Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating 40+ protein-related datasets and 40+ popular PLMs. All implementations are open-sourced on https://github.com/ai4protein/VenusFactory. A video introduction is available at https://www.youtube.com/watch?v=MT6lPH5kgCc.

Building query graphs from natural language questions is an important step in complex question answering over knowledge graph (Complex KGQA). In general, a question can be correctly answered if its query graph is built correctly and the right answer is then retrieved by issuing the query graph against the KG. Therefore, this paper focuses on query graph generation from natural language questions. Existing approaches for query graph generation ignore the semantic structure of a question, resulting in a large number of noisy query graph candidates that undermine prediction accuracies. In this paper, we define six semantic structures from common questions in KGQA and develop a novel Structure-BERT to predict the semantic structure of a question. By doing so, we can first filter out noisy candidate query graphs by the predicted semantic structures, and then rank the remaining candidates with a BERT-based ranking model. Extensive experiments on two popular benchmarks MetaQA and WebQuestionsSP (WSP) demonstrate the effectiveness of our method as compared to state-of-the-arts.

Knowledge graphs typically contain a large number of entities but often cover only a fraction of all relations between them (i.e., incompleteness). Zero-shot link prediction (ZSLP) is a popular way to tackle the problem by automatically identifying unobserved relations between entities. Most recent approaches use textual features of relations (e.g., surface name or textual descriptions) as auxiliary information to improve the encoded representation. These methods lack robustness as they are bound to support only tokens from a fixed vocabulary and unable to model out-of-vocabulary (OOV) words. Subword units such as character n-grams have the capability of generating more expressive representations for OOV words. Hence, in this paper, we propose a Hierarchical N-gram framework for Zero-Shot Link Prediction (HNZSLP) that leverages character n-gram information for ZSLP. Our approach works by first constructing a hierarchical n-gram graph from the surface name of relations. Subsequently, a new Transformer-based network models the hierarchical n-gram graph to learn a relation embedding for ZSLP. Experimental results show that our proposed HNZSLP method achieves state-of-the-art performance on two standard ZSLP datasets.