ML2Motif-Reliable extraction of discriminative sequence motifs from learning machines

Investigation of the Solubility of Elemental Sulfur (S) in Sulfur-Containing Natural Gas with Machine Learning Methods

Some natural gases are toxic because they contain hydrogen sulfide (H₂S). The solubility pattern of elemental sulfur (S) in toxic natural gas needs to be studied for environmental protection and life safety. Some methods (e.g., experiments) may pose safety risks. Measuring sulfur solubility using a machine learning (ML) method is fast and accurate. Considering the limited experimental data on sulfur solubility, this study used consensus nested cross-validation (cnCV) to obtain more information. The global search capability and learning efficiency of random forest (RF) and weighted least squares support vector machine (WLSSVM) models were enhanced via a whale optimization-genetic algorithm (WOA-GA). Hence, the WOA-GA-RF and WOA-GA-WLSSVM models were developed to accurately predict the solubility of sulfur and reveal its variation pattern. WOA-GA-RF outperformed six other similar models (e.g., RF model) and six other published studies (e.g., the model designed by Roberts et al.). Using the generic positional oligomer importance matrix (gPOIM), this study visualized the contribution of variables affecting sulfur solubility. The results show that temperature, pressure, and H₂S content all have positive effects on sulfur solubility. Sulfur solubility significantly increases when the H₂S content exceeds 10%, and other conditions (temperature, pressure) remain the same.

Interpretable machine learning for genomics

High-throughput technologies such as next-generation sequencing allow biologists to observe cell function with unprecedented resolution, but the resulting datasets are too large and complicated for humans to understand without the aid of advanced statistical methods. Machine learning (ML) algorithms, which are designed to automatically find patterns in data, are well suited to this task. Yet these models are often so complex as to be opaque, leaving researchers with few clues about underlying mechanisms. Interpretable machine learning (iML) is a burgeoning subdiscipline of computational statistics devoted to making the predictions of ML models more intelligible to end users. This article is a gentle and critical introduction to iML, with an emphasis on genomic applications. I define relevant concepts, motivate leading methodologies, and provide a simple typology of existing approaches. I survey recent examples of iML in genomics, demonstrating how such techniques are increasingly integrated into research workflows. I argue that iML solutions are required to realize the promise of precision medicine. However, several open challenges remain. I examine the limitations of current state-of-the-art tools and propose a number of directions for future research. While the horizon for iML in genomics is wide and bright, continued progress requires close collaboration across disciplines.