Soumyadeep Roy

Soumyadeep Roy, Jonas Wallat, Sowmya S Sundaram et al. · stanford

Large-scale language models such as DNABert and LOGO aim to learn optimal gene representations and are trained on the entire Human Reference Genome. However, standard tokenization schemes involve a simple sliding window of tokens like k-mers that do not leverage any gene-based semantics and thus may lead to (trivial) masking of easily predictable sequences and subsequently inefficient Masked Language Modeling (MLM) training. Therefore, we propose a novel masking algorithm, GeneMask, for MLM training of gene sequences, where we randomly identify positions in a gene sequence as mask centers and locally select the span around the mask center with the highest Normalized Pointwise Mutual Information (NPMI) to mask. We observe that in the absence of human-understandable semantics in the genomics domain (in contrast, semantic units like words and phrases are inherently available in NLP), GeneMask-based models substantially outperform the SOTA models (DNABert and LOGO) over four benchmark gene sequence classification datasets in five few-shot settings (10 to 1000-shot). More significantly, the GeneMask-based DNABert model is trained for less than one-tenth of the number of epochs of the original SOTA model. We also observe a strong correlation between top-ranked PMI tokens and conserved DNA sequence motifs, which may indicate the incorporation of latent genomic information. The codes (including trained models) and datasets are made publicly available at https://github.com/roysoumya/GeneMask.

Soumyadeep Roy, Shamik Sural, Niloy Ganguly

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. However, the typical tokenization methods employ a basic sliding window of tokens, such as k-mers, that fail to utilize gene-centric semantics. This could result in the (trivial) masking of easily predictable sequences, leading to inefficient MLM training. Time-variant training strategies are known to improve pretraining efficiency in both language and vision tasks. In this work, we focus on using curriculum masking where we systematically increase the difficulty of masked token prediction task by using a Pointwise Mutual Information-based difficulty criterion, as gene sequences lack well-defined semantic units similar to words or sentences of NLP domain. Our proposed Curriculum Masking-based Gene Masking Strategy (CM-GEMS) demonstrates superior representation learning capabilities compared to baseline masking approaches when evaluated on downstream gene sequence classification tasks. We perform extensive evaluation in both few-shot (five datasets) and full dataset settings (Genomic Understanding Evaluation benchmark consisting of 27 tasks). Our findings reveal that CM-GEMS outperforms state-of-the-art models (DNABert-2, Nucleotide transformer, DNABert) trained at 120K steps, achieving similar results in just 10K and 1K steps. We also demonstrate that Curriculum-Learned LOGO (a 2-layer DNABert-like model) can achieve nearly 90% of the state-of-the-art model performance of 120K steps. We will make the models and codes publicly available at https://github.com/roysoumya/curriculum-GeneMask.

Gunjan Balde, Soumyadeep Roy, Mainack Mondal et al.

Large language models pretrained on general-domain corpora often exhibit tokenization inefficiencies when applied to specialized domains. Although continual pretraining for domain adaptation partially alleviate performance degradation, it does not resolve the fundamental vocabulary mismatch. To address this gap, we introduce a targeted parameter-efficient domain adaptation approach that combines vocabulary adaptation with pretraining for LLM-based text summarization. Our unified framework augments pretrained tokenizers with domain-specific tokens while selectively replacing under-trained and unreachable tokens to limit parameter growth. We evaluate our approach on Llama-3.1-8B and Qwen2.5-7B across legal and medical summarization tasks on a challenge-oriented evaluation protocol focused on expert-driven text and summaries which typically has higher concentration of over-fragmented Out-of-Vocabulary (OOV) words. The vocabulary adaptation algorithm enhances the overall quality of the summarization model by improving semantic similarity between the generated summaries and their references. In addition, the adapted model produces summaries that incorporate more appropriate novel and domain-specific words, leading to improved coherence, relevance, and faithfulness. We further observe that our proposed approach significantly reduce training time by $35-55\%$ over continual pretraining and reduce parameter counts up to $37\%$ w.r.t expansion-only methods. We make the codebase publicly available at https://github.com/gb-kgp/VocabReplace-Then-Expand.

Soumyadeep Roy, Aparup Khatua, Fatemeh Ghoochani et al.

GPT-4 demonstrates high accuracy in medical QA tasks, leading with an accuracy of 86.70%, followed by Med-PaLM 2 at 86.50%. However, around 14% of errors remain. Additionally, current works use GPT-4 to only predict the correct option without providing any explanation and thus do not provide any insight into the thinking process and reasoning used by GPT-4 or other LLMs. Therefore, we introduce a new domain-specific error taxonomy derived from collaboration with medical students. Our GPT-4 USMLE Error (G4UE) dataset comprises 4153 GPT-4 correct responses and 919 incorrect responses to the United States Medical Licensing Examination (USMLE) respectively. These responses are quite long (258 words on average), containing detailed explanations from GPT-4 justifying the selected option. We then launch a large-scale annotation study using the Potato annotation platform and recruit 44 medical experts through Prolific, a well-known crowdsourcing platform. We annotated 300 out of these 919 incorrect data points at a granular level for different classes and created a multi-label span to identify the reasons behind the error. In our annotated dataset, a substantial portion of GPT-4's incorrect responses is categorized as a "Reasonable response by GPT-4," by annotators. This sheds light on the challenge of discerning explanations that may lead to incorrect options, even among trained medical professionals. We also provide medical concepts and medical semantic predications extracted using the SemRep tool for every data point. We believe that it will aid in evaluating the ability of LLMs to answer complex medical questions. We make the resources available at https://github.com/roysoumya/usmle-gpt4-error-taxonomy .

Gunjan Balde, Soumyadeep Roy, Mainack Mondal et al.

Large Language Models (LLMs) recently achieved great success in medical text summarization by simply using in-context learning. However, these recent efforts do not perform fine-grained evaluations under difficult settings where LLMs might fail. They typically report performance scores over the entire dataset. Through our benchmarking study, we show that LLMs show a significant performance drop for data points with high concentration of out-of-vocabulary (OOV) words or with high novelty. Vocabulary adaptation is an intuitive solution to this vocabulary mismatch issue where the LLM vocabulary gets updated with certain expert domain (here, medical) words or subwords. An interesting finding from our study is that Llama-3.1, even with a vocabulary size of around 128K tokens, still faces over-fragmentation issue with medical words. To that end, we show vocabulary adaptation helps improve the LLM summarization performance even in difficult settings. Through extensive experimentation of multiple vocabulary adaptation strategies, two continual pretraining strategies, and three benchmark medical summarization datasets, we gain valuable insights into the role of vocabulary adaptation strategies for customizing LLMs to the medical domain. We also performed a human evaluation study with medical experts where they found that vocabulary adaptation results in more relevant and faithful summaries. Our codebase is made publicly available at https://github.com/gb-kgp/LLM-MedicalSummarization-Benchmark.

Soumyadeep Roy, Shamik Sural, Niyati Chhaya et al.

A consumer-dependent (business-to-consumer) organization tends to present itself as possessing a set of human qualities, which is termed as the brand personality of the company. The perception is impressed upon the consumer through the content, be it in the form of advertisement, blogs or magazines, produced by the organization. A consistent brand will generate trust and retain customers over time as they develop an affinity towards regularity and common patterns. However, maintaining a consistent messaging tone for a brand has become more challenging with the virtual explosion in the amount of content which needs to be authored and pushed to the Internet to maintain an edge in the era of digital marketing. To understand the depth of the problem, we collect around 300K web page content from around 650 companies. We develop trait-specific classification models by considering the linguistic features of the content. The classifier automatically identifies the web articles which are not consistent with the mission and vision of a company and further helps us to discover the conditions under which the consistency cannot be maintained. To address the brand inconsistency issue, we then develop a sentence ranking system that outputs the top three sentences that need to be changed for making a web article more consistent with the company's brand personality.