Related papers: Deep Contextual Learners for Protein Networks

Identifying cultural capital (CC) themes in student reflections can offer valuable insights that help foster equitable learning environments in classrooms. However, themes such as aspirational goals or family support are often woven into…

We propose a principle for exploring context in machine learning models. Starting with a simple assumption that each observation may or may not depend on its context, a conditional probability distribution is decomposed into two parts:…

Although self-supervised learning enables us to bootstrap the training by exploiting unlabeled data, the generic self-supervised methods for natural images do not sufficiently incorporate the context. For medical images, a desirable method…

Explainability poses a major challenge to artificial intelligence (AI) techniques. Current studies on explainable AI (XAI) lack the efficiency of extracting global knowledge about the learning task, thus suffer deficiencies such as…

Attributed network embedding (ANE) is to learn low-dimensional vectors so that not only the network structure but also node attributes can be preserved in the embedding space. Existing ANE models do not consider the specific combination…

Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current…

Context plays a crucial role in visual recognition as it provides complementary clues for different learning tasks including image classification and annotation. As the performances of these tasks are currently reaching a plateau, any extra…

Gene expression (GE) data capture valuable condition-specific information ("condition" can mean a biological process, disease stage, age, patient, etc.) However, GE analyses ignore physical interactions between gene products, i.e.,…

With the wide application of electronic health records (EHR) in healthcare facilities, health event prediction with deep learning has gained more and more attention. A common feature of EHR data used for deep-learning-based predictions is…

Deep learning models have been efficient lately on image parsing tasks. However, deep learning models are not fully capable of exploiting visual and contextual information simultaneously. The proposed three-layer context-based deep…

Automatic art analysis aims to classify and retrieve artistic representations from a collection of images by using computer vision and machine learning techniques. In this work, we propose to enhance visual representations from neural…

Social network analysis provides meaningful information about behavior of network members that can be used for diverse applications such as classification, link prediction. However, network analysis is computationally expensive because of…

Understanding the intertwined contributions of amino acid sequence and spatial structure is essential to explain protein behaviour. Here, we introduce INFUSSE (Integrated Network Framework Unifying Structure and Sequence Embeddings), a deep…

Cellular nuclei recognition serves as a fundamental and essential step in the workflow of digital pathology. However, with disparate source organs and staining procedures among histology image clusters, the scanned tiles inherently conform…

The characterization of drug-protein interactions is crucial in the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without…

Graph neural networks (GNNs) have been shown to possess strong representation power, which can be exploited for downstream prediction tasks on graph-structured data, such as molecules and social networks. They typically learn…

The interpretability of deep learning is crucial for evaluating the reliability of medical imaging models and reducing the risks of inaccurate patient recommendations. This study addresses the "human out of the loop" and "trustworthiness"…

In the present article, we propose a paradigm shift on evolving Artificial Neural Networks (ANNs) towards a new bio-inspired design that is grounded on the structural properties, interactions, and dynamics of protein networks (PNs): the…

Motivation: Despite advances in the computational analysis of high-throughput molecular profiling assays (e.g. transcriptomics), a dichotomy exists between methods that are simple and interpretable, and ones that are complex but with lower…