BioMamba: A Pre-trained Biomedical Language Representation Model Leveraging Mamba

The advancement of natural language processing (NLP) in biology hinges on models' ability to interpret intricate biomedical literature. Traditional models often struggle with the complex and domain-specific language in this field. In this paper, we present BioMamba, a pre-trained model specifically designed for biomedical text mining. BioMamba builds upon the Mamba architecture and is pre-trained on an extensive corpus of biomedical literature. Our empirical studies demonstrate that BioMamba significantly outperforms models like BioBERT and general-domain Mamba across various biomedical tasks. For instance, BioMamba achieves a 100 times reduction in perplexity and a 4 times reduction in cross-entropy loss on the BioASQ test set. We provide an overview of the model architecture, pre-training process, and fine-tuning techniques. Additionally, we release the code and trained model to facilitate further research.

TrialEnroll: Predicting Clinical Trial Enrollment Success with Deep & Cross Network and Large Language Models

Clinical trials need to recruit a sufficient number of volunteer patients to demonstrate the statistical power of the treatment (e.g., a new drug) in curing a certain disease. Clinical trial recruitment has a significant impact on trial success. Forecasting whether the recruitment process would be successful before we run the trial would save many resources and time. This paper develops a novel deep & cross network with large language model (LLM)-augmented text feature that learns semantic information from trial eligibility criteria and predicts enrollment success. The proposed method enables interpretability by understanding which sentence/word in eligibility criteria contributes heavily to prediction. We also demonstrate the empirical superiority of the proposed method (0.7002 PR-AUC) over a bunch of well-established machine learning methods. The code and curated dataset are publicly available at https://anonymous.4open.science/r/TrialEnroll-7E12.

On the Robustness of Language Models for Tabular Question Answering

Large Language Models (LLMs), originally shown to ace various text comprehension tasks have also remarkably been shown to tackle table comprehension tasks without specific training. While previous research has explored LLM capabilities with tabular dataset tasks, our study assesses the influence of $\textit{in-context learning}$,$ \textit{model scale}$, $\textit{instruction tuning}$, and $\textit{domain biases}$ on Tabular Question Answering (TQA). We evaluate the robustness of LLMs on Wikipedia-based $\textbf{WTQ}$ and financial report-based $\textbf{TAT-QA}$ TQA datasets, focusing on their ability to robustly interpret tabular data under various augmentations and perturbations. Our findings indicate that instructions significantly enhance performance, with recent models like Llama3 exhibiting greater robustness over earlier versions. However, data contamination and practical reliability issues persist, especially with WTQ. We highlight the need for improved methodologies, including structure-aware self-attention mechanisms and better handling of domain-specific tabular data, to develop more reliable LLMs for table comprehension.