Meghana Kshirsagar

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee et al.

Differentially private (DP) synthetic data sets are a solution for sharing data while preserving the privacy of individual data providers. Understanding the effects of utilizing DP synthetic data in end-to-end machine learning pipelines impacts areas such as health care and humanitarian action, where data is scarce and regulated by restrictive privacy laws. In this work, we investigate the extent to which synthetic data can replace real, tabular data in machine learning pipelines and identify the most effective synthetic data generation techniques for training and evaluating machine learning models. We investigate the impacts of differentially private synthetic data on downstream classification tasks from the point of view of utility as well as fairness. Our analysis is comprehensive and includes representatives of the two main types of synthetic data generation algorithms: marginal-based and GAN-based. To the best of our knowledge, our work is the first that: (i) proposes a training and evaluation framework that does not assume that real data is available for testing the utility and fairness of machine learning models trained on synthetic data; (ii) presents the most extensive analysis of synthetic data set generation algorithms in terms of utility and fairness when used for training machine learning models; and (iii) encompasses several different definitions of fairness. Our findings demonstrate that marginal-based synthetic data generators surpass GAN-based ones regarding model training utility for tabular data. Indeed, we show that models trained using data generated by marginal-based algorithms can exhibit similar utility to models trained using real data. Our analysis also reveals that the marginal-based synthetic data generator MWEM PGM can train models that simultaneously achieve utility and fairness characteristics close to those obtained by models trained with real data.

Meghana Kshirsagar, Allen Nie, Ching-An Cheng et al.

We introduce RosettaSearch, an inference-time multi-objective optimization approach for protein sequence optimization. We use large language models (LLMs) as a generative optimizer within a search algorithm capable of controlled exploration and exploitation, using rewards computed from RosettaFold3, a structure prediction model. In a large-scale evaluation, we apply RosettaSearch to 400 suboptimal sequences generated by LigandMPNN (a state-of-the-art model trained for protein sequence design), recovering high-fidelity designs that LigandMPNN's single-pass decoding fails to produce. RosettaSearch's designs show improvements in structural fidelity metrics ranging between 18\% to 68\%, translating to a 2.5$\times$ improvement in design success rate. We observe that these gains in success rate are robust when RosettaSearch-designed sequences are evaluated with an independent structure prediction oracle (Chai-1) and generalize across two distinct LLM families (o4-mini and Gemini-3), with performance scaling consistently with reasoning capability. We further demonstrate that RosettaSearch improves sequence fidelity for ProteinMPNN-designed sequences on \textit{de novo} backbones from the Dayhoff atlas, showing that the approach generalizes beyond native protein structures to computationally generated backbones. We also demonstrate a multi-modal extension of RosettaSearch with vision-language models, where images of predicted protein structures are used as feedback to incorporate structural context to guide protein sequence generation. The sequence trajectories generated by our approach can be used as training data in sequence design models or in post-training and will be released along with the code and datasets upon publication.

Alison N. O'Connor, Stephen E. Ryan, Gauri Vaidya et al.

Increased healthcare demand is significantly straining European services. Digital solutions including advanced modelling techniques offer a promising solution to optimising patient flow without impacting day-to-day healthcare provision. In this work we outline an ongoing project that aims to optimise healthcare resources using agent-based simulations.

Mayana Pereira, Meghana Kshirsagar, Sumit Mukherjee et al.

Diferentially private (DP) synthetic datasets are a powerful approach for training machine learning models while respecting the privacy of individual data providers. The effect of DP on the fairness of the resulting trained models is not yet well understood. In this contribution, we systematically study the effects of differentially private synthetic data generation on classification. We analyze disparities in model utility and bias caused by the synthetic dataset, measured through algorithmic fairness metrics. Our first set of results show that although there seems to be a clear negative correlation between privacy and utility (the more private, the less accurate) across all data synthesizers we evaluated, more privacy does not necessarily imply more bias. Additionally, we assess the effects of utilizing synthetic datasets for model training and model evaluation. We show that results obtained on synthetic data can misestimate the actual model performance when it is deployed on real data. We hence advocate on the need for defining proper testing protocols in scenarios where differentially private synthetic datasets are utilized for model training and evaluation.

Meghana Kshirsagar, Eunho Yang, Aurélie C. Lozano

Sparse mapping has been a key methodology in many high-dimensional scientific problems. When multiple tasks share the set of relevant features, learning them jointly in a group drastically improves the quality of relevant feature selection. However, in practice this technique is used limitedly since such grouping information is usually hidden. In this paper, our goal is to recover the group structure on the sparsity patterns and leverage that information in the sparse learning. Toward this, we formulate a joint optimization problem in the task parameter and the group membership, by constructing an appropriate regularizer to encourage sparse learning as well as correct recovery of task groups. We further demonstrate that our proposed method recovers groups and the sparsity patterns in the task parameters accurately by extensive experiments.