arXiv subjects

Johan Pensar

Publications and source records attributed to Johan Pensar.

At least 19 recordsLinked to original sources

arXiv2026

path_boost: A Python Package for Interpretable Graph-Level Prediction using Path-Based Gradient Boosting

We present path_boost, a Python package for interpretable supervised learning on graph-structured input data. The package implements PathBoost, a gradient boosting algorithm that automatically discovers predictive labeled paths within graphs during the learning process. Unlike graph neural networks, which are generally difficult to interpret, PathBoost produces an additive prediction model over path-based features that explicitly reveals which substructures drive predictions. To avoid an exhaustive enumeration of all possible paths, the algorithm iteratively selects and extends paths during learning based on their predictive power, using boosting to combine weak learners into a strong ensemble. The package supports both regression and binary classification. Key features include compatibility with scikit-learn workflows, support for custom base learners and selectors, automatic starting node selection, parallel training across anchor nodes, and built-in variable importance computation. We demonstrate PathBoost on molecular property prediction of transition metal compounds, where atoms serve as nodes and bonds as edges, and further benchmark PathBoost against an established graph neural network and a graph kernel method across six molecular datasets. The package is available on PyPI and GitHub under an open-source license.

cs.LG↗

arXiv2026

Path-Based Gradient Boosting for Graph-Level Prediction

We propose PathBoost, a gradient tree boosting method for graph-level classification and regression that learns discriminative path-based features directly from the input graph structure. Building on a previous work, which was tailored to a specific chemistry application, PathBoost introduces three key extensions: (i) adaptation to binary classification through gradient boosting with a logistic loss, (ii) incorporation of multiple node and edge attributes into the path feature space via a prefix-based decomposition, and (iii) automatic anchor node selection based on categorical attribute diversity, eliminating the need for the user to specify the starting point of the considered path features. We compared PathBoost to graph neural networks and graph kernel approaches on several benchmark datasets, obtaining better results in half of them, and comparable results in the rest. PathBoost shows better performances on graphs with larger average node counts. Overall, the results demonstrate that path-based boosting methods can be competitive with more complex black-box approaches.

cs.LG↗

arXiv2026

tmQM-RDF Dataset: a Knowledge Graph Representing Transition Metal Complexes

Transition Metal Complexes (TMCs) have wide-ranging practical utility in chemistry, with possible applications that range from catalysis to medicinal chemistry. The study of TMCs and their properties is thus a field rich with potential, one in which machine learning and computational approaches can offer a substantial aid. For this reason, appropriate and accessible datasets, collecting a wide range of information, are required in order to facilitate the effective analysis and investigation of such compounds. This paper contributes to the data modelling effort via the introduction of the transition metal quantum mechanics RDF (tmQM-RDF) dataset, a knowledge graph constructed using the Resource Description Framework (RDF) vocabulary which collects rich and detailed descriptions of approximately 50k TMCs. These descriptions are both qualitative and quantitative in nature, encompassing the compositional nature of TMCs in terms of their constituting ligands, as well as the entirety of their molecular graphs. An example of the power of the proposed representation is presented, showcasing how the information available in tmQM-RDF can be exploited for TMC manipulation tasks, achieving promising performance even with relatively simple probabilistic models.

physics.chem-ph↗

arXiv2025

Causal inference amid missingness-specific independencies and mechanism shifts

The recovery of causal effects in structural models with missing data often relies on $m$-graphs, which assume that missingness mechanisms do not directly influence substantive variables. Yet, in many real-world settings, missing data can alter decision-making processes, as the absence of key information may affect downstream actions and states. To overcome this limitation, we introduce $lm$-SCMs and $lm$-graphs, which extend $m$-graphs by integrating a label set that represents relevant context-specific independencies (CSI), accounting for mechanism shifts induced by missingness. We define two causal effects within these systems: the Full Average Treatment Effect (FATE), which reflects the effect in a hypothetical scenario had no data been missing, and the Natural Average Treatment Effect (NATE), which captures the effect under the unaltered CSIs in the system. We propose recovery criteria for these queries and present doubly-robust estimators for a graphical model inspired by a real-world application. Simulations highlight key differences between these estimands and estimation methods. Findings from the application case suggest a small effect of ADHD treatment upon test achievement among Norwegian children, with a slight effect shift due to missing pre-tests scores.

stat.ME↗

arXiv2025

Bayesian estimation of causal effects from observational categorical data

We present a Bayesian procedure for estimation of pairwise intervention effects in a high-dimensional system of categorical variables. We assume that we have observational data generated from an unknown causal Bayesian network for which there are no latent confounders. Most of the existing methods developed for this setting assume that the underlying model is linear Gaussian, including the Bayesian IDA (BIDA) method that we build upon in this work. By combining a Bayesian backdoor estimator with model averaging, we obtain a posterior over the intervention distributions of a cause-effect pair that can be expressed as a mixture over stochastic linear combinations of Dirichlet distributions. Although there is no closed-form expression for the posterior density, it is straightforward to produce Monte Carlo approximations of target quantities through direct sampling, and we also derive closed-form expressions for a few selected moments. To scale up the proposed procedure, we employ Markov Chain Monte Carlo (MCMC), which also enables us to use more efficient adjustment sets compared to the current exact BIDA. Finally, we use Jensen-Shannon divergence to define a novel causal effect based on a set of intervention distributions in the general categorical setting. We compare our method to the original IDA method and existing Bayesian approaches in numerical simulations and show that categorical BIDA performs favorably against the existing alternative methods in terms of producing point estimates and discovering strong effects.

stat.ME↗

arXiv2025

The Probability of Tiered Benefit: Partial Identification with Robust and Stable Inference

We define the Probability of Tiered Benefit in scenarios with a binary exposure and an outcome that is either categorical with $K \geq 2$ ordered tiers or continuous partitioned by $K-1$ fixed thresholds into disjoint intervals. Similarly to other pure counterfactual queries, this parameter is not $g$-identifiable without additional assumptions. We demonstrate that strong monotonicity does not suffice for point identification when $K \geq 3$ and provide sharp bounds both with and without such constraint. Inference and uncertainty quantification for these bounds are challenging tasks due to potential nonregularity induced by ambiguities in the underlying individualized optimization problems. Such ambiguities can arise from immunities or null treatment effects in subpopulations with positive probability, affecting the lower bound estimate and hindering conservative inference. To address these issues, we extend the available Stabilized One-Step Correction (S1S) procedure by incorporating stratum-specific stabilizing matrices. Through simulations, we illustrate the benefits of this approach over existing alternatives. We apply our method to estimate bounds on the probabilities of tiered benefit and harm from pharmacological treatment for ADHD upon academic achievement, employing observational data from diagnosed Norwegian schoolchildren. Our findings indicate that while girls and children with low prior test performance could have moderate chances of both benefit and harm from treatment, a clear-cut recommendation remains uncertain across all strata.

stat.ME↗

arXiv2024

Recovery and inference of causal effects with sequential adjustment for confounding and attrition

Confounding bias and selection bias bring two significant challenges to the validity of conclusions drawn from applied causal inference. The latter can stem from informative missingness, such as in cases of attrition. We introduce the Sequential Adjustment Criteria (SAC), which extend available graphical conditions for recovering causal effects from confounding and attrition using sequential regressions, allowing for the inclusion of post-exposure and forbidden variables in the adjustment sets. We propose an estimator for the recovered Average Treatment Effect (ATE) based on Targeted Minimum-Loss Estimation (TMLE), which exhibits multiple robustness under certain technical conditions. This approach ensures consistency even in scenarios where the Double Inverse Probability Weighting (DIPW) and the naive plug-in sequential regressions approaches fall short. Through a simulation study, we assess the performance of the proposed estimator against alternative methods across different graph setups and model specification scenarios. As a motivating application, we examine the effect of pharmacological treatment for Attention-Deficit/Hyperactivity Disorder (ADHD) upon the scores obtained by diagnosed Norwegian schoolchildren in national tests using observational data ($n=9\,352$). Our findings align with the accumulated clinical evidence, affirming a positive but small impact of medication on academic achievement.

stat.ME↗

arXiv2023

Uncertainty quantification in automated valuation models with spatially weighted conformal prediction

Non-parametric machine learning models, such as random forests and gradient boosted trees, are frequently used to estimate house prices due to their predictive accuracy, but a main drawback of such methods is their limited ability to quantify prediction uncertainty. Conformal prediction (CP) is a model-agnostic framework for constructing confidence sets around predictions of machine learning models with minimal assumptions. However, due to the spatial dependencies observed in house prices, direct application of CP leads to confidence sets that are not calibrated everywhere, i.e., the confidence sets will be too large in certain geographical regions and too small in others. We survey various approaches to adjust the CP confidence set to account for this and demonstrate their performance on a data set from the housing market in Oslo, Norway. Our findings indicate that calibrating the confidence sets on a spatially weighted version of the non-conformity scores makes the coverage more consistently calibrated across geographical regions. We also perform a simulation study on synthetically generated sale prices to empirically explore the performance of CP on housing market data under idealized conditions with known data-generating mechanisms.

stat.ML↗

arXiv2022

DagSim: Combining DAG-based model structure with unconstrained data types and relations for flexible, transparent, and modularized data simulation

Data simulation is fundamental for machine learning and causal inference, as it allows exploration of scenarios and assessment of methods in settings with full control of ground truth. Directed acyclic graphs (DAGs) are well established for encoding the dependence structure over a collection of variables in both inference and simulation settings. However, while modern machine learning is applied to data of an increasingly complex nature, DAG-based simulation frameworks are still confined to settings with relatively simple variable types and functional forms. We here present DagSim, a Python-based framework for DAG-based data simulation without any constraints on variable types or functional relations. A succinct YAML format for defining the simulation model structure promotes transparency, while separate user-provided functions for generating each variable based on its parents ensure simulation code modularization. We illustrate the capabilities of DagSim through use cases where metadata variables control shapes in an image and patterns in bio-sequences.

cs.AI↗

arXiv2022

Improving generalization of machine learning-identified biomarkers with causal modeling: an investigation into immune receptor diagnostics

Machine learning is increasingly used to discover diagnostic and prognostic biomarkers from high-dimensional molecular data. However, a variety of factors related to experimental design may affect the ability to learn generalizable and clinically applicable diagnostics. Here, we argue that a causal perspective improves the identification of these challenges and formalizes their relation to the robustness and generalization of machine learning-based diagnostics. To make for a concrete discussion, we focus on a specific, recently established high-dimensional biomarker - adaptive immune receptor repertoires (AIRRs). Through simulations, we illustrate how major biological and experimental factors of the AIRR domain may influence the learned biomarkers. In conclusion, we argue that causal modeling improves machine learning-based biomarker robustness by identifying stable relations between variables and by guiding the adjustment of the relations and variables that vary between populations.

q-bio.QM↗

arXiv2021

Structure Learning of Contextual Markov Networks using Marginal Pseudo-likelihood

Markov networks are popular models for discrete multivariate systems where the dependence structure of the variables is specified by an undirected graph. To allow for more expressive dependence structures, several generalizations of Markov networks have been proposed. Here we consider the class of contextual Markov networks which takes into account possible context-specific independences among pairs of variables. Structure learning of contextual Markov networks is very challenging due to the extremely large number of possible structures. One of the main challenges has been to design a score, by which a structure can be assessed in terms of model fit related to complexity, without assuming chordality. Here we introduce the marginal pseudo-likelihood as an analytically tractable criterion for general contextual Markov networks. Our criterion is shown to yield a consistent structure estimator. Experiments demonstrate the favorable properties of our method in terms of predictive accuracy of the inferred models.

stat.ME↗

arXiv2020

High-dimensional structure learning of sparse vector autoregressive models using fractional marginal pseudo-likelihood

Learning vector autoregressive models from multivariate time series is conventionally approached through least squares or maximum likelihood estimation. These methods typically assume a fully connected model which provides no direct insight to the model structure and may lead to highly noisy estimates of the parameters. Because of these limitations, there has been an increasing interest towards methods that produce sparse estimates through penalized regression. However, such methods are computationally intensive and may become prohibitively time-consuming when the number of variables in the model increases. In this paper we adopt an approximate Bayesian approach to the learning problem by combining fractional marginal likelihood and pseudo-likelihood. We propose a novel method, PLVAR, that is both faster and produces more accurate estimates than the state-of-the-art methods based on penalized regression. We prove the consistency of the PLVAR estimator and demonstrate the attractive performance of the method on both simulated and real-world data.

stat.CO↗

arXiv2020

Towards Scalable Bayesian Learning of Causal DAGs

We give methods for Bayesian inference of directed acyclic graphs, DAGs, and the induced causal effects from passively observed complete data. Our methods build on a recent Markov chain Monte Carlo scheme for learning Bayesian networks, which enables efficient approximate sampling from the graph posterior, provided that each node is assigned a small number $K$ of candidate parents. We present algorithmic techniques to significantly reduce the space and time requirements, which make the use of substantially larger values of $K$ feasible. Furthermore, we investigate the problem of selecting the candidate parents per node so as to maximize the covered posterior mass. Finally, we combine our sampling method with a novel Bayesian approach for estimating causal effects in linear Gaussian DAG models. Numerical experiments demonstrate the performance of our methods in detecting ancestor-descendant relations, and in causal effect estimation our Bayesian method is shown to outperform previous approaches.

cs.LG↗

arXiv2019

Learning pairwise Markov network structures using correlation neighborhoods

Markov networks are widely studied and used throughout multivariate statistics and computer science. In particular, the problem of learning the structure of Markov networks from data without invoking chordality assumptions in order to retain expressiveness of the model class has been given a considerable attention in the recent literature, where numerous constraint-based or score-based methods have been introduced. Here we develop a new search algorithm for the network score-optimization that has several computational advantages and scales well to high-dimensional data sets. The key observation behind the algorithm is that the neighborhood of a variable can be efficiently captured using local penalized likelihood ratio (PLR) tests by exploiting an exponential decay of correlations across the neighborhood with an increasing graph-theoretic distance from the focus node. The candidate neighborhoods are then processed by a two-stage hill-climbing (HC) algorithm. Our approach, termed fully as PLRHC-BIC$_{0.5}$, compares favorably against the state-of-the-art methods in all our experiments spanning both low- and high-dimensional networks and a wide range of sample sizes. An efficient implementation of PLRHC-BIC$_{0.5}$ is freely available from the URL: https://github.com/jurikuronen/plrhc.

stat.ML↗

arXiv2019

High-dimensional structure learning of binary pairwise Markov networks: A comparative numerical study

Learning the undirected graph structure of a Markov network from data is a problem that has received a lot of attention during the last few decades. As a result of the general applicability of the model class, a myriad of methods have been developed in parallel in several research fields. Recently, as the size of the considered systems has increased, the focus of new methods has been shifted towards the high-dimensional domain. In particular, introduction of the pseudo-likelihood function has pushed the limits of score-based methods which were originally based on the likelihood function. At the same time, methods based on simple pairwise tests have been developed to meet the challenges arising from increasingly large data sets in computational biology. Apart from being applicable to high-dimensional problems, methods based on the pseudo-likelihood and pairwise tests are fundamentally very different. To compare the accuracy of the different types of methods, an extensive numerical study is performed on data generated by binary pairwise Markov networks. A parallelizable Gibbs sampler, based on restricted Boltzmann machines, is proposed as a tool to efficiently sample from sparse high-dimensional networks. The results of the study show that pairwise methods can be more accurate than pseudo-likelihood methods in settings often encountered in high-dimensional structure learning applications.

stat.CO↗

arXiv2016

Learning Gaussian Graphical Models With Fractional Marginal Pseudo-likelihood

We propose a Bayesian approximate inference method for learning the dependence structure of a Gaussian graphical model. Using pseudo-likelihood, we derive an analytical expression to approximate the marginal likelihood for an arbitrary graph structure without invoking any assumptions about decomposability. The majority of the existing methods for learning Gaussian graphical models are either restricted to decomposable graphs or require specification of a tuning parameter that may have a substantial impact on learned structures. By combining a simple sparsity inducing prior for the graph structures with a default reference prior for the model parameters, we obtain a fast and easily applicable scoring function that works well for even high-dimensional data. We demonstrate the favourable performance of our approach by large-scale comparisons against the leading methods for learning non-decomposable Gaussian graphical models. A theoretical justification for our method is provided by showing that it yields a consistent estimator of the graph structure.

stat.ML↗

arXiv2014

Context-specific independence in graphical log-linear models

Log-linear models are the popular workhorses of analyzing contingency tables. A log-linear parameterization of an interaction model can be more expressive than a direct parameterization based on probabilities, leading to a powerful way of defining restrictions derived from marginal, conditional and context-specific independence. However, parameter estimation is often simpler under a direct parameterization, provided that the model enjoys certain decomposability properties. Here we introduce a cyclical projection algorithm for obtaining maximum likelihood estimates of log-linear parameters under an arbitrary context-specific graphical log-linear model, which needs not satisfy criteria of decomposability. We illustrate that lifting the restriction of decomposability makes the models more expressive, such that additional context-specific independencies embedded in real data can be identified. It is also shown how a context-specific graphical model can correspond to a non-hierarchical log-linear parameterization with a concise interpretation. This observation can pave way to further development of non-hierarchical log-linear models, which have been largely neglected due to their believed lack of interpretability.

stat.ML↗

arXiv2014

Stratified Gaussian Graphical Models

Gaussian graphical models represent the backbone of the statistical toolbox for analyzing continuous multivariate systems. However, due to the intrinsic properties of the multivariate normal distribution, use of this model family may hide certain forms of context-specific independence that are natural to consider from an applied perspective. Such independencies have been earlier introduced to generalize discrete graphical models and Bayesian networks into more flexible model families. Here we adapt the idea of context-specific independence to Gaussian graphical models by introducing a stratification of the Euclidean space such that a conditional independence may hold in certain segments but be absent elsewhere. It is shown that the stratified models define a curved exponential family, which retains considerable tractability for parameter estimation and model selection.

math.ST↗