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1. Creating and Analyzing a Multimedia Dataset for Building Energy Efficiency Estimation

   Chen, G Q ; Kashyap, N ; Zhang, Z ; Kucheva, Y ; Bobker, M ; Zhu, Z ( March 2024 , International Conference on SMART MULTIMEDIA)

   This paper presents the results of a research that created and analyzed a Multimedia dataset for building energy efficiency estimation. First a new Multimedia Building Energy Efficiency (MMBEE) dataset was created from publicly available data. This work then explored the use of the window-to-wall ratio (WWR) information from building facade images and integrated it with traditional tabular data to create new training data, in order to predict building energy efficiency measures. Finally, we discuss potential applications and future research directions in using the MMBEE dataset for building energy efficiency prediction. Throughout the paper, a number of important processes and analyses were performed, which include feature selection, data correlation analysis, WWR extraction, and comparison of deep network and random forest models in building energy efficiency estimation. From this first attempt at using the Multimedia dataset for building energy efficiency estimation, we found the performances of deep models were better than traditional models such as random forest. We also found that there was an optimal point of what features shall be used for the prediction. Nonetheless, the incorporation of the current WWR estimation results did not yield the anticipated enhancement in estimation performance. Subsequently, a comprehensive investigation was conducted to ascertain potential contributing factors, and several avenues for future research were identified to enhance the predictive utility of the WWR feature. 

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2. Network-based drug sensitivity prediction

   https://doi.org/10.1186/s12920-020-00829-3  

   Ahmed, Khandakar Tanvir ; Park, Sunho ; Jiang, Qibing ; Yeu, Yunku ; Hwang, TaeHyun ; Zhang, Wei ( December 2020 , BMC Medical Genomics)

   null (Ed.)

   Abstract Background Drug sensitivity prediction and drug responsive biomarker selection on high-throughput genomic data is a critical step in drug discovery. Many computational methods have been developed to serve this purpose including several deep neural network models. However, the modular relations among genomic features have been largely ignored in these methods. To overcome this limitation, the role of the gene co-expression network on drug sensitivity prediction is investigated in this study. Methods In this paper, we first introduce a network-based method to identify representative features for drug response prediction by using the gene co-expression network. Then, two graph-based neural network models are proposed and both models integrate gene network information directly into neural network for outcome prediction. Next, we present a large-scale comparative study among the proposed network-based methods, canonical prediction algorithms (i.e., Elastic Net, Random Forest, Partial Least Squares Regression, and Support Vector Regression), and deep neural network models for drug sensitivity prediction. All the source code and processed datasets in this study are available at https://github.com/compbiolabucf/drug-sensitivity-prediction . Results In the comparison of different feature selection methods and prediction methods on a non-small cell lung cancer (NSCLC) cell line RNA-seq gene expression dataset with 50 different drug treatments, we found that (1) the network-based feature selection method improves the prediction performance compared to Pearson correlation coefficients; (2) Random Forest outperforms all the other canonical prediction algorithms and deep neural network models; (3) the proposed graph-based neural network models show better prediction performance compared to deep neural network model; (4) the prediction performance is drug dependent and it may relate to the drug’s mechanism of action. Conclusions Network-based feature selection method and prediction models improve the performance of the drug response prediction. The relations between the genomic features are more robust and stable compared to the correlation between each individual genomic feature and the drug response in high dimension and low sample size genomic datasets. 

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3. Predictive machine learning models trained on experimental datasets for electrochemical nitrogen reduction

   https://doi.org/10.1039/d3dd00151b  

   Rosser, Darik A ; Farris, Brianna R ; Leonard, Kevin C ( April 2024 , Digital Discovery)

   Obtaining useful insights from machine learning models trained on experimental datasets collected across different groups to improve the sustainability of chemical processes can be challenging due to the small size and heterogeneity of the dataset. Here we show that shallow learning models such as decision trees and random forest algorithms can be an effective tool for guiding experimental research in the sustainable chemistry field. This study trained four different machine learning algorithms (linear regression, decision tree, random forest, and multilayer perceptron) using different sized datasets containing up to 520 unique reaction conditions for the nitrogen reduction reaction (NRR) on heterogeneous electrocatalysts. Using the catalyst properties and experimental conditions as the features, we determined the ability of each model to regress the ammonia production rate and the faradaic efficiency. We observed that the shallow learning decision tree and random forest models had equal or better predictive power compared to the deep learning multilayer perceptron models and the simple linear regression models. Moreover, decision tree and random forest models enable the extraction of feature importance, which is a powerful tool in guiding experimental research. Analysis of the models showed the complex interaction between the applied potential and catalysts on the effective rate for the NRR. We also suggest some underexplored catalysts–electrolyte combinations to experimental researchers looking to improve both the rate and efficiency of the NRR reaction. 

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4. Application of Feature Selection and Deep Learning for Cancer Prediction Using DNA Methylation Markers

   https://doi.org/10.3390/genes13091557  

   Gomes, Rahul ; Paul, Nijhum ; He, Nichol ; Huber, Aaron Francis ; Jansen, Rick J ( September 2022 , Genes)

   DNA methylation is a process that can affect gene accessibility and therefore gene expression. In this study, a machine learning pipeline is proposed for the prediction of breast cancer and the identification of significant genes that contribute to the prediction. The current study utilized breast cancer methylation data from The Cancer Genome Atlas (TCGA), specifically the TCGA-BRCA dataset. Feature engineering techniques have been utilized to reduce data volume and make deep learning scalable. A comparative analysis of the proposed approach on Illumina 27K and 450K methylation data reveals that deep learning methodologies for cancer prediction can be coupled with feature selection models to enhance prediction accuracy. Prediction using 450K methylation markers can be accomplished in less than 13 s with an accuracy of 98.75%. Of the list of 685 genes in the feature selected 27K dataset, 578 were mapped to Ensemble Gene IDs. This reduced set was significantly (FDR < 0.05) enriched in five biological processes and one molecular function. Of the list of 1572 genes in the feature selected 450K data set, 1290 were mapped to Ensemble Gene IDs. This reduced set was significantly (FDR < 0.05) enriched in 95 biological processes and 17 molecular functions. Seven oncogene/tumor suppressor genes were common between the 27K and 450K feature selected gene sets. These genes were RTN4IP1, MYO18B, ANP32A, BRF1, SETBP1, NTRK1, and IGF2R. Our bioinformatics deep learning workflow, incorporating imputation and data balancing methods, is able to identify important methylation markers related to functionally important genes in breast cancer with high accuracy compared to deep learning or statistical models alone.

    

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5. Leveraging Scheme for Cross-Study Microbiome Machine Learning Prediction and Feature Evaluations

   https://doi.org/10.3390/bioengineering10020231  

   Song, Kuncheng ; Zhou, Yi-Hui ( February 2023 , Bioengineering)

   The microbiota has proved to be one of the critical factors for many diseases, and researchers have been using microbiome data for disease prediction. However, models trained on one independent microbiome study may not be easily applicable to other independent studies due to the high level of variability in microbiome data. In this study, we developed a method for improving the generalizability and interpretability of machine learning models for predicting three different diseases (colorectal cancer, Crohn’s disease, and immunotherapy response) using nine independent microbiome datasets. Our method involves combining a smaller dataset with a larger dataset, and we found that using at least 25% of the target samples in the source data resulted in improved model performance. We determined random forest as our top model and employed feature selection to identify common and important taxa for disease prediction across the different studies. Our results suggest that this leveraging scheme is a promising approach for improving the accuracy and interpretability of machine learning models for predicting diseases based on microbiome data.

    

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