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Bacteriophages, often referred to as the dark matter of the biosphere, play a critical role in regulating microbial ecosystems and in antibiotic alternatives. Thus, accurate interpretation of their genomes holds significant scientific and…

Vision-language models (VLMs) have exhibited remarkable generalization capabilities, and prompt learning for VLMs has attracted great attention for the ability to adapt pre-trained VLMs to specific downstream tasks. However, existing…

Recent years have witnessed a growing interest in automating labor-intensive and complex activities, i.e., those consisting of multiple atomic tasks, by deploying robots in dynamic and unpredictable environments such as industrial and…

Behavioral testing in NLP allows fine-grained evaluation of systems by examining their linguistic capabilities through the analysis of input-output behavior. Unfortunately, existing work on behavioral testing in Machine Translation (MT) is…

We investigate how to teach large language models (LLMs) to perform scientific reasoning by leveraging expert discussions as a learning signal. Focusing on the genomics domain, we develop an automated pipeline to extract trainable data and…

Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify…

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM…

Concept Bottleneck Models (CBMs) provide a basis for semantic abstractions within a neural network architecture. Such models have primarily been seen through the lens of interpretability so far, wherein they offer transparency by inferring…

Energy-based models (EBMs) are a simple yet powerful framework for generative modeling. They are based on a trainable energy function which defines an associated Gibbs measure, and they can be trained and sampled from via well-established…

Despite the large quantity of information available, thorough researches in various biological databases are still needed in order to reconstruct and understand the steps that lead to known or new phenomena. By using protein-protein…

The development of large language models and multi-modal models has enabled the appealing idea of generating novel molecules from text descriptions. Generative modeling would shift the paradigm from relying on large-scale chemical screening…

Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…

Machine learning and deep learning have gained popularity and achieved immense success in Drug discovery in recent decades. Historically, machine learning and deep learning models were trained on either structural data or chemical…

Protein Language Models (PLMs), pre-trained on extensive evolutionary data from natural proteins, have emerged as indispensable tools for protein design. While powerful, PLMs often struggle to produce proteins with precisely specified…

Extensive research has investigated the integration of large language models (LLMs) with knowledge graphs to enhance the reasoning process. However, understanding how models perform reasoning utilizing structured graph knowledge remains…

Recent advances in biochemical computing, i.e., information processing with cascades of primarily enzymatic reactions realizing computing gates, such as AND, OR, etc., as well as progress in networking these gates and coupling of the…

Large language models (LLMs) have shown remarkable performance on many tasks in different domains. However, their performance in closed-book biomedical machine reading comprehension (MRC) has not been evaluated in depth. In this work, we…

Cell movement in the early phase of C. elegans development is regulated by a highly complex process in which a set of rules and connections are formulated at distinct scales. Previous efforts have shown that agent-based, multi-scale…

Generalizable protein function prediction is increasingly constrained by the growing mismatch between exponentially expanding sequences of environmental proteins and the comparatively slow accumulation of experimentally verified functional…

Deep learning classifiers provide the most accurate means of automatically diagnosing diabetic retinopathy (DR) based on optical coherence tomography (OCT) and its angiography (OCTA). The power of these models is attributable in part to the…