Graphs for margins of Bayesian networks

Directed acyclic graph (DAG) models, also called Bayesian networks, impose conditional independence constraints on a multivariate probability distribution, and are widely used in probabilistic reasoning, machine learning and causal inference. If latent variables are included in such a model, then the set of possible marginal distributions over the remaining (observed) variables is generally complex, and not represented by any DAG. Larger classes of mixed graphical models, which use multiple edge types, have been introduced to overcome this; however, these classes do not represent all the models which can arise as margins of DAGs. In this paper we show that this is because ordinary mixed graphs are fundamentally insufficiently rich to capture the variety of marginal models. We introduce a new class of hyper-graphs, called mDAGs, and a latent projection operation to obtain an mDAG from the margin of a DAG. We show that each distinct marginal of a DAG model is represented by at least one mDAG, and provide graphical results towards characterizing when two such marginal models are the same. Finally we show that mDAGs correctly capture the marginal structure of causally-interpreted DAGs under interventions on the observed variables

A Unifying Framework for Characterizing and Computing Width Measures

Algorithms for computing or approximating optimal decompositions for decompositional parameters such as treewidth or clique-width have so far traditionally been tailored to specific width parameters. Moreover, for mim-width, no efficient algorithms for computing good decompositions were known, even under highly restrictive parameterizations. In this work we identify ?-branchwidth as a class of generic decompositional parameters that can capture mim-width, treewidth, clique-width as well as other measures. We show that while there is an infinite number of ?-branchwidth parameters, only a handful of these are asymptotically distinct. We then develop fixed-parameter and kernelization algorithms (under several structural parameterizations) that can approximate every possible ?-branchwidth, providing a unifying parameterized framework that can efficiently obtain near-optimal tree-decompositions, k-expressions, as well as optimal mim-width decompositions

Experimental Design for Causal Effect Identification

Pearl's do calculus is a complete axiomatic approach to learn the identifiable causal effects from observational data. When such an effect is not identifiable, it is necessary to perform a collection of often costly interventions in the system to learn the causal effect. In this work, we consider the problem of designing the collection of interventions with the minimum cost to identify the desired effect. First, we prove that this problem is NP-hard, and subsequently propose an algorithm that can either find the optimal solution or a logarithmic-factor approximation of it. This is done by establishing a connection between our problem and the minimum hitting set problem. Additionally, we propose several polynomial-time heuristic algorithms to tackle the computational complexity of the problem. Although these algorithms could potentially stumble on sub-optimal solutions, our simulations show that they achieve small regrets on random graphs.Comment: 53 pages, 13 figures, extending the findings of our ICML2022 pape

Reduction of dynamical biochemical reaction networks in computational biology

Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multi-scaleness is another property of these networks, that can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to simpler networks, in a way that depends only on the orders of magnitude and not on the exact values of the kinetic parameters. The main idea used for such robust simplifications of networks is the concept of dominance among model elements, allowing hierarchical organization of these elements according to their effects on the network dynamics. This concept finds a natural formulation in tropical geometry. We revisit, in the light of these new ideas, the main approaches to model reduction of reaction networks, such as quasi-steady state and quasi-equilibrium approximations, and provide practical recipes for model reduction of linear and nonlinear networks. We also discuss the application of model reduction to backward pruning machine learning techniques