Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tok-enization methods designed for natural language, which are unsuitable for DNA sequences due to their unique characteristics. In addition, the optimal approach to tokenize DNA remains largely under-explored, and may not be intuitively understood by humans even if discovered. To address these challenges, we introduce MxDNA, a novel framework where the model autonomously learns an effective DNA tokenization strategy through gradient decent.

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 due to their unique characteristics. In addition, the optimal approach to tokenize DNA remains largely under-explored, and may not be intuitively understood by humans even if discovered. To address these challenges, we introduce MxDNA, a novel framework where the model autonomously learns an effective DNA tokenization strategy through gradient decent. MxDNA employs a sparse Mixture of Convolution Experts coupled with a deformable convolution to model the tokenization process, with the discontinuous, overlapping, and ambiguous nature of meaningful genomic segments explicitly considered. On Nucleotide Transformer Benchmarks and Genomic Benchmarks, MxDNA demonstrates superior performance to existing methods with less pretraining data and time, highlighting its effectiveness. Finally, we show that MxDNA learns unique tokenization strategy distinct to those of previous methods and captures genomic functionalities at a token level during self-supervised pretraining. Our MxDNA aims to provide a new perspective on DNA tokenization, potentially offering broad applications in various domains and yielding profound insights.

Abstract--T okenization is fundamental in assembly code analysis, impacting intrinsic characteristics like vocabulary size, semantic coverage, and extrinsic performance in downstream tasks. Despite its significance, tokenization in the context of assembly code remains an underexplored area. This study aims to address this gap by evaluating the intrinsic properties of Natural Language Processing (NLP) tokenization models and parameter choices, such as vocabulary size. We explore prepro-cessing customization options and pre-tokenization rules tailored to the unique characteristics of assembly code. Additionally, we assess their impact on downstream tasks like function signature prediction--a critical problem in binary code analysis. T o this end, we conduct a thorough study on various tokeniza-tion models, systematically analyzing their efficiency in encoding assembly instructions and capturing semantic nuances. Through intrinsic evaluations, we compare tokenizers based on tokeniza-tion efficiency, vocabulary compression, and representational fidelity for assembly code. Using state-of-the-art pre-trained models such as the decoder-only Large Language Model (LLM) Llama 3.2, the encoder-only transformer BERT, and the encoder-decoder model BART, we evaluate the effectiveness of these tokenizers across multiple performance metrics. Preliminary findings indicate that tokenizer choice significantly influences downstream performance, with intrinsic metrics providing partial but incomplete predictability of extrinsic evaluation outcomes. These results reveal complex trade-offs between intrinsic tokenizer properties and their utility in practical assembly code tasks. Ultimately, this study provides valuable insights into optimizing tokenization models for low-level code analysis, contributing to the robustness and scalability of Natural Language Model (NLM)-based binary analysis workflows. Tokenization is critical in transforming raw input data into structured representations, a process of utmost importance for Machine Learning (ML) and NLM model tasks [1]-[3]. While tokenization strategies have been studied extensively for natural [4] and high-level programming languages [5], assembly code presents unique challenges due to its low-level operations, diverse instruction sets, and non-standardized syntax across architectures. These challenges highlight the need for specialized tokenization techniques that effectively capture assembly code's structural and semantic intricacies [2]. Despite its importance, the role of tokenization in assembly code processing remains underexplored, particularly in its impact on downstream tasks involving modern NLMs. Recent research underscores the significant influence of tokenization on NLM model performance.

Tokenization plays a critical role in processing agglutinative languages, where a single word can encode multiple morphemes carrying syntactic and semantic information. This study evaluates the impact of various tokenization strategies - word-level, character-level, n-gram, and Byte Pair Encoding (BPE) - on the quality of static word embeddings generated by Word2Vec for Turkish and Finnish. Using a 10,000-article Wikipedia corpus, we trained models under low-resource conditions and evaluated them on a Named Entity Recognition (NER) task. Despite the theoretical appeal of subword segmentation, word-level tokenization consistently outperformed all alternatives across all tokenization strategies tested. These findings suggest that in agglutinative, low-resource contexts, preserving boundaries via word-level tokenization may yield better embedding performance than complex statistical methods. This has practical implications for developing NLP pipelines for under-resourced languages where annotated data and computing power are limited.

Tokenization plays a pivotal role in natural language processing (NLP), shaping how text is segmented and interpreted by language models. While subword methods such as Byte Pair Encoding (BPE) and WordPiece have been effective, they often struggle with morphologically rich and agglutinative languages because they rely on frequency rather than linguistic structure. We introduce a hybrid tokenization framework that combines rule-based morphological analysis with statistical subword segmentation. The method uses phonological normalization, root-affix dictionaries, and a novel algorithm that balances morpheme preservation with vocabulary efficiency. It assigns shared identifiers to phonologically variant affixes (e.g., -ler and -lar) and altered root forms (e.g., kitap vs. kitabı), reducing redundancy while maintaining semantic integrity. Special tokens are added for whitespace and case, including an UPPERCASE marker to avoid vocabulary inflation from capitalization. BPE is integrated for out-of-vocabulary coverage without harming morphological coherence. On the TR-MMLU benchmark, the tokenizer achieves the highest Turkish Token Percentage (90.29\%) and Pure Token Percentage (85.8\%). Comparisons with tokenizers from LLaMA, Gemma, and GPT show more linguistically meaningful and coherent tokens. Although demonstrated on Turkish, the approach is language-independent and adaptable to other languages, offering a practical path toward more interpretable and effective multilingual NLP systems.

We established a rigorous benchmark for text-based recipe generation, a fundamental task in natural language generation. We present a comprehensive comparative study contrasting a fine-tuned GPT -2 large (774M) model against the GPT -2 small (124M) model and traditional LSTM/RNN baselines on the 5-cuisine corpus from RecipeDB. Our key contribution is a targeted tokenization strategy that augments the vocabulary with 23 common fraction tokens and custom structural markers. This approach addresses a critical limitation of generic tokenizers by preserving essential recipe structures and precise numerical quantities, thereby enhancing domain specificity. Performance is evaluated using a comprehensive suite of seven automatic metrics spanning fluency (BLEU-4, METEOR), coherence (ROUGE-L), semantic relevance (BERTScore), and diversity. Our experiments show that the large transformer-based approach yields a > 20% relative improvement in BERTScore (F1) (0.92 vs 0.72) over the best recurrent baseline, while reducing perplexity by 69.8%. We conclude with a discussion of remaining challenges, particularly regarding factual accuracy, and outline how this foundational study paves the way for integrating real-world constraints and multi-modal inputs in advanced recipe generation research.

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 which is superior. We compare k-mer segmentation with k=1,3,4,5,6, a 4,096-token BPE vocabulary, and three positional encoding methods--sinusoidal, AliBi, and RoPE. Each configuration is trained from scratch in 3, 6, 12, and 24-layer Transformer encoders and evaluated on GUE benchmark dataset. In general, BPE delivers higher and more stable performance across tasks by compressing frequent motifs into variable-length tokens, reducing sequence length, and improving model generalization. RoPE excels at capturing periodic motifs and extrapolating to long sequences, while AliBi also performs well on tasks driven by local dependencies. In terms of depth, we observe significant gains when increasing layers from 3 to 12, with only marginal improvements or slight overfitting at 24 layers. This study provides practical guidance for designing tokenization and positional encoding in DNA Transformer models.

Natural Language Processing (NLP) models are used for text-related tasks such as classification and generation. To complete these tasks, input data is first tokenized from human-readable text into a format the model can understand, enabling it to make inferences and understand context. Text classification models can be implemented to guard against threats such as prompt injection attacks against Large Language Models (LLMs), toxic input and cybersecurity risks such as spam emails. In this paper, we introduce TokenBreak: a novel attack that can bypass these protection models by taking advantage of the tokenization strategy they use. This attack technique manipulates input text in such a way that certain models give an incorrect classification. Importantly, the end target (LLM or email recipient) can still understand and respond to the manipulated text and therefore be vulnerable to the very attack the protection model was put in place to prevent. The tokenizer is tied to model architecture, meaning it is possible to predict whether or not a model is vulnerable to attack based on family. We also present a defensive strategy as an added layer of protection that can be implemented without having to retrain the defensive model.

Tokenization is a critical component of Natural Language Processing (NLP), especially for low resource languages, where subword segmentation influences vocabulary structure and downstream task accuracy. Although Byte Pair Encoding (BPE) is a standard tokenization method in multilingual language models, its suitability for Named Entity Recognition (NER) in low resource Indic languages remains underexplored due to its limitations in handling morphological complexity. In this work, we systematically compare BPE, SentencePiece, and Character Level tokenization strategies using IndicBERT for NER tasks in low resource Indic languages like Assamese, Bengali, Marathi, and Odia, as well as extremely low resource Indic languages like Santali, Manipuri, and Sindhi. We assess both intrinsic linguistic properties tokenization efficiency, out of vocabulary (OOV) rates, and morphological preservation as well as extrinsic downstream performance, including fine tuning and zero shot cross lingual transfer. Our experiments show that SentencePiece is a consistently better performing approach than BPE for NER in low resource Indic Languages, particularly in zero shot cross lingual settings, as it better preserves entity consistency. While BPE provides the most compact tokenization form, it is not capable of generalization because it misclassifies or even fails to recognize entity labels when tested on unseen languages. In contrast, SentencePiece constitutes a better linguistic structural preservation model, benefiting extremely low resource and morphologically rich Indic languages, such as Santali and Manipuri, for superior entity recognition, as well as high generalization across scripts, such as Sindhi, written in Arabic. The results point to SentencePiece as the more effective tokenization strategy for NER within multilingual and low resource Indic NLP applications.