Robust learning to rank models and their biomedical applications

There exist many real-world applications such as recommendation systems, document retrieval, and computational biology where the correct ordering of instances is of equal or greater importance than predicting the exact value of some discrete or continuous outcome. Learning-to-Rank (LTR) refers to a group of algorithms that apply machine learning techniques to tackle these ranking problems. Despite their empirical success, most existing LTR models are not built to be robust to errors in labeling or annotation, distributional data shift, or adversarial data perturbations. To fill this gap, we develop four LTR frameworks that are robust to various types of perturbations. First, Pairwise Elastic Net Regression Ranking (PENRR) is an elastic-net-based regression method for drug sensitivity prediction. PENRR infers robust predictors of drug responses from patient genomic information. The special design of this model (comparing each drug with other drugs in the same cell line and comparing that drug with itself in other cell lines) significantly enhances the accuracy of the drug prediction model under limited data. This approach is also able to solve the problem of fitting on the insensitive drugs that is commonly encountered in regression-based models. Second, Regression-based Ranking by Pairwise Cluster Comparisons (RRPCC) is a ridge-regression-based method for ranking clusters of similar protein complex conformations generated by an underlying docking program (i.e., ClusPro). Rather than using regression to predict scores, which would equally penalize deviations for either low-quality and high-quality clusters, we seek to predict the difference of scores for any pair of clusters corresponding to the same complex. RRPCC combines these pairwise assessments to form a ranked list of clusters, from higher to lower quality. We apply RRPCC to clusters produced by the automated docking server ClusPro and, depending on the training/validation strategy, we show. improvement by 24%–100% in ranking acceptable or better quality clusters first, and by 15%–100% in ranking medium or better quality clusters first. Third, Distributionally Robust Multi-Output Regression Ranking (DRMRR) is a listwise LTR model that induces robustness into LTR problems using the Distributionally Robust Optimization framework. Contrasting to existing methods, the scoring function of DRMRR was designed as a multivariate mapping from a feature vector to a vector of deviation scores, which captures local context information and cross-document interactions. DRMRR employs ranking metrics (i.e., NDCG) in its output. Particularly, we used the notion of position deviation to define a vector of relevance score instead of a scalar one. We then adopted the DRO framework to minimize a worst-case expected multi-output loss function over a probabilistic ambiguity set that is defined by the Wasserstein metric. We also presented an equivalent convex reformulation of the DRO problem, which is shown to be tighter than the ones proposed by the previous studies. Fourth, Inversion Transformer-based Neural Ranking (ITNR) is a Transformer-based model to predict drug responses using RNAseq gene expression profiles, drug descriptors, and drug fingerprints. It utilizes a Context-Aware-Transformer architecture as its scoring function that ensures the modeling of inter-item dependencies. We also introduced a new loss function using the concept of Inversion and approximate permutation matrices. The accuracy and robustness of these LTR models are verified through three medical applications, namely cluster ranking in protein-protein docking, medical document retrieval, and drug response prediction

Fuzzy Gilmore and Gomory algorithm: Application in robotic flow shops with the effects of job-dependent transportation and set-ups

This paper addresses the scheduling of robotic cells with job-dependent transportation and set-up effects with fuzzy methodology. Since transportation and set-up times are a large portion of the production time in a flexible manufacturing cell, ignoring these parameters may cause significant errors in determining the optimal makespan. Furthermore, determining the exact values of these time parameters is a challenging task. To overcome this problem, we represent these parameters using fuzzy L-R numbers. Using the capability of fuzzy numbers to represent approximate values, we can represent these parameters without losing valuable information. For generating the optimal part sequencing in the cells, the Gilmore and Gomory algorithm is modified, and instead, a fuzzy Gilmore and Gomory algorithm is developed. We compare the results of the proposed fuzzy method with those of crisp ones. The results indicate the superiority of the proposed algorithm in terms of robustness, flexibility, and reduction of makespan

Social determinants of health and the prediction of missed breast imaging appointments

Abstract Background Predictive models utilizing social determinants of health (SDH), demographic data, and local weather data were trained to predict missed imaging appointments (MIA) among breast imaging patients at the Boston Medical Center (BMC). Patients were characterized by many different variables, including social needs, demographics, imaging utilization, appointment features, and weather conditions on the date of the appointment. Methods This HIPAA compliant retrospective cohort study was IRB approved. Informed consent was waived. After data preprocessing steps, the dataset contained 9,970 patients and 36,606 appointments from 1/1/2015 to 12/31/2019. We identified 57 potentially impactful variables used in the initial prediction model and assessed each patient for MIA. We then developed a parsimonious model via recursive feature elimination, which identified the 25 most predictive variables. We utilized linear and non-linear models including support vector machines (SVM), logistic regression (LR), and random forest (RF) to predict MIA and compared their performance. Results The highest-performing full model is the nonlinear RF, achieving the highest Area Under the ROC Curve (AUC) of 76% and average F1 score of 85%. Models limited to the most predictive variables were able to attain AUC and F1 scores comparable to models with all variables included. The variables most predictive of missed appointments included timing, prior appointment history, referral department of origin, and socioeconomic factors such as household income and access to caregiving services. Conclusions Prediction of MIA with the data available is inherently limited by the complex, multifactorial nature of MIA. However, the algorithms presented achieved acceptable performance and demonstrated that socioeconomic factors were useful predictors of MIA. In contrast with non-modifiable demographic factors, we can address SDH to decrease the incidence of MIA