Abstract Specialized transformers-based models (such as BioBERT and BioMegatron) are adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We investigate the encoding and representation of biological knowledge in these models, and its potential utility to support inference in cancer precision medicine—namely, the interpretation of the clinical significance of genomic alterations. We compare the performance of different transformer baselines; we use probing to determine the consistency of encodings for distinct entities; and we use clustering methods to compare and contrast the internal properties of the embeddings for genes, variants, drugs, and diseases. We show that these models do indeed encode biological knowledge, although some of this is lost in fine-tuning for specific tasks. Finally, we analyze how the models behave with regard to biases and imbalances in the dataset.

Regenerating natural language explanations in the scientific domain has been proposed as a benchmark to evaluate complex multi-hop and explainable inference. In this context, large language models can achieve state-of-the-art performance when employed as cross-encoder architectures and fine-tuned on human-annotated explanations. However, while much attention has been devoted to the quality of the explanations, the problem of performing inference efficiently is largely under studied. Cross-encoders, in fact, are intrinsically not scalable, possessing limited applicability to real-world scenarios that require inference on massive facts banks. To enable complex multi-hop reasoning at scale, this paper focuses on bi-encoder architectures, investigating the problem of scientific explanation regeneration at the intersection of dense and sparse models. Specifically, we present SCAR (for Scalable Autoregressive Inference), a hybrid framework that iteratively combines a Transformer-based bi-encoder with a sparse model of explanatory power, designed to leverage explicit inference patterns in the explanations. Our experiments demonstrate that the hybrid framework significantly outperforms previous sparse models, achieving performance comparable with that of state-of-the-art cross-encoders while being approx 50 times faster and scalable to corpora of millions of facts. Further analyses on semantic drift and multi-hop question answering reveal that the proposed hybridisation boosts the quality of the most challenging explanations, contributing to improved performance on downstream inference tasks.

Abstract This paper presents Diff-Explainer, the first hybrid framework for explainable multi-hop inference that integrates explicit constraints with neural architectures through differentiable convex optimization. Specifically, Diff- Explainer allows for the fine-tuning of neural representations within a constrained optimization framework to answer and explain multi-hop questions in natural language. To demonstrate the efficacy of the hybrid framework, we combine existing ILP-based solvers for multi-hop Question Answering (QA) with Transformer-based representations. An extensive empirical evaluation on scientific and commonsense QA tasks demonstrates that the integration of explicit constraints in a end-to-end differentiable framework can significantly improve the performance of non- differentiable ILP solvers (8.91%–13.3%). Moreover, additional analysis reveals that Diff-Explainer is able to achieve strong performance when compared to standalone Transformers and previous multi-hop approaches while still providing structured explanations in support of its predictions.

Mathematical statements written in natural language are usually composed of two different modalities: mathematical elements and natural language.These two modalities have several distinct linguistic and semantic properties.State-of-the-art representation techniques have demonstrated an inability in capturing such an entangled style of discourse.In this work, we propose STAR, a model that uses crossmodal attention to learn how to represent mathematical text for the task of Natural Language Premise Selection.This task uses conjectures written in both natural and mathematical language to recommend premises that most likely will be relevant to prove a particular statement.We found that STAR not only outperforms baselines that do not distinguish between natural language and mathematical elements, but it also achieves better performance than state-ofthe-art models.

The discovery of supporting evidence for addressing complex mathematical problems is a semantically challenging task, which is still unexplored in the field of natural language processing for mathematical text.The natural language premise selection task consists in using conjectures written in both natural language and mathematical formulae to recommend premises that most likely will be useful to prove a particular statement.We propose an approach to solve this task as a link prediction problem, using Deep Convolutional Graph Neural Networks.This paper also analyses how different baselines perform in this task and shows that a graph structure can provide higher F1-score, especially when considering multi-hop premise selection.

Mathematical text is written using a combination of words and mathematical expressions. This combination, along with a specific way of structuring sentences makes it challenging for state-of-art NLP tools to understand and reason on top of mathematical discourse. In this work, we propose a new NLP task, the natural premise selection, which is used to retrieve supporting definitions and supporting propositions that are useful for generating an informal mathematical proof for a particular statement. We also make available a dataset, NL-PS, which can be used to evaluate different approaches for the natural premise selection task. Using different baselines, we demonstrate the underlying interpretation challenges associated with the task.