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In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations:…

Machine Learning · Computer Science 2025-03-12 Taojie Kuang , Qianli Ma , Athanasios V. Vasilakos , Yu Wang , Qiang , Cheng , Zhixiang Ren

Bone repair using BMP-2 is a promising therapeutic approach in clinical practices, however, high dosages required to be effective pose issues of cost and safety. The present study explores the potential of low dose BMP-2 treatment via…

Biomolecules · Quantitative Biology 2020-11-24 Swati Dubey , Rutusmita Mishra , Partha Roy , R. P. Singh

Predicting clinical outcomes from preclinical data is essential for identifying safe and effective drug combinations, reducing late-stage clinical failures, and accelerating the development of precision therapies. Current AI models rely on…

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate…

Biological neural networks (BNNs) have been established as a powerful and adaptive substrate that offer the potential for incredibly energy and data efficient information processing with distinct learning mechanisms. Yet a core challenge to…

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a…

Computation and Language · Computer Science 2024-10-11 Peng Zhou , Jianmin Wang , Chunyan Li , Zixu Wang , Yiping Liu , Siqi Sun , Jianxin Lin , Leyi Wei , Xibao Cai , Houtim Lai , Wei Liu , Longyue Wang , Yuansheng Liu , Xiangxiang Zeng

Explainable ML for molecular toxicity prediction is a promising approach for efficient drug development and chemical safety. A predictive ML model of toxicity can reduce experimental cost and time while mitigating ethical concerns by…

Quantitative Methods · Quantitative Biology 2022-04-15 Bhanushee Sharma , Vijil Chenthamarakshan , Amit Dhurandhar , Shiranee Pereira , James A. Hendler , Jonathan S. Dordick , Payel Das

Generative models have been very successful over the years and have received significant attention for synthetic data generation. As deep learning models are getting more and more complex, they require large amounts of data to perform…

Image and Video Processing · Electrical Eng. & Systems 2023-02-24 Usama Tariq , Rizwan Qureshi , Anas Zafar , Danyal Aftab , Jia Wu , Tanvir Alam , Zubair Shah , Hazrat Ali

Designing compounds with desired properties is a key element of the drug discovery process. However, measuring progress in the field has been challenging due to the lack of realistic retrospective benchmarks, and the large cost of…

Biomolecules · Quantitative Biology 2023-06-16 Tobiasz Cieplinski , Tomasz Danel , Sabina Podlewska , Stanislaw Jastrzebski

Virtual screening plays a pivotal role in early drug discovery, traditionally dominated by physics-based methods. While these approaches offer detailed insights, they are often hindered by high computational costs, limited sampling, and…

Biomolecules · Quantitative Biology 2024-09-20 Temitope Sobodu , Adeshina Yusuf , Dan Kiel , Dong Kong

Small molecules in biological samples are studied to provide information about disease states, environmental toxins, natural product drug discovery, and many other applications. The primary window into the composition of small molecule…

Machine Learning · Computer Science 2023-05-08 Gennady Voronov , Rose Lightheart , Joe Davison , Christoph A. Krettler , David Healey , Thomas Butler

Stochastic neural networks such as Restricted Boltzmann Machines (RBMs) have been successfully used in applications ranging from speech recognition to image classification. Inference and learning in these algorithms use a Markov Chain Monte…

Neural and Evolutionary Computing · Computer Science 2016-11-17 Bruno U. Pedroni , Srinjoy Das , John V. Arthur , Paul A. Merolla , Bryan L. Jackson , Dharmendra S. Modha , Kenneth Kreutz-Delgado , Gert Cauwenberghs

This work introduces a method to tune a sequence-based generative model for molecular de novo design that through augmented episodic likelihood can learn to generate structures with certain specified desirable properties. We demonstrate how…

Artificial Intelligence · Computer Science 2017-08-30 Marcus Olivecrona , Thomas Blaschke , Ola Engkvist , Hongming Chen

Robust and generalizable segmentation of brain tumors on multi-parametric magnetic resonance imaging (MRI) remains difficult because tumor types differ widely. The BraTS 2025 Lighthouse Challenge benchmarks segmentation methods on diverse…

Molecular design and synthesis planning are two critical steps in the process of molecular discovery that we propose to formulate as a single shared task of conditional synthetic pathway generation. We report an amortized approach to…

Machine Learning · Computer Science 2022-03-15 Wenhao Gao , Rocío Mercado , Connor W. Coley

As spiking-based deep learning inference applications are increasing in embedded systems, these systems tend to integrate neuromorphic accelerators such as $\mu$Brain to improve energy efficiency. We propose a $\mu$Brain-based scalable…

Neural and Evolutionary Computing · Computer Science 2021-11-24 M. Lakshmi Varshika , Adarsha Balaji , Federico Corradi , Anup Das , Jan Stuijt , Francky Catthoor

The intersection of artificial intelligence and bioinformatics has enabled significant advancements in drug discovery, particularly through the application of machine learning models. In this study, we present a combined approach using…

Biomolecules · Quantitative Biology 2024-08-15 Ricardo Romero

Timely brain tumor diagnosis remains challenging in low-resource clinical environments where expert neuroradiology interpretation, high-end MRI hardware, and invasive biopsy procedures may be limited. Although deep learning has achieved…

Image and Video Processing · Electrical Eng. & Systems 2025-12-30 Areeb Ehsan

Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the…

Machine Learning · Computer Science 2024-10-11 Haitao Lin , Guojiang Zhao , Odin Zhang , Yufei Huang , Lirong Wu , Zicheng Liu , Siyuan Li , Cheng Tan , Zhifeng Gao , Stan Z. Li

De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on…

Quantitative Methods · Quantitative Biology 2021-01-05 Nathan Brown , Marco Fiscato , Marwin H. S. Segler , Alain C. Vaucher