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Recent advances in Language Models have enabled the protein modeling community with a powerful tool since protein sequences can be represented as text. Specifically, by taking advantage of Transformers, sequence-to-property prediction will…

Biomolecules · Quantitative Biology 2023-09-07 Chakradhar Guntuboina , Adrita Das , Parisa Mollaei , Seongwon Kim , Amir Barati Farimani

Advances in artificial intelligence (AI) promise autonomous discovery, yet most systems still resurface knowledge latent in their training data. We present Sparks, a multi-modal multi-agent AI model that executes the entire discovery cycle…

Artificial Intelligence · Computer Science 2025-04-29 Alireza Ghafarollahi , Markus J. Buehler

Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the…

Machine Learning · Computer Science 2022-08-29 Ashish Ranjan , Md Shah Fahad , David Fernandez-Baca , Akshay Deepak , Sudhakar Tripathi

Enzymes and proteins are live driven biochemicals, which has a dramatic impact over the environment, in which it is active. So, therefore, it is highly looked-for to build such a robust and highly accurate automatic and computational model…

Biomolecules · Quantitative Biology 2021-01-11 Zaheer Ullah Khan , Dechang Pi , Izhar Ahmed Khan , Asif Nawaz , Jamil Ahmad , Mushtaq Hussain

Background & Purpose: Chest X-Ray (CXR) use in pre-MRI safety screening for Lead-Less Implanted Electronic Devices (LLIEDs), easily overlooked or misidentified on a frontal view (often only acquired), is common. Although most LLIED types…

Image and Video Processing · Electrical Eng. & Systems 2022-04-28 Mutlu Demirer , Richard D. White , Vikash Gupta , Ronnie A. Sebro , Barbaros S. Erdal

X-ray is one of the prevalent image modalities for the detection and diagnosis of the human body. X-ray provides an actual anatomical structure of an organ present with disease or absence of disease. Segmentation of disease in chest X-ray…

Image and Video Processing · Electrical Eng. & Systems 2024-05-21 Nand Lal Yadav , Satyendra Singh , Rajesh Kumar , Sudhakar Singh

Medical images used in clinical practice are heterogeneous and not the same quality as scans studied in academic research. Preprocessing breaks down in extreme cases when anatomy, artifacts, or imaging parameters are unusual or protocols…

Image and Video Processing · Electrical Eng. & Systems 2022-08-31 Mostafa Mehdipour Ghazi , Mads Nielsen

Virtual Screening (VS) of vast compound libraries guided by Artificial Intelligence (AI) models is a highly productive approach to early drug discovery. Data splitting is crucial for better benchmarking of such AI models. Traditional random…

Quantitative Methods · Quantitative Biology 2024-07-02 Qianrong Guo , Saiveth Hernandez-Hernandez , Pedro J Ballester

Physiological responses to pain have received increasing attention among researchers for developing an automated pain recognition sensing system. Though less explored, Blood Volume Pulse (BVP) is one of the candidate physiological measures…

Machine Learning · Computer Science 2023-03-21 Fatemeh Pouromran , Yingzi Lin , Sagar Kamarthi

In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…

Biomolecules · Quantitative Biology 2019-10-07 Simona Cocco , Christoph Feinauer , Matteo Figliuzzi , Remi Monasson , Martin Weigt

In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each…

Machine Learning · Computer Science 2021-11-04 Damiano Perri , Marco Simonetti , Andrea Lombardi , Noelia Faginas-Lago , Osvaldo Gervasi

Survival analysis studies time-modeling techniques for an event of interest occurring for a population. Survival analysis found widespread applications in healthcare, engineering, and social sciences. However, the data needed to train…

Machine Learning · Computer Science 2023-02-22 Alberto Archetti , Eugenio Lomurno , Francesco Lattari , André Martin , Matteo Matteucci

Semi-supervised learning (SSL) has seen great strides when labeled data is scarce but unlabeled data is abundant. Critically, most recent work assume that such unlabeled data is drawn from the same distribution as the labeled data. In this…

Computer Vision and Pattern Recognition · Computer Science 2022-06-15 Amin Banitalebi-Dehkordi , Pratik Gujjar , Yong Zhang

Significant advances have been made in predicting new topological materials using high-throughput empirical descriptors or symmetry-based indicators. To date, these approaches have been applied to materials in existing databases, and are…

Identification of antimicrobial peptides is an important and necessary issue in today's era. Antimicrobial peptides are essential as an alternative to antibiotics for biomedical applications and many other practical applications. These…

Machine Learning · Computer Science 2025-12-17 Reyhaneh Keshavarzpour , Eghbal Mansoori

Artificial intelligence-assisted drug design is revolutionizing the pharmaceutical industry. Effective molecular features are crucial for accurate machine learning predictions, and advanced mathematics plays a key role in designing these…

Biomolecules · Quantitative Biology 2024-08-27 Hongsong Feng , Li Shen , Jian Liu , Guo-Wei Wei

Deep learning has transformed protein design, enabling accurate structure prediction, sequence optimization, and de novo protein generation. Advances in single-chain protein structure prediction via AlphaFold2, RoseTTAFold, ESMFold, and…

Machine Learning · Computer Science 2025-02-27 Gregory W. Kyro , Tianyin Qiu , Victor S. Batista

Lack of transparency in AI systems poses challenges in critical real-life applications. It is important to be able to explain the decisions of an AI system to ensure trust on the system. Explainable AI (XAI) algorithms play a vital role in…

Machine Learning · Computer Science 2026-05-15 Sayantani Ghosh , Amit Kumar Das , Amlan Chakrabarti

Understanding and predicting polymer solubility in various solvents is critical for applications ranging from recycling to pharmaceutical formulation. This work presents a deep learning framework that predicts polymer solubility, expressed…

Machine Learning · Computer Science 2025-12-11 Andrew Reinhard

Ischemic heart disease (IHD), particularly in its chronic stable form, is a subtle pathology due to its silent behavior before developing in unstable angina, myocardial infarction or sudden cardiac death. Machine learning techniques applied…

Signal Processing · Electrical Eng. & Systems 2020-11-20 Giulia Silveri , Marco Merlo , Luca Restivo , Gianfranco Sinagra , Agostino Accardo