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Protein engineering seeks to identify protein sequences with optimized properties. When guided by machine learning, protein sequence generation methods can draw on prior knowledge and experimental efforts to improve this process. In this…

Quantitative Methods · Quantitative Biology 2021-05-28 Zachary Wu , Kadina E. Johnston , Frances H. Arnold , Kevin K. Yang

Deep generative models that learn from the distribution of natural protein sequences and structures may enable the design of new proteins with valuable functions. While the majority of today's models focus on generating either sequences or…

Biomolecules · Quantitative Biology 2024-10-03 Chentong Wang , Sarah Alamdari , Carles Domingo-Enrich , Ava Amini , Kevin K. Yang

Deep learning approaches have produced substantial breakthroughs in fields such as image classification and natural language processing and are making rapid inroads in the area of protein design. Many generative models of proteins have been…

Machine Learning · Computer Science 2021-09-29 Alexey Strokach , Philip M. Kim

Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…

Machine Learning · Computer Science 2019-12-05 John Bradshaw , Brooks Paige , Matt J. Kusner , Marwin H. S. Segler , José Miguel Hernández-Lobato

In this paper, we introduce an alternative approach, namely GEN (Genetic Evolution Network) Model, to the deep learning models. Instead of building one single deep model, GEN adopts a genetic-evolutionary learning strategy to build a group…

Machine Learning · Computer Science 2018-06-06 Jiawei Zhang , Limeng Cui , Fisher B. Gouza

Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous studies have primarily focused on generating gene expression or haplotype…

Genomics · Quantitative Biology 2025-08-14 Sihan Xie , Thierry Tribout , Didier Boichard , Blaise Hanczar , Julien Chiquet , Eric Barrey

We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…

Quantitative Methods · Quantitative Biology 2023-03-10 Mehedi Hasan Sarkar , Adnan Ferdous Ashrafi

Generative artificial intelligence models learn probability distributions from data and produce novel samples that capture the salient properties of their training sets. Proteins are particularly attractive for such approaches given their…

Biomolecules · Quantitative Biology 2026-02-27 Filippo Stocco , Michele Garibbo , Noelia Ferruz

Password guessing approaches via deep learning have recently been investigated with significant breakthroughs in their ability to generate novel, realistic password candidates. In the present work we study a broad collection of deep…

Machine Learning · Computer Science 2020-12-18 David Biesner , Kostadin Cvejoski , Bogdan Georgiev , Rafet Sifa , Erik Krupicka

This paper introduces a new generative deep learning network for human motion synthesis and control. Our key idea is to combine recurrent neural networks (RNNs) and adversarial training for human motion modeling. We first describe an…

Graphics · Computer Science 2018-06-25 Zhiyong Wang , Jinxiang Chai , Shihong Xia

Taking inspiration from biological evolution, we explore the idea of "Can deep neural networks evolve naturally over successive generations into highly efficient deep neural networks?" by introducing the notion of synthesizing new highly…

Computer Vision and Pattern Recognition · Computer Science 2017-02-08 Mohammad Javad Shafiee , Akshaya Mishra , Alexander Wong

This work addresses the scarcity of annotated hyperspectral data required to train deep neural networks. Especially, we investigate generative adversarial networks and their application to the synthesis of consistent labeled spectra. By…

Neural and Evolutionary Computing · Computer Science 2018-06-08 Nicolas Audebert , Bertrand Le Saux , Sébastien Lefèvre

Deep neural networks (DNNs) have demonstrated state-of-the-art results on many pattern recognition tasks, especially vision classification problems. Understanding the inner workings of such computational brains is both fascinating basic…

Neural and Evolutionary Computing · Computer Science 2016-11-24 Anh Nguyen , Alexey Dosovitskiy , Jason Yosinski , Thomas Brox , Jeff Clune

Optimizing a neural network's performance is a tedious and time taking process, this iterative process does not have any defined solution which can work for all the problems. Optimization can be roughly categorized into - Architecture and…

Machine Learning · Computer Science 2019-12-16 Siddhartha Dhar Choudhury , Shashank Pandey , Kunal Mehrotra

Generative methods (Gen-AI) are reviewed with a particular goal of solving tasks in machine learning and Bayesian inference. Generative models require one to simulate a large training dataset and to use deep neural networks to solve a…

Computation · Statistics 2025-05-20 Maria Nareklishvili , Nick Polson , Vadim Sokolov

There are a number of ways to procedurally generate interesting three-dimensional shapes, and a method where a cellular neural network is combined with a mesh growth algorithm is presented here. The aim is to create a shape from a genetic…

Neural and Evolutionary Computing · Computer Science 2016-03-30 Hugo Martay

Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes…

Artificial Intelligence · Computer Science 2022-08-02 Dai Hai Nguyen , Koji Tsuda

Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…

Biomolecules · Quantitative Biology 2021-02-02 Zichao Yan , William L. Hamilton , Mathieu Blanchette

Recent work introduced progressive network growing as a promising way to ease the training for large GANs, but the model design and architecture-growing strategy still remain under-explored and needs manual design for different image data.…

Computer Vision and Pattern Recognition · Computer Science 2021-06-17 Lanlan Liu , Yuting Zhang , Jia Deng , Stefano Soatto

Designing DNA and protein sequences with improved function has the potential to greatly accelerate synthetic biology. Machine learning models that accurately predict biological fitness from sequence are becoming a powerful tool for…

Machine Learning · Computer Science 2022-03-17 Johannes Linder , Georg Seelig
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