Aya Laajil

Aya Laajil, Elnura Zhalieva, Naomi Desobry et al.

The goal of probabilistic prediction is to issue predictive distributions that are as informative as possible, subject to being calibrated. Despite substantial progress in the univariate setting, achieving multivariate calibration remains challenging. Recent work has introduced pre-rank functions, scalar projections of multivariate forecasts and observations, as flexible diagnostics for assessing specific aspects of multivariate calibration, but their use has largely been limited to post-hoc evaluation. We propose a regularization-based calibration method that enforces multivariate calibration during training of multivariate distributional regression models using pre-rank functions. We further introduce a novel PCA-based pre-rank that projects predictions onto principal directions of the predictive distribution. Through simulation studies and experiments on 18 real-world multi-output regression datasets, we show that the proposed approach substantially improves multivariate pre-rank calibration without compromising predictive accuracy, and that the PCA pre-rank reveals dependence-structure misspecifications that are not detected by existing pre-ranks.

Aya Laajil, Abduragim Shtanchaev, Sajan Muhammad et al.

Designing mRNA sequences is a major challenge in developing next-generation therapeutics, since it involves exploring a vast space of possible nucleotide combinations while optimizing sequence properties like stability, translation efficiency, and protein expression. While Generative Flow Networks are promising for this task, their training is hindered by sparse, long-horizon rewards and multi-objective trade-offs. We propose Curriculum-Augmented GFlowNets (CAGFN), which integrate curriculum learning with multi-objective GFlowNets to generate de novo mRNA sequences. CAGFN integrates a length-based curriculum that progressively adapts the maximum sequence length guiding exploration from easier to harder subproblems. We also provide a new mRNA design environment for GFlowNets which, given a target protein sequence and a combination of biological objectives, allows for the training of models that generate plausible mRNA candidates. This provides a biologically motivated setting for applying and advancing GFlowNets in therapeutic sequence design. On different mRNA design tasks, CAGFN improves Pareto performance and biological plausibility, while maintaining diversity. Moreover, CAGFN reaches higher-quality solutions faster than a GFlowNet trained with random sequence sampling (no curriculum), and enables generalization to out-of-distribution sequences.