Related papers: DNABERT-2: Efficient Foundation Model and Benchmar…

DNA language models have advanced genomics, but their downstream performance varies widely due to differences in tokenization, pretraining data, and architecture. We argue that a major bottleneck lies in tokenizing sparse and unevenly…

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…

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…

The task of understanding and interpreting the complex information encoded within genomic sequences remains a grand challenge in biological research and clinical applications. In this context, recent advancements in large language model…

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…

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…

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…

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…

This paper presents the Ensemble Nucleotide Byte-level Encoder-Decoder (ENBED) foundation model, analyzing DNA sequences at byte-level precision with an encoder-decoder Transformer architecture. ENBED uses a sub-quadratic implementation of…

In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained comparisons among organisms within the same kingdom of…

Gene transformer models such as Nucleotide Transformer, DNABert, and LOGO are trained to learn optimal gene sequence representations by using the Masked Language Modeling (MLM) training objective over the complete Human Reference Genome.…

The success of large pretrained Transformers is closely tied to tokenizers, which convert raw input into discrete symbols. Extending these models to graph-structured data remains a significant challenge. In this work, we introduce a graph…

Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory…

Automated malware analysis increasingly relies on machine learning, yet most existing methods remain task-specific and depend on handcrafted features or narrowly scoped models. Recent developments in binary-level foundation models suggest a…

Sequence models for binary analysis are bottlenecked by byte-level tokenization: raw bytes waste precious context window capacity for transformers and other neural network architectures, and many existing text-oriented tokenizers fail on…

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that…

Pre-trained language models such as BERT have been successful at tackling many natural language processing tasks. However, the unsupervised sub-word tokenization methods commonly used in these models (e.g., byte-pair encoding - BPE) are…

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…

Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits…

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…