Vivian Viallon

Laurent El Ghaoui, Vivian Viallon, Tarek Rabbani

We describe a fast method to eliminate features (variables) in l1 -penalized least-square regression (or LASSO) problems. The elimination of features leads to a potentially substantial reduction in running time, specially for large values of the penalty parameter. Our method is not heuristic: it only eliminates features that are guaranteed to be absent after solving the LASSO problem. The feature elimination step is easy to parallelize and can test each feature for elimination independently. Moreover, the computational effort of our method is negligible compared to that of solving the LASSO problem - roughly it is the same as single gradient step. Our method extends the scope of existing LASSO algorithms to treat larger data sets, previously out of their reach. We show how our method can be extended to general l1 -penalized convex problems and present preliminary results for the Sparse Support Vector Machine and Logistic Regression problems.

Marie Breeur, George Stepaniants, Pekka Keski-Rahkonen et al.

Untargeted metabolomic profiling through liquid chromatography-mass spectrometry (LC-MS) measures a vast array of metabolites within biospecimens, advancing drug development, disease diagnosis, and risk prediction. However, the low throughput of LC-MS poses a major challenge for biomarker discovery, annotation, and experimental comparison, necessitating the merging of multiple datasets. Current data pooling methods encounter practical limitations due to their vulnerability to data variations and hyperparameter dependence. Here we introduce GromovMatcher, a flexible and user-friendly algorithm that automatically combines LC-MS datasets using optimal transport. By capitalizing on feature intensity correlation structures, GromovMatcher delivers superior alignment accuracy and robustness compared to existing approaches. This algorithm scales to thousands of features requiring minimal hyperparameter tuning. Manually curated datasets for validating alignment algorithms are limited in the field of untargeted metabolomics, and hence we develop a dataset split procedure to generate pairs of validation datasets to test the alignments produced by GromovMatcher and other methods. Applying our method to experimental patient studies of liver and pancreatic cancer, we discover shared metabolic features related to patient alcohol intake, demonstrating how GromovMatcher facilitates the search for biomarkers associated with lifestyle risk factors linked to several cancer types.