Related papers: Classification Framework and Structure-Activity-Re…
Explainable artificial intelligence (XAI) approaches have been increasingly applied in drug discovery to learn molecular representations and identify substructures driving property predictions. However, building end-to-end explainable…
Silicon nanoparticles are widely used in the medical area and until now they have not manifested toxicological effects in humans beings. In order to understand the physical properties that determine their low-toxicity, we perform ab initio…
It is well known that tumors originating from the same tissue have different prognosis and sensitivity to treatments. Over the last decade, cancer genomics consortia like the Cancer Genome Atlas (TCGA) have been generating thousands of…
Spatial-temporal data, that is information about objects that exist at a particular location and time period, are rich in value and, as a consequence, the target of so many initiative efforts. Clustering approaches aim at grouping…
PROTACs, as a highly promising new. therapeutic paradigm, have attracted widespread attention from the academic and pharmaceutical communities in recent years. To date, the design and validation of PROTACs molecule's druggability primarily…
Molecules with identical graph connectivity can exhibit different physical and biological properties if they exhibit stereochemistry-a spatial structural characteristic. However, modern neural architectures designed for learning…
Dynamic treatment regimes (DTRs) are critical to precision medicine, optimizing long-term outcomes through personalized, real-time decision-making in evolving clinical contexts, but require careful supervision for unsafe treatment risks.…
An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study…
The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these transcriptional regulatory networks (TRNs) in bacteria have an inherently hierarchical…
With the advent of high-throughput sequencing (HTS) in molecular biology and medicine, the need for scalable statistical solutions for modeling complex biological systems has become of critical importance. The increasing number of platforms…
Phenotype-based screening has attracted much attention for identifying cell-active compounds. Transcriptional and proteomic profiles of cell population or single cells are informative phenotypic measures of cellular responses to…
Background: The problem of predicting whether a drug combination of arbitrary orders is likely to induce adverse drug reactions is considered in this manuscript. Methods: Novel kernels over drug combinations of arbitrary orders are…
Detecting toxicity in multimodal data remains a significant challenge, as harmful meanings often lurk beneath seemingly benign individual modalities: only emerging when modalities are combined and semantic associations are activated. To…
We aim to explore how developers document their refactoring activities during the software life cycle. We call such activity Self-Affirmed Refactoring (SAR), which indicates developers' documentation of their refactoring activities. SAR is…
New sensitivity-based methods are developed for determining identifiability and observability of nonsmooth input-output systems. More specifically, lexicographic calculus is used to construct nonsmooth sensitivity rank condition (SERC)…
In directed graphs, a cycle can be seen as a structure that allows its vertices to loop back to themselves, or as a structure that allows pairs of vertices to reach each other through distinct paths. We extend these concepts to temporal…
Antimicrobial resistance (AMR) is escalating and outpacing current antibiotic development. Thus, discovering antibiotics effective against emerging pathogens is becoming increasingly critical. However, existing approaches cannot rapidly…
The evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore…
Human Activity Recognition (HAR) plays a significant role in the everyday life of people because of its ability to learn extensive high-level information about human activity from wearable or stationary devices. A substantial amount of…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…