Related papers: Piggy-backing protein domains with Formal Concept …
Malware applications typically use a command and control (C&C) server to manage bots to perform malicious activities. Domain Generation Algorithms (DGAs) are popular methods for generating pseudo-random domain names that can be used to…
The identification of compound-protein interactions (CPI) plays a critical role in drug screening, drug repurposing, and combination therapy studies. The effectiveness of CPI prediction relies heavily on the features extracted from both…
Modern malware typically makes use of a domain generation algorithm (DGA) to avoid command and control domains or IPs being seized or sinkholed. This means that an infected system may attempt to access many domains in an attempt to contact…
Machine learning algorithms minimizing the average training loss usually suffer from poor generalization performance due to the greedy exploitation of correlations among the training data, which are not stable under distributional shifts.…
Formal Concept Analysis has proven to be an effective method of restructuring complete lattices and various algebraic domains. In this paper, the notions of attribute continuous formal context and continuous formal concept are introduced by…
Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and…
Malicious domains are increasingly common and pose a severe cybersecurity threat. Specifically, many types of current cyber attacks use URLs for attack communications (e.g., C\&C, phishing, and spear-phishing). Despite the continuous…
A pseudo independent (PI) model is a probabilistic domain model (PDM) where proper subsets of a set of collectively dependent variables display marginal independence. PI models cannot be learned correctly by many algorithms that rely on a…
Domain adaptation is a popular paradigm in modern machine learning which aims at tackling the problem of divergence (or shift) between the labeled training and validation datasets (source domain) and a potentially large unlabeled dataset…
Formal Concept Analysis (FCA) provides a method called attribute exploration which helps a domain expert discover structural dependencies in knowledge domains that can be represented by a formal context (a cross table of objects and…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
Intrinsically disordered proteins (IDPs) are important for biological functions. In contrast to folded proteins, molecular recognition among certain IDPs is "fuzzy" in that their binding and/or phase separation are stochastically governed…
Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…
Domain generalization (DG) aims to learn predictive models that can generalize to unseen domains. Most existing DG approaches focus on learning domain-invariant representations under the assumption of conditional distribution shift (i.e.,…
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…
Artificial Intelligence (AI) has become an integral part of modern-day security solutions for its ability to learn very complex functions and handling "Big Data". However, the lack of explainability and interpretability of successful AI…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our…
Deep learning models for medical image analysis easily suffer from distribution shifts caused by dataset artifacts bias, camera variations, differences in the imaging station, etc., leading to unreliable diagnoses in real-world clinical…
Prediction-powered inference (PPI) enables valid statistical inference by combining experimental data with machine learning predictions. When a sufficient number of high-quality predictions is available, PPI results in more accurate…