Related papers: DNAMotifTokenizer: Towards Biologically Informed T…

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…

Tokens serve as the basic units of representation in DNA language models (DNALMs), yet their design remains underexplored. Unlike natural language, DNA lacks inherent token boundaries or predefined compositional rules, making tokenization a…

Tokenization is a foundational step in natural language processing (NLP) tasks, bridging raw text and language models. Existing tokenization approaches like Byte-Pair Encoding (BPE) originate from the field of data compression, and it has…

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…

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 crucial step in processing protein sequences for machine learning models, as proteins are complex sequences of amino acids that require meaningful segmentation to capture their functional and structural properties.…

Tokenization underlies every large language model, yet it remains an under-theorized and inconsistently designed component. Common subword approaches such as Byte Pair Encoding (BPE) offer scalability but often misalign with linguistic…

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…

The emergence of telomere-to-telomere (T2T) genome assemblies has opened new avenues for comparative genomics, yet effective tokenization strategies for genomic sequences remain underexplored. In this pilot study, we apply Byte Pair…

Tokenization sits at the boundary between high-throughput genomic input and GPU compute, posing challenges in both algorithm design and system throughput. Overlapping k-mer tokenization can introduce information leakage under masked…

The best performing transformer-based language models use subword tokenization techniques, such as Byte-Pair-Encoding (BPE). However, these approaches often overlook linguistic principles, such as morphological segmentation, which we…

The pretraining data of today's strongest language models is opaque; in particular, little is known about the proportions of various domains or languages represented. In this work, we tackle a task which we call data mixture inference,…

DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases…

Subword tokenization has become the prevailing standard in the field of natural language processing (NLP) over recent years, primarily due to the widespread utilization of pre-trained language models. This shift began with Byte-Pair…

Subword tokenization methods, such as Byte-Pair Encoding (BPE), significantly impact the performance and efficiency of large language models (LLMs). The standard approach involves training a general-purpose tokenizer that uniformly…

Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed for natural language, which are unsuitable for DNA sequences…

As a cornerstone in language modeling, tokenization involves segmenting text inputs into pre-defined atomic units. Conventional statistical tokenizers often disrupt constituent boundaries within words, thereby corrupting semantic…

Traditional greedy tokenization methods have been a critical step in Natural Language Processing (NLP), influencing how text is converted into tokens and directly impacting model performance. While subword tokenizers like Byte-Pair Encoding…

Tokenization is the first -- and often least scrutinized -- step of most NLP pipelines. Standard algorithms for learning tokenizers rely on frequency-based objectives, which favor languages dominant in the training data and consequently…