Related papers: SMISS: A protein function prediction server by int…
With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary information. The resulting…
Protein design using structure prediction models such as AlphaFold2 has shown remarkable success, but existing approaches like relaxed sequence optimization (RSO) rely on single-path gradient descent and ignore sequence-space constraints,…
AI-based protein structure prediction pipelines, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence Alignments (MSAs) as inputs to learn the co-evolution information from…
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…
Summary: The F2CS server provides access to the software, F2CS2.00, that implements an automated prediction method of SCOP and CATH classifications of proteins, based on their FSSP Z-scores (Getz et al., 2002), Availability: Free, at…
In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated…
Multimodal semantic communication has great potential to enhance downstream task performance by integrating complementary information across modalities. This paper introduces ProMSC-MIS, a novel Prompt-based Multimodal Semantic…
Virtual screening of small molecules against protein targets can accelerate drug discovery and development by predicting drug-target interactions (DTIs). However, structure-based methods like molecular docking are too slow to allow for…
Natural Language Inference (NLI) is a fundamental and challenging task in Natural Language Processing (NLP). Most existing methods only apply one-pass inference process on a mixed matching feature, which is a concatenation of different…
Most of the web user's requirements are search or navigation time and getting correctly matched result. These constrains can be satisfied with some additional modules attached to the existing search engines and web servers. This paper…
Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" become a verb, describing the act of performing sequence search and alignment. However, if one needs…
Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability…
We present two new approaches for point prediction with streaming data. One is based on the Count-Min sketch (CMS) and the other is based on Gaussian process priors with a random bias. These methods are intended for the most general…
Short Message Service (SMS) based Information Systems (SMSbIS) provide an excellent alternative to a traditional approach of obtaining specific information by direct (through phone) or indirect (IVRS, Web, Email) probing. Information and…
Software systems are complex, and behavioral comprehension with the increasing amount of AI components challenges traditional testing and maintenance strategies.The lack of tools and methodologies for behavioral software comprehension…
Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…
Neuromorphic Systems-on-Chip (NSoCs) are becoming heterogeneous by integrating general-purpose processors (GPPs) and neural processing units (NPUs) on the same SoC. For embedded systems, an NSoC may need to execute user applications built…
Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent…
Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural information from it.…
Large language models (LLMs) have garnered considerable attention for their proficiency in tackling intricate tasks, particularly leveraging their capacities for zero-shot and in-context learning. However, their utility has been…