Related papers: CHERRY: a Computational metHod for accuratE pRedic…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
Community search aims at finding densely connected subgraphs for query vertices in a graph. While this task has been studied widely in the literature, most of the existing works only focus on finding homogeneous communities rather than…
Microorganisms are found in almost every environment, including the soil, water, air, and inside other organisms, like animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as…
The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate…
This thesis develops computational methods in similarity-preserving hashing, classification, and cancer genomics. Standard space partitioning-based hashing relies on Binary Search Trees (BSTs), but their exponential growth and sparsity…
Graphs are a common model for complex relational data such as social networks and protein interactions, and such data can evolve over time (e.g., new friendships) and be noisy (e.g., unmeasured interactions). Link prediction aims to predict…
An active area of research interest is the inference of ecological models of complex microbial communities. Inferring such ecological models entails understanding the interactions between microbes and how they affect each other's growth.…
Locating lesions is important in the computer-aided diagnosis of X-ray images. However, box-level annotation is time-consuming and laborious. How to locate lesions accurately with few, or even without careful annotations is an urgent…
We describe a novel dataset for the automated recognition of named taxonomic and other entities relevant to the association of viruses with their hosts. We further describe some initial results using pre-trained models on the named-entity…
Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
Learning program semantics from raw source code is challenging due to the complexity of real-world programming language syntax and due to the difficulty of reconstructing long-distance relational information implicitly represented in…
Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial…
Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…
Rule-based systems must solve complex matching problems within tight time constraints to be effective in real-time applications, such as planning and reactive control for AI agents, as well as low-latency relational database querying.…
In this paper, we propose a hybrid bankcard response model, which integrates decision tree based chi-square automatic interaction detection (CHAID) into logistic regression. In the first stage of the hybrid model, CHAID analysis is used to…
Ecological networks offer powerful insights into community function, but without first characterizing these networks accurately, our ability to detect and interpret changes under environmental stress is limited. We develop an approach to…
Network ecology is a rising field of quantitative biology representing ecosystems as complex networks. A suitable example is parasite spreading: several parasites may be transmitted among their hosts through different mechanisms, each one…
Complex systems are often characterized by distinct types of interactions between the same entities. These can be described as a multilayer network where each layer represents one type of interaction. These layers may be interdependent in…
Uncovering the underlying causal mechanisms of complex real-world systems remains a significant challenge, as these systems often entail high data collection costs and involve unknown interventions. We introduce MetaCaDI, the first…