Michael Ibrahim

Mathieu Chevalley, Jacob Sackett-Sanders, Yusuf Roohani et al.

In drug discovery, mapping interactions between genes within cellular systems is a crucial early step. Such maps are not only foundational for understanding the molecular mechanisms underlying disease biology but also pivotal for formulating hypotheses about potential targets for new medicines. Recognizing the need to elevate the construction of these gene-gene interaction networks, especially from large-scale, real-world datasets of perturbed single cells, the CausalBench Challenge was initiated. This challenge aimed to inspire the machine learning community to enhance state-of-the-art methods, emphasizing better utilization of expansive genetic perturbation data. Using the framework provided by the CausalBench benchmark, participants were tasked with refining the current methodologies or proposing new ones. This report provides an analysis and summary of the methods submitted during the challenge to give a partial image of the state of the art at the time of the challenge. Notably, the winning solutions significantly improved performance compared to previous baselines, establishing a new state of the art for this critical task in biology and medicine.

Michael Ibrahim, Heraldo Rozas, Nagi Gebraeel

We study the problem of multiclass classification for settings where data features $\mathbf{x}$ and their labels $\mathbf{y}$ are uncertain. We identify that distributionally robust one-vs-all (OVA) classifiers often struggle in settings with imbalanced data. To address this issue, we use Wasserstein distributionally robust optimization to develop a robust version of the multiclass support vector machine (SVM) characterized by the Crammer-Singer (CS) loss. First, we prove that the CS loss is bounded from above by a Lipschitz continuous function for all $\mathbf{x} \in \mathcal{X}$ and $\mathbf{y} \in \mathcal{Y}$, then we exploit strong duality results to express the dual of the worst-case risk problem, and we show that the worst-case risk minimization problem admits a tractable convex reformulation due to the regularity of the CS loss. Moreover, we develop a kernel version of our proposed model to account for nonlinear class separation, and we show that it admits a tractable convex upper bound. We also propose a projected subgradient method algorithm for a special case of our proposed linear model to improve scalability. Our numerical experiments demonstrate that our model outperforms state-of-the art OVA models in settings where the training data is highly imbalanced. We also show through experiments on popular real-world datasets that our proposed model often outperforms its regularized counterpart as the first accounts for uncertain labels unlike the latter.

Michael Ibrahim, Nagi Gebraeel, Weijun Xie

We study the problem of federated clustering when the total number of clusters $K$ across clients is unknown, and the clients have heterogeneous but potentially overlapping cluster sets in their local data. To that end, we develop FedGEM: a federated generalized expectation-maximization algorithm for the training of mixture models with an unknown number of components. Our proposed algorithm relies on each of the clients performing EM steps locally, and constructing an uncertainty set around the maximizer associated with each local component. The central server utilizes the uncertainty sets to learn potential cluster overlaps between clients, and infer the global number of clusters via closed-form computations. We perform a thorough theoretical study of our algorithm, presenting probabilistic convergence guarantees under common assumptions. Subsequently, we study the specific setting of isotropic GMMs, providing tractable, low-complexity computations to be performed by each client during each iteration of the algorithm, as well as rigorously verifying assumptions required for algorithm convergence. We perform various numerical experiments, where we empirically demonstrate that our proposed method achieves comparable performance to centralized EM, and that it outperforms various existing federated clustering methods.

Michael Ibrahim, Hanqi Zhao, Eli Sennesh et al.

Poisson-distributed latent variable models are widely used in computational neuroscience, but differentiating through discrete stochastic samples remains challenging. Two approaches address this: Exponential Arrival Time (EAT) simulation and Gumbel-SoftMax (GSM) relaxation. We provide the first systematic comparison of these methods, along with practical guidance for practitioners. Our main technical contribution is a modification to the EAT method that theoretically guarantees an unbiased first moment (exactly matching the firing rate), and reduces second-moment bias. We evaluate these methods on their distributional fidelity, gradient quality, and performance on two tasks: (1) variational autoencoders with Poisson latents, and (2) partially observable generalized linear models, where latent neural connectivity must be inferred from observed spike trains. Across all metrics, our modified EAT method exhibits better overall performance (often comparable to exact gradients), and substantially higher robustness to hyperparameter choices. Together, our results clarify the trade-offs between these methods and offer concrete recommendations for practitioners working with Poisson latent variable models.