AmalREC: A Dataset for Relation Extraction and Classification Leveraging Amalgamation of Large Language Models

Existing datasets for relation classification and extraction often exhibit limitations such as restricted relation types and domain-specific biases. This work presents a generic framework to generate well-structured sentences from given tuples with the help of Large Language Models (LLMs). This study has focused on the following major questions: (i) how to generate sentences from relation tuples, (ii) how to compare and rank them, (iii) can we combine strengths of individual methods and amalgamate them to generate an even bette quality of sentences, and (iv) how to evaluate the final dataset? For the first question, we employ a multifaceted 5-stage pipeline approach, leveraging LLMs in conjunction with template-guided generation. We introduce Sentence Evaluation Index(SEI) that prioritizes factors like grammatical correctness, fluency, human-aligned sentiment, accuracy, and complexity to answer the first part of the second question. To answer the second part of the second question, this work introduces a SEI-Ranker module that leverages SEI to select top candidate generations. The top sentences are then strategically amalgamated to produce the final, high-quality sentence. Finally, we evaluate our dataset on LLM-based and SOTA baselines for relation classification. The proposed dataset features 255 relation types, with 15K sentences in the test set and around 150k in the train set organized in, significantly enhancing relational diversity and complexity. This work not only presents a new comprehensive benchmark dataset for RE/RC task, but also compare different LLMs for generation of quality sentences from relational tuples.

A Benchmark Dataset for Multimodal Prediction of Enzymatic Function Coupling DNA Sequences and Natural Language

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.