Rafael Cabañas

Marco Zaffalon, Alessandro Antonucci, Rafael Cabañas et al.

We address the problem of integrating data from multiple, possibly biased, observational and interventional studies, to eventually compute counterfactuals in structural causal models. We start from the case of a single observational dataset affected by a selection bias. We show that the likelihood of the available data has no local maxima. This enables us to use the causal expectation-maximisation scheme to approximate the bounds for partially identifiable counterfactual queries, which are the focus of this paper. We then show how the same approach can address the general case of multiple datasets, no matter whether interventional or observational, biased or unbiased, by remapping it into the former one via graphical transformations. Systematic numerical experiments and a case study on palliative care show the effectiveness of our approach, while hinting at the benefits of fusing heterogeneous data sources to get informative outcomes in case of partial identifiability.

Marco Zaffalon, Alessandro Antonucci, Rafael Cabañas et al.

We assume to be given structural equations over discrete variables inducing a directed acyclic graph, namely, a structural causal model, together with data about its internal nodes. The question we want to answer is how we can compute bounds for partially identifiable counterfactual queries from such an input. We start by giving a map from structural casual models to credal networks. This allows us to compute exact counterfactual bounds via algorithms for credal nets on a subclass of structural causal models. Exact computation is going to be inefficient in general given that, as we show, causal inference is NP-hard even on polytrees. We target then approximate bounds via a causal EM scheme. We evaluate their accuracy by providing credible intervals on the quality of the approximation; we show through a synthetic benchmark that the EM scheme delivers accurate results in a fair number of runs. In the course of the discussion, we also point out what seems to be a neglected limitation to the trending idea that counterfactual bounds can be computed without knowledge of the structural equations. We also present a real case study on palliative care to show how our algorithms can readily be used for practical purposes.

Marco Zaffalon, Alessandro Antonucci, Rafael Cabañas et al.

Causal analysis may be affected by selection bias, which is defined as the systematic exclusion of data from a certain subpopulation. Previous work in this area focused on the derivation of identifiability conditions. We propose instead a first algorithm to address both identifiable and unidentifiable queries. We prove that, in spite of the missingness induced by the selection bias, the likelihood of the available data is unimodal. This enables us to use the causal expectation-maximisation scheme to obtain the values of causal queries in the identifiable case, and to compute bounds otherwise. Experiments demonstrate the approach to be practically viable. Theoretical convergence characterisations are provided.

Marco Zaffalon, Alessandro Antonucci, David Huber et al.

We address the problem of integrating data from multiple, possibly biased, observational and interventional studies, to eventually compute counterfactuals in structural causal models. We start from the case of a single observational dataset affected by a selection bias. We show that the likelihood of the available data has no local maxima. This enables us to use the causal expectation-maximisation scheme to compute approximate bounds for partially identifiable counterfactual queries, which are the focus of this paper. We then show how the same approach can solve the general case of multiple datasets, no matter whether interventional or observational, biased or unbiased, by remapping it into the former one via graphical transformations. Systematic numerical experiments and a case study on palliative care show the effectiveness and accuracy of our approach, while hinting at the benefits of integrating heterogeneous data to get informative bounds in case of partial identifiability.

Joel Castaño, Rafael Cabañas, Antonio Salmerón et al.

The proliferation of Machine Learning (ML) models and their open-source implementations has transformed Artificial Intelligence research and applications. Platforms like Hugging Face (HF) enable this evolving ecosystem, yet a large-scale longitudinal study of how these models change is lacking. This study addresses this gap by analyzing over 680,000 commits from 100,000 models and 2,251 releases from 202 of these models on HF using repository mining and longitudinal methods. We apply an extended ML change taxonomy to classify commits and use Bayesian networks to model temporal patterns in commit and release activities. Our findings show that commit activities align with established data science methodologies, such as the Cross-Industry Standard Process for Data Mining (CRISP-DM), emphasizing iterative refinement. Release patterns tend to consolidate significant updates, particularly in model outputs, sharing, and documentation, distinguishing them from granular commits. Furthermore, projects with higher popularity exhibit distinct evolutionary paths, often starting from a more mature baseline with fewer foundational commits in their public history. In contrast, those with intensive collaboration show unique documentation and technical evolution patterns. These insights enhance the understanding of model changes on community platforms and provide valuable guidance for best practices in model maintenance.

Andrés R. Masegosa, Ana M. Martínez, Darío Ramos-López et al.

The AMIDST Toolbox is a software for scalable probabilistic machine learning with a spe- cial focus on (massive) streaming data. The toolbox supports a flexible modeling language based on probabilistic graphical models with latent variables and temporal dependencies. The specified models can be learnt from large data sets using parallel or distributed implementa- tions of Bayesian learning algorithms for either streaming or batch data. These algorithms are based on a flexible variational message passing scheme, which supports discrete and continu- ous variables from a wide range of probability distributions. AMIDST also leverages existing functionality and algorithms by interfacing to software tools such as Flink, Spark, MOA, Weka, R and HUGIN. AMIDST is an open source toolbox written in Java and available at http://www.amidsttoolbox.com under the Apache Software License version 2.0.

Anna Rodum Bjøru, Rafael Cabañas, Helge Langseth et al.

Recently, Bjøru et al. proposed a novel divide-and-conquer algorithm for bounding counterfactual probabilities in structural causal models (SCMs). They assumed that the SCMs were learned from purely observational data, leading to an imprecise characterization of the marginal distributions of exogenous variables. Their method leveraged the canonical representation of structural equations to decompose a general SCM with high-cardinality exogenous variables into a set of sub-models with low-cardinality exogenous variables. These sub-models had precise marginals over the exogenous variables and therefore admitted efficient exact inference. The aggregated results were used to bound counterfactual probabilities in the original model. The approach was developed for Markovian models, where each exogenous variable affects only a single endogenous variable. In this paper, we investigate extending the methodology to \textit{semi-Markovian} SCMs, where exogenous variables may influence multiple endogenous variables. Such models are capable of representing confounding relationships that Markovian models cannot. We illustrate the challenges of this extension using a minimal example, which motivates a set of alternative solution strategies. These strategies are evaluated both theoretically and through a computational study.

Rafael Cabañas, Ana D. Maldonado, María Morales et al.

Causal and counterfactual reasoning are emerging directions in data science that allow us to reason about hypothetical scenarios. This is particularly useful in fields like environmental and ecological sciences, where interventional data are usually not available. Structural causal models are probabilistic models for causal analysis that simplify this kind of reasoning due to their graphical representation. They can be regarded as extensions of the so-called Bayesian networks, a well known modeling tool commonly used in environmental and ecological problems. The main contribution of this paper is to analyze the relations of necessity and sufficiency between the variables of a socioecological system using counterfactual reasoning with Bayesian networks. In particular, we consider a case study involving socioeconomic factors and land-uses in southern Spain. In addition, this paper aims to be a coherent overview of the fundamental concepts for applying counterfactual reasoning, so that environmental researchers with a background in Bayesian networks can easily take advantage of the structural causal model formalism.

Luis A. Ortega, Rafael Cabañas, Andrés R. Masegosa

Ensembles are widely used in machine learning and, usually, provide state-of-the-art performance in many prediction tasks. From the very beginning, the diversity of an ensemble has been identified as a key factor for the superior performance of these models. But the exact role that diversity plays in ensemble models is poorly understood, specially in the context of neural networks. In this work, we combine and expand previously published results in a theoretically sound framework that describes the relationship between diversity and ensemble performance for a wide range of ensemble methods. More precisely, we provide sound answers to the following questions: how to measure diversity, how diversity relates to the generalization error of an ensemble, and how diversity is promoted by neural network ensemble algorithms. This analysis covers three widely used loss functions, namely, the squared loss, the cross-entropy loss, and the 0-1 loss; and two widely used model combination strategies, namely, model averaging and weighted majority vote. We empirically validate this theoretical analysis with neural network ensembles.

Rafael Cabañas, Alessandro Antonucci

Credal networks are a popular class of imprecise probabilistic graphical models obtained as a Bayesian network generalization based on, so-called credal, sets of probability mass functions. A Java library called CREMA has been recently released to model, process and query credal networks. Despite the NP-hardness of the (exact) task, a number of algorithms is available to approximate credal network inferences. In this paper we present CREPO, an open repository of synthetic credal networks, provided together with the exact results of inference tasks on these models. A Python tool is also delivered to load these data and interact with CREMA, thus making extremely easy to evaluate and compare existing and novel inference algorithms. To demonstrate such benchmarking scheme, we propose an approximate heuristic to be used inside variable elimination schemes to keep a bound on the maximum number of vertices generated during the combination step. A CREPO-based validation against approximate procedures based on linearization and exact techniques performed in CREMA is finally discussed.

Marco Zaffalon, Alessandro Antonucci, Rafael Cabañas

Structural causal models are the basic modelling unit in Pearl's causal theory; in principle they allow us to solve counterfactuals, which are at the top rung of the ladder of causation. But they often contain latent variables that limit their application to special settings. This appears to be a consequence of the fact, proven in this paper, that causal inference is NP-hard even in models characterised by polytree-shaped graphs. To deal with such a hardness, we introduce the causal EM algorithm. Its primary aim is to reconstruct the uncertainty about the latent variables from data about categorical manifest variables. Counterfactual inference is then addressed via standard algorithms for Bayesian networks. The result is a general method to approximately compute counterfactuals, be they identifiable or not (in which case we deliver bounds). We show empirically, as well as by deriving credible intervals, that the approximation we provide becomes accurate in a fair number of EM runs. These results lead us finally to argue that there appears to be an unnoticed limitation to the trending idea that counterfactual bounds can often be computed without knowledge of the structural equations.

Marco Zaffalon, Alessandro Antonucci, Rafael Cabañas

A structural causal model is made of endogenous (manifest) and exogenous (latent) variables. We show that endogenous observations induce linear constraints on the probabilities of the exogenous variables. This allows to exactly map a causal model into a credal network. Causal inferences, such as interventions and counterfactuals, can consequently be obtained by standard algorithms for the updating of credal nets. These natively return sharp values in the identifiable case, while intervals corresponding to the exact bounds are produced for unidentifiable queries. A characterization of the causal models that allow the map above to be compactly derived is given, along with a discussion about the scalability for general models. This contribution should be regarded as a systematic approach to represent structural causal models by credal networks and hence to systematically compute causal inferences. A number of demonstrative examples is presented to clarify our methodology. Extensive experiments show that approximate algorithms for credal networks can immediately be used to do causal inference in real-size problems.

Javier Cózar, Rafael Cabañas, Antonio Salmerón et al.

InferPy is a Python package for probabilistic modeling with deep neural networks. It defines a user-friendly API that trades-off model complexity with ease of use, unlike other libraries whose focus is on dealing with very general probabilistic models at the cost of having a more complex API. In particular, this package allows to define, learn and evaluate general hierarchical probabilistic models containing deep neural networks in a compact and simple way. InferPy is built on top of Tensorflow Probability and Keras.

Andrés R. Masegosa, Rafael Cabañas, Helge Langseth et al.

Recent advances in statistical inference have significantly expanded the toolbox of probabilistic modeling. Historically, probabilistic modeling has been constrained to (i) very restricted model classes where exact or approximate probabilistic inference were feasible, and (ii) small or medium-sized data sets which fit within the main memory of the computer. However, developments in variational inference, a general form of approximate probabilistic inference originated in statistical physics, are allowing probabilistic modeling to overcome these restrictions: (i) Approximate probabilistic inference is now possible over a broad class of probabilistic models containing a large number of parameters, and (ii) scalable inference methods based on stochastic gradient descent and distributed computation engines allow to apply probabilistic modeling over massive data sets. One important practical consequence of these advances is the possibility to include deep neural networks within a probabilistic model to capture complex non-linear stochastic relationships between random variables. These advances in conjunction with the release of novel probabilistic modeling toolboxes have greatly expanded the scope of application of probabilistic models, and allow these models to take advantage of the recent strides made by the deep learning community. In this paper we review the main concepts, methods and tools needed to use deep neural networks within a probabilistic modeling framework.