<i>De Novo</i> Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization by Alberga Domenico (9356272)

“…In the present study, we conceived a novel pair-based multiobjective approach implemented in an adapted SMILES generative algorithm based on recurrent neural networks for the automated <i>de novo</i> design of new molecules whose overall features are optimized by finding the best trade-offs among relevant physicochemical properties (MW, logP, HBA, HBD) and additional similarity-based constraints biasing specific biological targets. …”

RosettaAMRLD: A Reaction-Driven Approach for Structure-Based Drug Design from Combinatorial Libraries with Monte Carlo Metropolis Algorithms by Yidan Tang (6623693)

“…The Rosetta automated Monte Carlo reaction-based ligand design (RosettaAMRLD) integrates a Monte Carlo Metropolis (MCM) algorithm and reaction-driven molecule proposal to enhance structure-based <i>de novo</i> drug discovery. …”

Fine-Tuning a Genetic Algorithm for CAMD: A Screening-Guided Warm Start by Yifan Wang (380120)

“…In response to these challenges, this work presents a method to fine-tune a genetic algorithm for CAMD. The proposed method builds on the COSMO-CAMD framework that utilizes a genetic algorithm for solving optimization-based molecular design problems and COSMO-RS for predicting physical properties of molecules. …”

Fine-Tuning a Genetic Algorithm for CAMD: A Screening-Guided Warm Start by Yifan Wang (380120)

“…In response to these challenges, this work presents a method to fine-tune a genetic algorithm for CAMD. The proposed method builds on the COSMO-CAMD framework that utilizes a genetic algorithm for solving optimization-based molecular design problems and COSMO-RS for predicting physical properties of molecules. …”

Hierarchical clustering to infer a binary tree with <i>K</i> = 4 sampled populations. by Tristan Mary-Huard (3864)

“…After <i>K</i> − 2 = 2 steps, the resulting tree is binary and the algorithm stops.</p>…”

<i>hi</i>PRS algorithm process flow. by Michela C. Massi (14599915)

“…<b>(B)</b> Focusing on the positive class only, the algorithm exploits FIM (<i>apriori</i> algorithm) to build a list of candidate interactions of any desired order, retaining those that have an empirical frequency above a given threshold <i>δ</i>. …”

Acceleration of Inverse Molecular Design by Using Predictive Techniques by Jos L. Teunissen (1911856)

“…This study addresses one of the most important drawbacks inherently related to molecular searches in chemical compound space by greedy algorithms such as Best First Search and Genetic Algorithm, i.e., the large computational cost required to optimize one or more quantum-chemical properties. …”

FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology by Pieter B. Burger (4172578)

“…In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. …”

FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology by Pieter B. Burger (4172578)

“…In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. …”

FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology by Pieter B. Burger (4172578)

“…In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. …”

FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology by Pieter B. Burger (4172578)

“…In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. …”

FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology by Pieter B. Burger (4172578)

“…In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. …”

FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology by Pieter B. Burger (4172578)

“…In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. …”

FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology by Pieter B. Burger (4172578)

“…In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. …”

Presentation_1_Calibrating Seed-Based Heuristics to Map Short Reads With Sesame.zip by Guillaume J. Filion (9027317)

tUbenet Foundation Model Weights by Natalie Holroyd (7099391)

Cheminformatics-Guided Cell-Free Exploration of Peptide Natural Products by Jarrett M. Pelton (18143785)

“…To assess the peptide NP space that is directly accessible to current cell-free technologies, we developed a peptide parsing algorithm that breaks down peptide NPs into building blocks based on ribosomal translation logic. …”

Seed mix selection model by Bethanne Bruninga-Socolar (10923639)

“…</p> <p>  </p> <p>We applied the seed mix selection model using a binary genetic algorithm to select seed mixes (R package ‘GA’; Scrucca 2013; Scrucca 2017). …”

Supporting data for "clinical-oriented surgical planning based on finite element method and automate-generated surgical templates assisting the spinal surgery" by Tianchi Wu (11062323)

“…Remaining algorithm needed was reimplemented from open-source libraries.…”

hIPPYlib: An Extensible Software Framework for Large-scale Inverse Problems by Olalekan A. Babaniyi (767286)

“…The key property of the algorithms implemented in hIPPYlib is that the solution is computed at a cost, measured in forward PDE solves, that is independent of the parameter dimension. …”