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Design of new drugs is a challenging process: a candidate molecule should satisfy multiple conditions to act properly and make the least side-effect -- perfect candidates selectively attach to and influence only targets, leaving off-targets…

Biomolecules · Quantitative Biology 2024-05-07 Andrij Rovenchak , Maksym Druchok

Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…

Biomolecules · Quantitative Biology 2024-02-09 Song Yin , Xuenan Mi , Diwakar Shukla

We show that neural networks trained by evolutionary reinforcement learning can enact efficient molecular self-assembly protocols. Presented with molecular simulation trajectories, networks learn to change temperature and chemical potential…

Statistical Mechanics · Physics 2020-06-01 Stephen Whitelam , Isaac Tamblyn

Predicting human performance in interaction tasks allows designers or developers to understand the expected performance of a target interface without actually testing it with real users. In this work, we present a deep neural net to model…

Human-Computer Interaction · Computer Science 2018-03-15 Yang Li , Samy Bengio , Gilles Bailly

Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…

Quantitative Methods · Quantitative Biology 2023-08-02 Dhananjay Bhaskar , William Y. Zhang , Alexandria Volkening , Björn Sandstede , Ian Y. Wong

Current pharmaceutical formulation development still strongly relies on the traditional trial-and-error approach by individual experiences of pharmaceutical scientists, which is laborious, time-consuming and costly. Recently, deep learning…

Machine Learning · Computer Science 2018-12-05 Yilong Yang , Zhuyifan Ye , Yan Su , Qianqian Zhao , Xiaoshan Li , Defang Ouyang

Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…

Quantitative Methods · Quantitative Biology 2024-06-14 Alex Jihun Lee , Reza Abbasi-Asl

The characterization of dynamical processes in living systems provides important clues for their mechanistic interpretation and link to biological functions. Thanks to recent advances in microscopy techniques, it is now possible to…

Data Analysis, Statistics and Probability · Physics 2023-11-29 Jesús Pineda , Benjamin Midtvedt , Harshith Bachimanchi , Sergio Noé , Daniel Midtvedt , Giovanni Volpe , Carlo Manzo

Amphiphilic molecules spontaneously form self-assembled structures of various shapes depending on their molecular structures, the temperature, and other physical conditions. The functionalities of these structures are dictated by their…

Soft Condensed Matter · Physics 2024-04-18 Takeo Sudo , Satoki Ishiai , Yuuki Ishiwatari , Takahiro Yokoyama , Kenji Yasuoka , Noriyoshi Arai

Topology optimization of microstructures plays a critical role in optimizing functional performance across diverse engineering applications. While metamaterials with enhanced mechanical properties -- such as hyperelasticity, energy…

Soft Condensed Matter · Physics 2025-01-27 Weiming Wang , Yanhao Hou , Renbo Su , Weiguang Wang , Charlie C. L. Wang

Using machine learning, we explore the utility of various deep neural networks (NN) when applied to high harmonic generation (HHG) scenarios. First, we train the NNs to predict the time-dependent dipole and spectra of HHG emission from…

Optics · Physics 2023-03-07 M. Lytova , M. Spanner , I. Tamblyn

Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather…

Machine Learning tools are nowadays widely applied extensively to the prediction of the properties of molecular materials, using datasets extracted from high-throughput computational models. In several cases of scientific and technological…

Materials Science · Physics 2021-02-10 Fabio Le Piane , Matteo Baldoni , Francesco Mercuri

Histopathological images are widely used for the analysis of diseased (tumor) tissues and patient treatment selection. While the majority of microscopy image processing was previously done manually by pathologists, recent advances in…

Image and Video Processing · Electrical Eng. & Systems 2024-07-12 Andrey Ignatov , Josephine Yates , Valentina Boeva

With the advancements in computer technology, there is a rapid development of intelligent systems to understand the complex relationships in data to make predictions and classifications. Artificail Intelligence based framework is rapidly…

Machine Learning · Computer Science 2021-07-30 G Jignesh Chowdary , Suganya G , Premalatha M , Asnath Victy Phamila Y , Karunamurthy K

Automatic classification of active tuberculosis from chest X-ray images has the potential to save lives, especially in low- and mid-income countries where skilled human experts can be scarce. Given the lack of available labeled data to…

Computer Vision and Pattern Recognition · Computer Science 2024-10-10 Özgür Acar Güler , Manuel Günther , André Anjos

We investigate the potential of machine learning models for the prediction of visual improvement after macular hole surgery from preoperative data (retinal images and clinical features). Collecting our own data for the task, we end up with…

Image and Video Processing · Electrical Eng. & Systems 2021-11-16 M. Godbout , A. Lachance , F. Antaki , A. Dirani , A. Durand

Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…

Biomolecules · Quantitative Biology 2023-02-27 Gabriele Corso

Adhering cells actively probe the mechanical properties of their environment and use the resulting information to position and orient themselves. We show that a large body of experimental observations can be consistently explained from one…

Soft Condensed Matter · Physics 2009-11-10 I. B. Bischofs , U. S. Schwarz

Learning to interact with the environment not only empowers the agent with manipulation capability but also generates information to facilitate building of action understanding and imitation capabilities. This seems to be a strategy adopted…

Robotics · Computer Science 2022-12-06 M. Y. Seker , A. Ahmetoglu , Y. Nagai , M. Asada , E. Oztop , E. Ugur