Emilie Devijver

Clément Yvernes, Emilie Devijver, Marianne Clausel et al.

The do-calculus defines a general system of inference for interventional queries, allowing causal quantities to be transformed through successive applications of its rules. This process induces a rich space of equivalent interventional expressions, but combining and ordering these rules remains challenging. In this work, we introduce derivation graphs, which represent how do-calculus rules are applied and combined, and characterize the full space of observational and interventional probabilities which are equivalent under the do-calculus. The structure of these graphs yields a simple procedure that uses at most four applications of do-calculus rules. Finally, we show how applying identification algorithms to equivalent causal queries produces multiple valid estimands for the same causal quantity, eventually yielding more efficient estimators.

Daria Bystrova, Charles K. Assaad, Julyan Arbel et al.

Constraint-based methods and noise-based methods are two distinct families of methods proposed for uncovering causal graphs from observational data. However, both operate under strong assumptions that may be challenging to validate or could be violated in real-world scenarios. In response to these challenges, there is a growing interest in hybrid methods that amalgamate principles from both methods, showing robustness to assumption violations. This paper introduces a novel comprehensive framework for hybridizing constraint-based and noise-based methods designed to uncover causal graphs from observational time series. The framework is structured into two classes. The first class employs a noise-based strategy to identify a super graph, containing the true graph, followed by a constraint-based strategy to eliminate unnecessary edges. In the second class, a constraint-based strategy is applied to identify a skeleton, which is then oriented using a noise-based strategy. The paper provides theoretical guarantees for each class under the condition that all assumptions are satisfied, and it outlines some properties when assumptions are violated. To validate the efficacy of the framework, two algorithms from each class are experimentally tested on simulated data, realistic ecological data, and real datasets sourced from diverse applications. Notably, two novel datasets related to Information Technology monitoring are introduced within the set of considered real datasets. The experimental results underscore the robustness and effectiveness of the hybrid approaches across a broad spectrum of datasets.

Charles K. Assaad, Emilie Devijver, Eric Gaussier et al.

We study the problem of identifiability of the total effect of an intervention from observational time series in the situation, common in practice, where one only has access to abstractions of the true causal graph. We consider here two abstractions: the extended summary causal graph, which conflates all lagged causal relations but distinguishes between lagged and instantaneous relations, and the summary causal graph which does not give any indication about the lag between causal relations. We show that the total effect is always identifiable in extended summary causal graphs and provide sufficient conditions for identifiability in summary causal graphs. We furthermore provide adjustment sets allowing to estimate the total effect whenever it is identifiable.

Ali Aït-Bachir, Charles K. Assaad, Christophe de Bignicourt et al.

Information technology (IT) systems are vital for modern businesses, handling data storage, communication, and process automation. Monitoring these systems is crucial for their proper functioning and efficiency, as it allows collecting extensive observational time series data for analysis. The interest in causal discovery is growing in IT monitoring systems as knowing causal relations between different components of the IT system helps in reducing downtime, enhancing system performance and identifying root causes of anomalies and incidents. It also allows proactive prediction of future issues through historical data analysis. Despite its potential benefits, applying causal discovery algorithms on IT monitoring data poses challenges, due to the complexity of the data. For instance, IT monitoring data often contains misaligned time series, sleeping time series, timestamp errors and missing values. This paper presents case studies on applying causal discovery algorithms to different IT monitoring datasets, highlighting benefits and ongoing challenges.

Lies Hadjadj, Emilie Devijver, Remi Molinier et al.

Machine learning methods usually rely on large sample size to have good performance, while it is difficult to provide labeled set in many applications. Pool-based active learning methods are there to detect, among a set of unlabeled data, the ones that are the most relevant for the training. We propose in this paper a meta-approach for pool-based active learning strategies in the context of multi-class classification tasks based on Proper Topological Regions. PTR, based on topological data analysis (TDA), are relevant regions used to sample cold-start points or within the active learning scheme. The proposed method is illustrated empirically on various benchmark datasets, being competitive to the classical methods from the literature.

Clément Yvernes, Emilie Devijver, Adèle H. Ribeiro et al.

Cluster DAGs (C-DAGs) provide an abstraction of causal graphs in which nodes represent clusters of variables, and edges encode both cluster-level causal relationships and dependencies arisen from unobserved confounding. C-DAGs define an equivalence class of acyclic causal graphs that agree on cluster-level relationships, enabling causal reasoning at a higher level of abstraction. However, when the chosen clustering induces cycles in the resulting C-DAG, the partition is deemed inadmissible under conventional C-DAG semantics. In this work, we extend the C-DAG framework to support arbitrary variable clusterings by relaxing the partition admissibility constraint, thereby allowing cyclic C-DAG representations. We extend the notions of d-separation and causal calculus to this setting, significantly broadening the scope of causal reasoning across clusters and enabling the application of C-DAGs in previously intractable scenarios. Our calculus is both sound and atomically complete with respect to the do-calculus: all valid interventional queries at the cluster level can be derived using our rules, each corresponding to a primitive do-calculus step.

Charles K. Assaad, Emilie Devijver, Eric Gaussier

This study addresses the problem of learning an extended summary causal graph on time series. The algorithms we propose fit within the well-known constraint-based framework for causal discovery and make use of information-theoretic measures to determine (in)dependencies between time series. We first introduce generalizations of the causation entropy measure to any lagged or instantaneous relations, prior to using this measure to construct extended summary causal graphs by adapting two well-known algorithms, namely PC and FCI. The behavior of our methods is illustrated through several experiments run on simulated and real datasets.

Clément Yvernes, Emilie Devijver, Eric Gaussier

The identifiability problem for interventions aims at assessing whether the total causal effect can be written with a do-free formula, and thus be estimated from observational data only. We study this problem, considering multiple interventions, in the context of time series when only an abstraction of the true causal graph, in the form of a summary causal graph, is available. We propose in particular both necessary and sufficient conditions for the adjustment criterion, which we show is complete in this setting, and provide a pseudo-linear algorithm to decide whether the query is identifiable or not.

Lei Zan, Charles K. Assaad, Emilie Devijver et al.

This paper introduces a new structural causal model tailored for representing threshold-based IT systems and presents a new algorithm designed to rapidly detect root causes of anomalies in such systems. When root causes are not causally related, the method is proven to be correct; while an extension is proposed based on the intervention of an agent to relax this assumption. Our algorithm and its agent-based extension leverage causal discovery from offline data and engage in subgraph traversal when encountering new anomalies in online data. Our extensive experiments demonstrate the superior performance of our methods, even when applied to data generated from alternative structural causal models or real IT monitoring data.

Morad Laglil, Emilie Devijver, Eric Gaussier et al.

Inspired by recent advances in large language models, foundation models have been developed for zero-shot time series forecasting, enabling prediction on datasets unseen during pretraining. These large-scale models, trained on vast collections of time series, learn generalizable representations for both point and probabilistic forecasting, reducing the need for task-specific architectures and manual tuning. In this work, we review the main architectures, pretraining strategies, and optimization methods used in such models, and study the effect of fine-tuning after pretraining to enhance their performance on specific datasets. Our empirical results show that fine-tuning generally improves zero-shot forecasting capabilities, especially for long-term horizons.

Clément Yvernes, Emilie Devijver, Marianne Clausel et al.

Identifying the effect of a treatment from observational data typically requires assuming a fully specified causal diagram. However, such diagrams are rarely known in practice, especially in complex or high-dimensional settings. To overcome this limitation, recent works have explored the use of causal abstractions-simplified representations that retain partial causal information. In this paper, we consider causal abstractions formalized as collections of causal diagrams, and focus on the identifiability of causal queries within such collections. We introduce and formalize several identifiability criteria under this setting. Our main contribution is to organize these criteria into a structured hierarchy, highlighting their relationships. This hierarchical view enables a clearer understanding of what can be identified under varying levels of causal knowledge. We illustrate our framework through examples from the literature and provide tools to reason about identifiability when full causal knowledge is unavailable.

Clément Yvernes, Charles K. Assaad, Emilie Devijver et al.

The identifiability problem for interventions aims at assessing whether the total effect of some given interventions can be written with a do-free formula, and thus be computed from observational data only. We study this problem, considering multiple interventions and multiple effects, in the context of time series when only abstractions of the true causal graph in the form of summary causal graphs are available. We focus in this study on identifiability by a common backdoor set, and establish, for time series with and without consistency throughout time, conditions under which such a set exists. We also provide algorithms of limited complexity to decide whether the problem is identifiable or not.

Alexandre Seiller, Éric Gaussier, Emilie Devijver et al.

Tree-based ensemble methods such as random forests, gradient-boosted trees, and Bayesianadditive regression trees have been successfully used for regression problems in many applicationsand research studies. In this paper, we study ensemble versions of probabilisticregression trees that provide smooth approximations of the objective function by assigningeach observation to each region with respect to a probability distribution. We prove thatthe ensemble versions of probabilistic regression trees considered are consistent, and experimentallystudy their bias-variance trade-off and compare them with the state-of-the-art interms of performance prediction.

Ashna Jose, Emilie Devijver, Massih-Reza Amini et al.

Supervised machine learning often requires large training sets to train accurate models, yet obtaining large amounts of labeled data is not always feasible. Hence, it becomes crucial to explore active learning methods for reducing the size of training sets while maintaining high accuracy. The aim is to select the optimal subset of data for labeling from an initial unlabeled set, ensuring precise prediction of outcomes. However, conventional active learning approaches are comparable to classical random sampling. This paper proposes a wrapper active learning method for classification, organizing the sampling process into a tree structure, that improves state-of-the-art algorithms. A classification tree constructed on an initial set of labeled samples is considered to decompose the space into low-entropy regions. Input-space based criteria are used thereafter to sub-sample from these regions, the total number of points to be labeled being decomposed into each region. This adaptation proves to be a significant enhancement over existing active learning methods. Through experiments conducted on various benchmark data sets, the paper demonstrates the efficacy of the proposed framework by being effective in constructing accurate classification models, even when provided with a severely restricted labeled data set.

Massih-Reza Amini, Vasilii Feofanov, Loic Pauletto et al.

Semi-supervised algorithms aim to learn prediction functions from a small set of labeled observations and a large set of unlabeled observations. Because this framework is relevant in many applications, they have received a lot of interest in both academia and industry. Among the existing techniques, self-training methods have undoubtedly attracted greater attention in recent years. These models are designed to find the decision boundary on low density regions without making additional assumptions about the data distribution, and use the unsigned output score of a learned classifier, or its margin, as an indicator of confidence. The working principle of self-training algorithms is to learn a classifier iteratively by assigning pseudo-labels to the set of unlabeled training samples with a margin greater than a certain threshold. The pseudo-labeled examples are then used to enrich the labeled training data and to train a new classifier in conjunction with the labeled training set. In this paper, we present self-training methods for binary and multi-class classification; as well as their variants and two related approaches, namely consistency-based approaches and transductive learning. We examine the impact of significant self-training features on various methods, using different general and image classification benchmarks, and we discuss our ideas for future research in self-training. To the best of our knowledge, this is the first thorough and complete survey on this subject.

Vasilii Feofanov, Emilie Devijver, Massih-Reza Amini

Self-learning is a classical approach for learning with both labeled and unlabeled observations which consists in giving pseudo-labels to unlabeled training instances with a confidence score over a predetermined threshold. At the same time, the pseudo-labeling technique is prone to error and runs the risk of adding noisy labels into unlabeled training data. In this paper, we present a probabilistic framework for analyzing self-learning in the multi-class classification scenario with partially labeled data. First, we derive a transductive bound over the risk of the multi-class majority vote classifier. Based on this result, we propose to automatically choose the threshold for pseudo-labeling that minimizes the transductive bound. Then, we introduce a mislabeling error model to analyze the error of the majority vote classifier in the case of the pseudo-labeled data. We derive a probabilistic C-bound over the majority vote error when an imperfect label is given. Empirical results on different data sets show the effectiveness of our framework compared to several state-of-the-art semi-supervised approaches.

Charles K. Assaad, Emilie Devijver, Eric Gaussier

This study addresses the problem of learning a summary causal graph on time series with potentially different sampling rates. To do so, we first propose a new causal temporal mutual information measure for time series. We then show how this measure relates to an entropy reduction principle that can be seen as a special case of the probability raising principle. We finally combine these two ingredients in PC-like and FCI-like algorithms to construct the summary causal graph. There algorithm are evaluated on several datasets, which shows both their efficacy and efficiency.

Vasilii Feofanov, Emilie Devijver, Massih-Reza Amini

In this paper, we propose a new wrapper feature selection approach with partially labeled training examples where unlabeled observations are pseudo-labeled using the predictions of an initial classifier trained on the labeled training set. The wrapper is composed of a genetic algorithm for proposing new feature subsets, and an evaluation measure for scoring the different feature subsets. The selection of feature subsets is done by assigning weights to characteristics and recursively eliminating those that are irrelevant. The selection criterion is based on a new multi-class $\mathcal{C}$-bound that explicitly takes into account the mislabeling errors induced by the pseudo-labeling mechanism, using a probabilistic error model. Empirical results on different data sets show the effectiveness of our framework compared to several state-of-the-art semi-supervised feature selection approaches.

Myriam Tami, Marianne Clausel, Emilie Devijver et al.

Tree-based ensemble methods, as Random Forests and Gradient Boosted Trees, have been successfully used for regression in many applications and research studies. Furthermore, these methods have been extended in order to deal with uncertainty in the output variable, using for example a quantile loss in Random Forests (Meinshausen, 2006). To the best of our knowledge, no extension has been provided yet for dealing with uncertainties in the input variables, even though such uncertainties are common in practical situations. We propose here such an extension by showing how standard regression trees optimizing a quadratic loss can be adapted and learned while taking into account the uncertainties in the inputs. By doing so, one no longer assumes that an observation lies into a single region of the regression tree, but rather that it belongs to each region with a certain probability. Experiments conducted on several data sets illustrate the good behavior of the proposed extension.

Emilie Devijver, Mélina Gallopin, Emeline Perthame

Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological observations might be heterogeneous and correspond to different biological mechanisms. Secondly, the gene expression variables used to predict the phenotype are potentially highly correlated since genes interact though unknown regulatory networks. In this paper, we present a novel approach designed to predict quantitative trait from transcriptomic data, taking into account the heterogeneity in biological samples and the hidden gene regulatory networks underlying different biological mechanisms. The proposed model performs well on prediction but it is also fully parametric, which facilitates the downstream biological interpretation. The model provides clusters of individuals based on the relation between gene expression data and the phenotype, and also leads to infer a gene regulatory network specific for each cluster of individuals. We perform numerical simulations to demonstrate that our model is competitive with other prediction models, and we demonstrate the predictive performance and the interpretability of our model to predict alcohol sensitivity from transcriptomic data on real data from Drosophila Melanogaster Genetic Reference Panel (DGRP).

Emilie Devijver, Mélina Gallopin

Gaussian graphical models are widely utilized to infer and visualize networks of dependencies between continuous variables. However, inferring the graph is difficult when the sample size is small compared to the number of variables. To reduce the number of parameters to estimate in the model, we propose a non-asymptotic model selection procedure supported by strong theoretical guarantees based on an oracle inequality and a minimax lower bound. The covariance matrix of the model is approximated by a block-diagonal matrix. The structure of this matrix is detected by thresholding the sample covariance matrix, where the threshold is selected using the slope heuristic. Based on the block-diagonal structure of the covariance matrix, the estimation problem is divided into several independent problems: subsequently, the network of dependencies between variables is inferred using the graphical lasso algorithm in each block. The performance of the procedure is illustrated on simulated data. An application to a real gene expression dataset with a limited sample size is also presented: the dimension reduction allows attention to be objectively focused on interactions among smaller subsets of genes, leading to a more parsimonious and interpretable modular network.