Pablo Millan Arias

Pablo Millan Arias, Niousha Sadjadi, Monireh Safari et al.

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 life. Although machine learning algorithms specifically designed for the analysis of DNA barcodes are becoming more popular, most existing methodologies rely on generic supervised training algorithms. We introduce BarcodeBERT, a family of models tailored to biodiversity analysis and trained exclusively on data from a reference library of 1.5M invertebrate DNA barcodes. We compared the performance of BarcodeBERT on taxonomic identification tasks against a spectrum of machine learning approaches including supervised training of classical neural architectures and fine-tuning of general DNA foundation models. Our self-supervised pretraining strategies on domain-specific data outperform fine-tuned foundation models, especially in identification tasks involving lower taxa such as genera and species. We also compared BarcodeBERT with BLAST, one of the most widely used bioinformatics tools for sequence searching, and found that our method matched BLAST's performance in species-level classification while being 55 times faster. Our analysis of masking and tokenization strategies also provides practical guidance for building customized DNA language models, emphasizing the importance of aligning model training strategies with dataset characteristics and domain knowledge. The code repository is available at https://github.com/bioscan-ml/BarcodeBERT.

Zahra Gharaee, Scott C. Lowe, ZeMing Gong et al.

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, geographical, and size information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at https://github.com/bioscan-ml/BIOSCAN-5M.

Kevin Lee, Pablo Millan Arias

Layer-wise Relevance Propagation (LRP) provides principled attribution for neural networks through conservation properties and foundations in Deep Taylor Decomposition. However, existing implementations operate at the module level, requiring architecture-specific propagation rules and modifications. These limit the generality of target model and sustainability of implementations as architectures evolve. We introduce DynamicLRP, a model-agnostic LRP framework operating at the tensor operation level. By decomposing attribution to individual operations within computation graphs and introducing a novel mechanism for deferred activation resolution, named the Promise System, our approach achieves true architecture agnosticity while maintaining LRP's theoretical guarantees. This design operates independently of backpropagation machinery, enabling operation on arbitrary computation graphs without model modification and side-by-side execution with gradient backpropagation. Being based on computation graphs, this method is theoretically extensible to other deep learning libraries that support auto-differentiation. We demonstrate faithfulness matching or exceeding specialized implementations (1.77 vs 1.69 ABPC on VGG, equivalent performance on ViT, 93.70\% and 95.06\% top-1 attribution accuracy for explaining RoBERTa-large and Flan-T5-large answers on SQuADv2, respectively) while maintaining practical efficiency on models with hundreds of millions of parameters. We achieved 99.92\% node coverage across 31,465 computation graph nodes from 15 diverse architectures, including state-space models (Mamba), audio transformers (Whisper), and multimodal systems (DePlot) without any model-specific code with rules for 47 fundamental operations implemented. Our operation-level decomposition and Promise System establish a sustainable, extensible foundation for LRP across evolving architectures.

Monireh Safari, Pablo Millan Arias, Scott C. Lowe et al.

Masked language modelling (MLM) as a pretraining objective has been widely adopted in genomic sequence modelling. While pretrained models can successfully serve as encoders for various downstream tasks, the distribution shift between pretraining and inference detrimentally impacts performance, as the pretraining task is to map [MASK] tokens to predictions, yet the [MASK] is absent during downstream applications. This means the encoder does not prioritize its encodings of non-[MASK] tokens, and expends parameters and compute on work only relevant to the MLM task, despite this being irrelevant at deployment time. In this work, we propose a modified encoder-decoder architecture based on the masked autoencoder framework, designed to address this inefficiency within a BERT-based transformer. We empirically show that the resulting mismatch is particularly detrimental in genomic pipelines where models are often used for feature extraction without fine-tuning. We evaluate our approach on the BIOSCAN-5M dataset, comprising over 2 million unique DNA barcodes. We achieve substantial performance gains in both closed-world and open-world classification tasks when compared against causal models and bidirectional architectures pretrained with MLM tasks.