Related papers: ppiTrim: Constructing non-redundant and up-to-date…
This paper introduces reAnalyst, a framework designed to facilitate the study of reverse engineering (RE) practices through the semi-automated annotation of RE activities across various RE tools. By integrating tool-agnostic data collection…
Based on developer needs and usage scenarios, API (Application Programming Interface) recommendation is the process of assisting developers in finding the required API among numerous candidate APIs. Previous studies mainly modeled API…
Protein-protein interaction (PPI) prediction is an important problem in machine learning and computational biology. However, there is no data set for training or evaluation purposes, where all the instances are accurately labeled. Instead,…
A referring expression (RE) is a description that identifies a set of instances unambiguously. Mining REs from data finds applications in natural language generation, algorithmic journalism, and data maintenance. Since there may exist…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…
In several natural language tasks, labeled sequences are available in separate domains (say, languages), but the goal is to label sequences with mixed domain (such as code-switched text). Or, we may have available models for labeling whole…
Evaluating conversational systems in multi-turn settings remains a fundamental challenge. Conventional pipelines typically rely on manually defined rubrics and fixed conversational context$-$a static approach that limits coverage and fails…
Aptamers are single-stranded DNA/RNAs or short peptides with unique tertiary structures that selectively bind to specific targets. They have great potential in the detection and medical fields. Here, we present SelfTrans-Ensemble, a deep…
Protein-protein interactions (PPIs) are of fundamental importance for the human body, and the knowledge of their existence can facilitate very important tasks like drug target developing and therapy design. The high-throughput experiments…
Artificial Intelligence (AI) development is inherently iterative and experimental. Over the course of normal development, especially with the advent of automated AI, hundreds or thousands of experiments are generated and are often lost or…
Knowledge about protein-protein interactions is essential in understanding the biological processes such as metabolic pathways, DNA replication, and transcription etc. However, a majority of the existing Protein-Protein Interaction (PPI)…
Multi-turn interactions between large language models (LLMs) and users naturally include implicit feedback signals. If an LLM responds in an unexpected way to an instruction, the user is likely to signal it by rephrasing the request,…
Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements…
Dynamic text-attributed graphs (DyTAGs) provide a powerful framework for modeling evolving systems in which node semantics and time-dependent interactions are tightly coupled. Recently, multimodal learning has emerged as a promising yet…
Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps…
Interactive documents help readers engage with complex ideas through dynamic visualization, interactive animations, and exploratory interfaces. However, creating such documents remains costly, as it requires both domain expertise and web…
Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo…
Complex systems often involve higher-order interactions which require us to go beyond their description in terms of pairwise networks. Triadic interactions are a fundamental type of higher-order interaction that occurs when one node…
Lipid-protein interactions play essential roles in cellular signaling and membrane dynamics, yet their systematic characterization has long been hindered by the inherent biochemical properties of lipids. Recent advances in functionalized…
Adaptive experiments automatically optimize their design throughout the data collection process, which can bring substantial benefits compared to conventional experimental settings. Potential applications include, among others: computerized…