We propose SemCSE-Multi, a novel unsupervised framework for generating multifaceted embeddings of scientific abstracts, evaluated in the domains of invasion biology and medicine. These embeddings capture distinct, individually specifiable aspects in isolation, thus enabling fine-grained and controllable similarity assessments as well as adaptive, user-driven visualizations of scientific domains. Our approach relies on an unsupervised procedure that produces aspect-specific summarizing sentences and trains embedding models to map semantically related summaries to nearby positions in the embedding space. We then distill these aspect-specific embedding capabilities into a unified embedding model that directly predicts multiple aspect embeddings from a scientific abstract in a single, efficient forward pass. In addition, we introduce an embedding decoding pipeline that decodes embeddings back into natural language descriptions of their associated aspects. Notably, we show that this decoding remains effective even for unoccupied regions in low-dimensional visualizations, thus offering vastly improved interpretability in user-centric settings.

This study explores strategies for efficiently classifying scientific full texts using both small, BERT-based models and local large language models like Llama-3.1 8B. We focus on developing methods for selecting subsets of input sentences to reduce input size while simultaneously enhancing classification performance. To this end, we compile a novel dataset consisting of full-text scientific papers from the field of invasion biology, specifically addressing the impacts of invasive species. These papers are aligned with publicly available impact assessments created by researchers for the International Union for Conservation of Nature (IUCN). Through extensive experimentation, we demonstrate that various sources like human evidence annotations, LLM-generated annotations or explainability scores can be used to train sentence selection models that improve the performance of both encoder- and decoder-based language models while optimizing efficiency through the reduction in input length, leading to improved results even if compared to models like ModernBERT that are able to handle the complete text as input. Additionally, we find that repeated sampling of shorter inputs proves to be a very effective strategy that, at a slightly increased cost, can further improve classification performance.

We investigate the use of LLM-generated data for continual pretraining of transformer encoder models in specialized domains with limited training data, using the scientific domain of invasion biology as a case study. To this end, we leverage domain-specific ontologies by enriching them with LLM-generated data and pretraining the encoder model as an ontology-informed embedding model for concept definitions. To evaluate the effectiveness of this method, we compile a benchmark specifically designed for assessing model performance in invasion biology. After demonstrating substantial improvements over standard MLM pretraining, we investigate the feasibility of applying the proposed approach to domains without comprehensive ontologies by substituting ontological concepts with concepts automatically extracted from a small corpus of scientific abstracts and establishing relationships between concepts through distributional statistics. Our results demonstrate that this automated approach achieves comparable performance using only a small set of scientific abstracts, resulting in a fully automated pipeline for enhancing domain-specific understanding of small encoder models that is especially suited for application in low-resource settings and achieves performance comparable to masked language modeling pretraining on much larger datasets.

We introduce SemCSE, an unsupervised method for learning semantic embeddings of scientific texts. Building on recent advances in contrastive learning for text embeddings, our approach leverages LLM-generated summaries of scientific abstracts to train a model that positions semantically related summaries closer together in the embedding space. This resulting objective ensures that the model captures the true semantic content of a text, in contrast to traditional citation-based approaches that do not necessarily reflect semantic similarity. To validate this, we propose a novel benchmark designed to assess a model’s ability to understand and encode the semantic content of scientific texts, demonstrating that our method enforces a stronger semantic separation within the embedding space. Additionally, we evaluate SemCSE on the comprehensive SciRepEval benchmark for scientific text embeddings, where it achieves state-of-the-art performance among models of its size, thus highlighting the benefits of a semantically focused training approach.

We propose an end-to-end differentiable training paradigm for stable training of a rationalized transformer classifier. Our approach results in a single model that simultaneously classifies a sample and scores input tokens based on their relevance to the classification. To this end, we build on the widely-used three-player-game for training rationalized models, which typically relies on training a rationale selector, a classifier and a complement classifier. We simplify this approach by making a single model fulfill all three roles, leading to a more efficient training paradigm that is not susceptible to the common training instabilities that plague existing approaches. Further, we extend this paradigm to produce class-wise rationales while incorporating recent advances in parameterizing and regularizing the resulting rationales, thus leading to substantially improved and state-of-the-art alignment with human annotations without any explicit supervision.

Concurrent with the rapid progress in neural network-based models in NLP, the need for creating explanations for the predictions of these black-box models has risen steadily. Yet, especially for complex inputs like texts or images, existing interpretability methods still struggle with deriving easily interpretable explanations that also accurately represent the basis for the model’s decision. To this end, we propose a new, model-agnostic method to generate extractive explanations for predictions made by neural networks, that is based on masking parts of the input which the model does not consider to be indicative of the respective class. The masking is done using gradient-based optimization combined with a new regularization scheme that enforces sufficiency, comprehensiveness, and compactness of the generated explanation. Our method achieves state-of-the-art results in a challenging paragraph-level rationale extraction task, showing that this task can be performed without training a specialized model. We further apply our method to image inputs and obtain high-quality explanations for image classifications, which indicates that the objectives for optimizing explanation masks in text generalize to inputs of other modalities.

We investigate the problem of identifying the major hypothesis that is addressed in a scientific paper. To this end, we present a dataset from the domain of invasion biology that organizes a set of 954 papers into a network of fine-grained domain-specific categories of hypotheses. We carry out experiments on classifying abstracts according to these categories and present a pilot study on annotating hypothesis statements within the text. We find that hypothesis statements in our dataset are complex, varied and more or less explicit, and, importantly, spread over the whole abstract. Experiments with BERT-based classifiers show that these models are able to classify complex hypothesis statements to some extent, without being trained on sentence-level text span annotations.