相关论文: Hybrid Tokenization Strategy for DNA Language Mode…

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…

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…

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…

Current language models (LMs) use a fixed, static subword tokenizer. This default choice typically results in degraded efficiency and language capabilities, especially in languages other than English. To address this issue, we challenge the…

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 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…

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…

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…

Existing Machine Translation (MT) research often suggests a single, fixed set of hyperparameters for word segmentation models, symmetric Byte Pair Encoding (BPE), which applies the same number of merge operations (NMO) to train tokenizers…

The Byte Pair Encoding algorithm can be safely batched to merge hundreds of pairs of tokens at a time when building up a tokenizer's vocabulary. This technique combined with reducing the memory footprint of text used in vocabulary training…

Subword tokenization schemes are the dominant technique used in current NLP models. However, such schemes can be rigid and tokenizers built on one corpus do not adapt well to other parallel corpora. It has also been observed that in…

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…

The success of pretrained transformer language models (LMs) in natural language processing has led to a wide range of pretraining setups. In particular, these models employ a variety of subword tokenization methods, most notably byte-pair…

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…

DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…

Data representation remains a fundamental challenge in machine learning, particularly when adapting sequence-based architectures like Transformers and Large Language Models (LLMs) for structured tabular data. Existing methods often fail to…

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 this work, we show a fundamental limitation in vocabulary adaptation approaches that use Byte-Pair Encoding (BPE) tokenization scheme for fine-tuning pretrained language models (PLMs) to expert domains. Current approaches trivially…

Byte pair encoding (BPE) emerges as an effective tokenization method for tackling the out-of-vocabulary (OOV) challenge in various natural language and speech processing tasks. Recent research highlights the dependency of BPE subword…