17 accepted papers
Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a global alignment approach to learn the knowledge from differ…
Immunoglobulins are crucial proteins produced by the immune system to identify and bind to foreign substances, playing an essential role in shielding organisms from infections and diseases. Designing specific antibodies opens new pathways for disease treatment. With the rise of deep learning, AI-dri…
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 functionalities or properties due to inherent challenges in contr…
One individual human’s immune repertoire consists of a huge set of adaptive immune receptors at a certain time point, representing the individual's adaptive immune state. Immune repertoire classification and associated receptor identification have the potential to make a transformative contribution…
Protein optimization is a fundamental biological task aimed at enhancing theperformance of proteins by modifying their sequences. Computational methodsprimarily rely on evolutionary information (EI) encoded by protein languagemodels (PLMs) to predict fitness landscape for optimization. However, thes…
Directed evolution, a cornerstone of protein optimization, is to harness natural mutational processes to enhance protein functionality. Existing Machine Learning-assisted Directed Evolution (MLDE) methodologies typically rely on data-driven strategies and often overlook the profound domain knowledge…
The decoder-only Transformer architecture with causal masking and relative position encoding (RPE) has become the de facto choice in language modeling. Despite its exceptional performance across various tasks, we have identified two limitations: First, it prevents all attended tokens from having zer…
Immune repertoire classification, a typical multiple instance learning (MIL) problem, is a frontier research topic in computational biology that makes transformative contributions to new vaccines and immune therapies. However, the traditional instance-space MIL, directly assigning bag-level labels t…
"Detecting and segmenting objects within whole slide images is essential in computational pathology workflow. Self-supervised learning (SSL) is appealing to such annotation-heavy tasks. Despite the extensive benchmarks in natural images for dense tasks, such studies are, unfortunately, absent in cur…
Integration of heterogeneous and high-dimensional data (e.g., multiomics) is becoming increasingly important. Existing multimodal classification algorithms mainly focus on improving performance by exploiting the complementarity from different modalities. However, conventional approaches are basicall…
Few-shot learning is an established topic in natural images for years, but few work is attended to histology images, which is of high clinical value since well-labeled datasets and rare abnormal samples are expensive to collect. Here, we facilitate the study of few-shot learning in histology images…
Morphology of neuron trees is a key indicator to delineate neuronal cell-types, analyze brain development process, and evaluate pathological changes in neurological diseases. Traditional analysis mostly relies on heuristic features and visual inspections. A quantitative, informative, and comprehensi…
Subpopulation shift widely exists in many real-world machine learning applications, referring to the training and test distributions containing the same subpopulation groups but varying in subpopulation frequencies. Importance reweighting is a normal way to handle the subpopulation shift issue by im…
Metastatic involvement of lymph nodes is one of the most important prognostic variables for many cancers. Several deep learning based algorithms have been developed to segment metastatic regions in pathological images to help predict prognosis. However, the training of these methods requires a large…
Multiple instance learning (MIL) is a typical weakly-supervised learning method where the label is associated with a bag of instances instead of a single instance. Despite extensive research over past years, effectively deploying MIL remains an open and challenging problem, especially when the commo…
Despite the recent advances in automatically describing image contents, their applications have been mostly limited to image caption datasets containing natural images (e.g., Flickr 30k, MSCOCO). In this paper, we present a deep learning model to efficiently detect a disease from an image and annota…
Despite tremendous progress in computer vision, effective learning on very large-scale (>100K patients) medical image databases has been vastly hindered. We present an interleaved text/image deep learning system to extract and mine the semantic interactions of radiology images and reports from a nat…