<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. …”

Relative predictive performance when using default algorithm hyperparameters and all features vs. tuning hyperparameters or selecting features. by Stephen R. Piccolo (8367780)

Classification algorithm hyperparameter combinations. by Stephen R. Piccolo (8367780)

Feature-selection algorithm hyperparameter combinations. by Stephen R. Piccolo (8367780)

Comparison of ranks for classification algorithms across performance metrics. by Stephen R. Piccolo (8367780)

A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters by José Manuel Vásquez-Pérez (12843737)

“…The Fortran implementation of the algorithm is available as an open source library (https://github.com/qcuaeh/molalignlib) and is suitable to be used in global optimization methods for the identification of local minima or basins.…”

Relative classification performance per combination of feature-selection and classification algorithm. by Stephen R. Piccolo (8367780)

Relative performance of classification algorithms using gene-expression and clinical predictors and performing feature selection. by Stephen R. Piccolo (8367780)

Flat optimization method. by Nisha Ann Viswan (20371285)

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. …”

Addressing Imbalanced Classification Problems in Drug Discovery and Development Using Random Forest, Support Vector Machine, AutoGluon-Tabular, and H2O AutoML by Ayush Garg (21090944)

“…The important findings of our studies are as follows: (i) there is no effect of threshold optimization on ranking metrics such as AUC and AUPR, but AUC and AUPR get affected by class-weighting and SMOTTomek; (ii) for ML methods RF and SVM, significant percentage improvement up to 375, 33.33, and 450 over all the data sets can be achieved, respectively, for F1 score, MCC, and balanced accuracy, which are suitable for performance evaluation of imbalanced data sets; (iii) for AutoML libraries AutoGluon-Tabular and H2O AutoML, significant percentage improvement up to 383.33, 37.25, and 533.33 over all the data sets can be achieved, respectively, for F1 score, MCC, and balanced accuracy; (iv) the general pattern of percentage improvement in balanced accuracy is that the percentage improvement increases when the class ratio is systematically decreased from 0.5 to 0.1; in the case of F1 score and MCC, maximum improvement is achieved at the class ratio of 0.3; (v) for both ML and AutoML with balancing, it is observed that any individual class-balancing technique does not outperform all other methods on a significantly higher number of data sets based on F1 score; (vi) the three external balancing techniques combined outperformed the internal balancing methods of the ML and AutoML; (vii) AutoML tools perform as good as the ML models and in some cases perform even better for handling imbalanced classification when applied with imbalance handling techniques. …”

Fig 7 - by Muhammad Usman Tariq (11022141)

2D UMAP visualization of embedded spectra and peptide vectors generated by SpeCollate. by Muhammad Usman Tariq (11022141)

Using Variable Data-Independent Acquisition for Capillary Electrophoresis-Based Untargeted Metabolomics by Saki Kiuchi (19374255)

“…Capillary electrophoresis coupled with tandem mass spectrometry (CE-MS/MS) offers advantages in peak capacity and sensitivity for metabolic profiling owing to the electroosmotic flow-based separation. However, the utilization of data-independent MS/MS acquisition (DIA) is restricted due to the absence of an optimal procedure for analytical chemistry and its related informatics framework. …”

Using Variable Data-Independent Acquisition for Capillary Electrophoresis-Based Untargeted Metabolomics by Saki Kiuchi (19374255)

“…Capillary electrophoresis coupled with tandem mass spectrometry (CE-MS/MS) offers advantages in peak capacity and sensitivity for metabolic profiling owing to the electroosmotic flow-based separation. However, the utilization of data-independent MS/MS acquisition (DIA) is restricted due to the absence of an optimal procedure for analytical chemistry and its related informatics framework. …”

Performance of the SPP. by Virgile Andreani (17087764)

SHAP bar plot. by Meng Cao (105914)

“…The optimal model was further assessed for predictor importance utilizing the SHAP method and deployed on a web platform using the Streamlit library.…”

Sample screening flowchart. by Meng Cao (105914)

“…The optimal model was further assessed for predictor importance utilizing the SHAP method and deployed on a web platform using the Streamlit library.…”

Descriptive statistics for variables. by Meng Cao (105914)

“…The optimal model was further assessed for predictor importance utilizing the SHAP method and deployed on a web platform using the Streamlit library.…”