Panagiotis Misiakos

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.

Panagiotis Misiakos, Markus Püschel

We introduce SpinSVAR, a novel method for estimating a structural vector autoregression (SVAR) from time-series data under sparse input assumption. Unlike prior approaches using Gaussian noise, we model the input as independent Laplacian variables, enforcing sparsity and yielding a maximum likelihood estimator (MLE) based on least absolute error regression. We provide theoretical consistency guarantees for the MLE under mild assumptions. SpinSVAR is efficient: it can leverage GPU acceleration to scale to thousands of nodes. On synthetic data with Laplacian or Bernoulli-uniform inputs, SpinSVAR outperforms state-of-the-art methods in accuracy and runtime. When applied to S&P 500 data, it clusters stocks by sectors and identifies significant structural shocks linked to major price movements, demonstrating the viability of our sparse input assumption.

Panagiotis Misiakos, Chris Wendler, Markus Püschel

We present a novel perspective and algorithm for learning directed acyclic graphs (DAGs) from data generated by a linear structural equation model (SEM). First, we show that a linear SEM can be viewed as a linear transform that, in prior work, computes the data from a dense input vector of random valued root causes (as we will call them) associated with the nodes. Instead, we consider the case of (approximately) few root causes and also introduce noise in the measurement of the data. Intuitively, this means that the DAG data is produced by few data-generating events whose effect percolates through the DAG. We prove identifiability in this new setting and show that the true DAG is the global minimizer of the $L^0$-norm of the vector of root causes. For data with few root causes, with and without noise, we show superior performance compared to prior DAG learning methods.