE subword tokenization but lack a systematic evaluation to determine…

Tokenization is a foundational step in the text process of Large Language Models (LLMs). Texts must be first tokenized into token IDs, which are then input to LLMs. Inefficient tokenization results in long token-ID sequences and will slow…

Multimodal Large Language Models have made significant strides in integrating visual and textual information, yet they often struggle with effectively aligning these modalities. We introduce a novel image tokenizer that bridges this gap by…

Large language models have made remarkable progress in the field of molecular science, particularly in understanding and generating functional small molecules. This success is largely attributed to the effectiveness of molecular…

Tokenization is the first - and often underappreciated - layer of computation in language models. While Chain-of-Thought (CoT) prompting enables transformer models to approximate recurrent computation by externalizing intermediate steps, we…

Due in part to their discontinuous and discrete default encodings for numbers, Large Language Models (LLMs) have not yet been commonly used to process numerically-dense scientific datasets. Rendering datasets as text, however, could help…