Decision tree-based identification of important molecular fragments for protein-ligand binding

Fragment-based drug design is an emerging technology in pharmaceutical research and development. One of the key aspects of this technology is the identification and quantitative characterization of molecular fragments. This study presents a strategy for identifying important molecular fragments based on molecular fingerprints and decision tree algorithms and verifies its feasibility in predicting protein-ligand binding affinity. Specifically, the three-dimensional (3D) structures of protein-ligand complexes are encoded using extended-connectivity fingerprints (ECFP), and three decision tree models, namely Random Forest, XGBoost, and LightGBM, are used to quantitatively characterize the feature importance, thereby extracting important molecular fragments with high reliability. Few-shot learning reveals that the extracted molecular fragments contribute significantly and consistently to the binding affinity even with a small sample size. Despite the absence of location and distance information for molecular fragments in ECFP, 3D visualization, in combination with the reverse ECFP process, shows that the majority of the extracted fragments are located at the binding interface of the protein and the ligand. This alignment with the distance constraints critical for binding affinity further supports the reliability of the strategy for identifying important molecular fragments.

Hepatic Involvement across the Metabolic Syndrome Spectrum: Non-Invasive Assessment and Risk Prediction Using Machine Learning

Metabolic-dysfunction-associated steatotic liver disease (MASLD) and metabolic syndrome (MetS) are inextricably linked conditions, both of which are experiencing an upward trend in prevalence, thereby exerting a substantial clinical and economic burden. The presence of MetS should prompt the search for metabolic-associated liver disease. Liver fibrosis is the main predictor of liver-related morbidity and mortality. Non-invasive tests (NIT) such as the Fibrosis-4 index (FIB4), aspartate aminotransferase-to-platelet ratio index (APRI), aspartate aminotransferase-to-alanine aminotransferase ratio (AAR), hepatic steatosis index (HIS), transient elastography (TE), and combined scores (AGILE3+, AGILE4) facilitate the detection of liver fibrosis or steatosis. Our study enrolled 217 patients with suspected MASLD, 109 of whom were diagnosed with MetS. We implemented clinical and biological evaluations complemented by transient elastography (TE) to discern the most robust predictors for liver disease manifestation patterns. Patients with MetS had significantly higher values of FIB4, APRI, HSI, liver stiffness, and steatosis parameters measured by TE, as well as AGILE3+ and AGILE4 scores. Machine-learning algorithms enhanced our evaluation. A two-step cluster algorithm yielded three clusters with reliable model quality. Cluster 1 contained patients without significant fibrosis or steatosis, while clusters 2 and 3 showed a higher prevalence of significant liver fibrosis or at least moderate steatosis as measured by TE. A decision tree algorithm identified age, BMI, liver enzyme levels, and metabolic syndrome characteristics as significant factors in predicting cluster membership with an overall accuracy of 89.4%. Combining NITs improves the accuracy of detecting patterns of liver involvement in patients with suspected MASLD.

Betting Against the Odds: The Mysterious Case of the Clinical Override in Risk Assessment of Adult Convicted Offenders

Various tools were designed to guide practitioners in the risk assessment of offenders, including the Level of Service and Case Management Inventory (LS/CMI). This instrument is based on risk assessment principles prioritizing the actuarial approach to clinical judgment. However, the tool's architects allowed subjective judgment from the practitioners-referred to as clinical override-to modify an offender's risk category under certain circumstances. Few studies, however, have examined these circumstances. Therefore, the current study used decision tree analyses among a quasi-population of Quebec offenders (n = 15,744) to identify whether there are offenders more likely to be subjected to this discretion based on their characteristics. The results suggest that, although the override is rare, it occurred under few specific combinations of circumstances. More precisely, these findings propose that the utilization of the clinical override stems from a perceived discrepancy between risk prediction and management.

Molecular Decision Tree Algorithms Predict Individual Recurrence Pattern for Locally Advanced Nasopharyngeal Carcinoma

Background: Recurrence remains one of the key reasons of relapse after the radical radiation for locally advanced nasopharyngeal carcinoma (NPC). Here, the multiple molecular and clinical variables integrated decision tree algorithms were designed to predict individual recurrence patterns (with VS without recurrence) for locally advanced NPC.

Methods: A total of 136 locally advanced NPC patients retrieved from a randomized controlled phase III trial, were included. For each patient, the expression levels of 33 clinicopathological biomarkers in tumor specimen, 3 Epstein-Barr virus related serological antibody titer and 5 clinicopathological variables, were detected and collected to construct the decision tree algorithm. The expression level of 33 clinicopathological biomarkers in tumor specimen was evaluated by immunohistochemistry staining.

Results: Three algorithm classifiers, augmented by the adaptive boosting algorithm for variable selection and classification, were designed to predict individual recurrence pattern. The classifiers were trained in the training subset and further tested using a 10-fold cross-validation scheme in the validation subset. In total, 13 molecules expression level in tumor specimen, including AKT1, Aurora-A, Bax, Bcl-2, N-Cadherin, CENP-H, HIF-1α, LMP-1, C-Met, MMP-2, MMP-9, Pontin and Stathmin, and N stage were selected to construct three 10-fold cross-validation decision tree classifiers. These classifiers showed high predictive sensitivity (87.2-93.3%), specificity (69.0-100.0%), and overall accuracy (84.5-95.2%) to predict recurrence pattern individually. Multivariate analyses confirmed the decision tree classifier was an independent prognostic factor to predict individual recurrence (algorithm 1: hazard ration (HR) 0.07, 95% confidence interval (CI) 0.03-0.16, P < 0.01; algorithm 2: HR 0.13, 95% CI 0.04-0.44, P < 0.01; algorithm 3: HR 0.13, 95% CI 0.03-0.68, P = 0.02).

Conclusion: Multiple molecular and clinicopathological variables integrated decision tree algorithms may individually predict the recurrence pattern for locally advanced NPC. This decision tree algorism provides a potential tool to select patients with high recurrence risk for intensive follow-up, and to diagnose recurrence at an earlier stage for salvage treatment in the NPC endemic region.