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Ricardo Silva

Ricardo Silva appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Machine LearningMethodologyArtificial IntelligenceApplicationsphysics.soc-phComputationComputer Visioneess.SPQuantitative Methods

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Published work

25 published item(s)

preprint2026arXiv

Correcting heterogeneous diagnostic bias when developing clinical prediction models using causal hidden Markov models

In routine care, individuals identified a priori as high-risk are usually tested for conditions more frequently. Protected attributes, such as sex or ethnicity may also determine testing frequency. Such heterogeneous detection rates across a population induce label error. This causes systematic model error for specific groups and biases performance metrics during validation. This paper proposes a method to correct for such bias in prediction models due to differential diagnostic delay. We use a causal inference framework to define our target estimand: an individual's diagnosis probability in a counterfactual scenario where their diagnosis rate matches that of a reference group. We model the longitudinal process as a hidden Markov model, in which confirmatory test results are emissions from a latent progressive disease stage. We validate our approach in simulated data and apply it to a case study of chronic kidney disease prediction using electronic health records. In simulations, our method reduces prediction bias and improves calibration-in-the-large, correcting the Observed:Expected ratio in the underdiagnosed group from 1.34 (standard deviation: 0.09) in a model developed without any correction for underdiagnosis bias to 1.02 (0.09). Violations of assumptions in the simulation affected the estimation of model parameters, but the proposed approach nonetheless remained better calibrated than the standard model. In the clinical case study, we identify diabetes as the main driver of observability, with an odds ratio of 10.36 (95% confidence interval, 9.80 - 11.02) in 6-month urine albumin-creatinine ratio testing rate. Using our approach to predict the counterfactual diagnostic rate in patients without diabetes, we improved the Observed:Expected ratio of a developed clinical prediction model from 1.55 (1.51 - 1.59) to 1.01 (0.98 - 1.04).

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

IV-ICL: Bounding Causal Effects with Instrumental Variables via In-Context Learning

The instrumental-variables (IV) setting is standard for partial identification of causal effects when unobserved confounding makes point identification impossible. Existing approaches face methodological bottlenecks: closed-form bound estimands are required -- e.g., Balke-Pearl equations in binary IV -- and even when available, designing accurate estimators requires manual effort tailored to each estimand. While direct Bayesian inference of the causal effects, instead of the bounds, circumvents these challenges, it is often computationally intensive and suffers from high prior sensitivity or under-dispersed posteriors. As a remedy, we introduce IV-ICL, an amortized Bayesian in-context learning method that learns the marginal posterior distribution of the causal effects directly and derives bounds as its quantiles. Unlike standard variational inference that optimizes exclusive KL divergence, amortized Bayesian inference minimizes the expected inclusive KL, a mass-covering objective. We empirically observe that optimizing inclusive KL can recover the entire identified set across diverse data-generating processes, while exclusive-KL (e.g. with variational inference) of the same Bayesian formulation collapses onto a single mode and fails to cover the identified set. We evaluate IV-ICL on synthetic and semi-synthetic IV benchmarks and show it produces intervals that are more reliably valid and more informative compared to efficient semi-parametric, Bayesian, and plug-in baselines, at 20-500x lower inference time. Beyond methodology, we propose a procedure to convert randomized controlled trials into IV benchmarks with provably preserved ground-truth causal effects that enables a more realistic evaluation of partial-identification methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Causal discovery under a confounder blanket

Inferring causal relationships from observational data is rarely straightforward, but the problem is especially difficult in high dimensions. For these applications, causal discovery algorithms typically require parametric restrictions or extreme sparsity constraints. We relax these assumptions and focus on an important but more specialized problem, namely recovering the causal order among a subgraph of variables known to descend from some (possibly large) set of confounding covariates, i.e. a $\textit{confounder blanket}$. This is useful in many settings, for example when studying a dynamic biomolecular subsystem with genetic data providing background information. Under a structural assumption called the $\textit{confounder blanket principle}$, which we argue is essential for tractable causal discovery in high dimensions, our method accommodates graphs of low or high sparsity while maintaining polynomial time complexity. We present a structure learning algorithm that is provably sound and complete with respect to a so-called $\textit{lazy oracle}$. We design inference procedures with finite sample error control for linear and nonlinear systems, and demonstrate our approach on a range of simulated and real-world datasets. An accompanying $\texttt{R}$ package, $\texttt{cbl}$, is available from $\texttt{CRAN}$.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Causal Inference with Treatment Measurement Error: A Nonparametric Instrumental Variable Approach

We propose a kernel-based nonparametric estimator for the causal effect when the cause is corrupted by error. We do so by generalizing estimation in the instrumental variable setting. Despite significant work on regression with measurement error, additionally handling unobserved confounding in the continuous setting is non-trivial: we have seen little prior work. As a by-product of our investigation, we clarify a connection between mean embeddings and characteristic functions, and how learning one simultaneously allows one to learn the other. This opens the way for kernel method research to leverage existing results in characteristic function estimation. Finally, we empirically show that our proposed method, MEKIV, improves over baselines and is robust under changes in the strength of measurement error and to the type of error distributions.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

FCN-Pose: A Pruned and Quantized CNN for Robot Pose Estimation for Constrained Devices

IoT devices suffer from resource limitations, such as processor, RAM, and disc storage. These limitations become more evident when handling demanding applications, such as deep learning, well-known for their heavy computational requirements. A case in point is robot pose estimation, an application that predicts the critical points of the desired image object. One way to mitigate processing and storage problems is compressing that deep learning application. This paper proposes a new CNN for the pose estimation while applying the compression techniques of pruning and quantization to reduce his demands and improve the response time. While the pruning process reduces the total number of parameters required for inference, quantization decreases the precision of the floating-point. We run the approach using a pose estimation task for a robotic arm and compare the results in a high-end device and a constrained device. As metrics, we consider the number of Floating-point Operations Per Second(FLOPS), the total of mathematical computations, the calculation of parameters, the inference time, and the number of video frames processed per second. In addition, we undertake a qualitative evaluation where we compare the output image predicted for each pruned network with the corresponding original one. We reduce the originally proposed network to a 70% pruning rate, implying an 88.86% reduction in parameters, 94.45% reduction in FLOPS, and for the disc storage, we reduced the requirement in 70% while increasing error by a mere $1\%$. With regard input image processing, this metric increases from 11.71 FPS to 41.9 FPS for the Desktop case. When using the constrained device, image processing augmented from 2.86 FPS to 10.04 FPS. The higher processing rate of image frames achieved by the proposed approach allows a much shorter response time.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

The Causal Marginal Polytope for Bounding Treatment Effects

Due to unmeasured confounding, it is often not possible to identify causal effects from a postulated model. Nevertheless, we can ask for partial identification, which usually boils down to finding upper and lower bounds of a causal quantity of interest derived from all solutions compatible with the encoded structural assumptions. One appealing way to derive such bounds is by casting it in terms of a constrained optimization method that searches over all causal models compatible with evidence, as introduced in the classic work of Balke and Pearl (1994) for discrete data. Although by construction this guarantees tight bounds, it poses a formidable computational challenge. To cope with this issue, alternatives include algorithms that are not guaranteed to be tight, or by introducing restrictions on the class of models. In this paper, we introduce a novel alternative: inspired by ideas coming from belief propagation, we enforce compatibility between marginals of a causal model and data, without constructing a global causal model. We call this collection of locally consistent marginals the causal marginal polytope. As global independence constraints disappear when considering small dimensional tractable marginals, this also leads to a rethinking of how to elicit and express causal knowledge. We provide an explicit algorithm and implementation of this idea, and assess its practicality with numerical experiments.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

A Bayesian inference approach for determining player abilities in football

We consider the task of determining a football player's ability for a given event type, for example, scoring a goal. We propose an interpretable Bayesian model which is fit using variational inference methods. We implement a Poisson model to capture occurrences of event types, from which we infer player abilities. Our approach also allows the visualisation of differences between players, for a specific ability, through the marginal posterior variational densities. We then use these inferred player abilities to extend the Bayesian hierarchical model of Baio and Blangiardo (2010) which captures a team's scoring rate (the rate at which they score goals). We apply the resulting scheme to the English Premier League, capturing player abilities over the 2013/2014 season, before using output from the hierarchical model to predict whether over or under 2.5 goals will be scored in a given game in the 2014/2015 season. This validates our model as a way of providing insights into team formation and the individual success of sports teams.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Differentiable Causal Backdoor Discovery

Discovering the causal effect of a decision is critical to nearly all forms of decision-making. In particular, it is a key quantity in drug development, in crafting government policy, and when implementing a real-world machine learning system. Given only observational data, confounders often obscure the true causal effect. Luckily, in some cases, it is possible to recover the causal effect by using certain observed variables to adjust for the effects of confounders. However, without access to the true causal model, finding this adjustment requires brute-force search. In this work, we present an algorithm that exploits auxiliary variables, similar to instruments, in order to find an appropriate adjustment by a gradient-based optimization method. We demonstrate that it outperforms practical alternatives in estimating the true causal effect, without knowledge of the full causal graph.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Learning Joint Nonlinear Effects from Single-variable Interventions in the Presence of Hidden Confounders

We propose an approach to estimate the effect of multiple simultaneous interventions in the presence of hidden confounders. To overcome the problem of hidden confounding, we consider the setting where we have access to not only the observational data but also sets of single-variable interventions in which each of the treatment variables is intervened on separately. We prove identifiability under the assumption that the data is generated from a nonlinear continuous structural causal model with additive Gaussian noise. In addition, we propose a simple parameter estimation method by pooling all the data from different regimes and jointly maximizing the combined likelihood. We also conduct comprehensive experiments to verify the identifiability result as well as to compare the performance of our approach against a baseline on both synthetic and real-world data.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Neural Likelihoods via Cumulative Distribution Functions

We leverage neural networks as universal approximators of monotonic functions to build a parameterization of conditional cumulative distribution functions (CDFs). By the application of automatic differentiation with respect to response variables and then to parameters of this CDF representation, we are able to build black box CDF and density estimators. A suite of families is introduced as alternative constructions for the multivariate case. At one extreme, the simplest construction is a competitive density estimator against state-of-the-art deep learning methods, although it does not provide an easily computable representation of multivariate CDFs. At the other extreme, we have a flexible construction from which multivariate CDF evaluations and marginalizations can be obtained by a simple forward pass in a deep neural net, but where the computation of the likelihood scales exponentially with dimensionality. Alternatives in between the extremes are discussed. We evaluate the different representations empirically on a variety of tasks involving tail area probabilities, tail dependence and (partial) density estimation.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Neural Network Approximation of Graph Fourier Transforms for Sparse Sampling of Networked Flow Dynamics

Infrastructure monitoring is critical for safe operations and sustainability. Water distribution networks (WDNs) are large-scale networked critical systems with complex cascade dynamics which are difficult to predict. Ubiquitous monitoring is expensive and a key challenge is to infer the contaminant dynamics from partial sparse monitoring data. Existing approaches use multi-objective optimisation to find the minimum set of essential monitoring points, but lack performance guarantees and a theoretical framework. Here, we first develop Graph Fourier Transform (GFT) operators to compress networked contamination spreading dynamics to identify the essential principle data collection points with inference performance guarantees. We then build autoencoder (AE) inspired neural networks (NN) to generalize the GFT sampling process and under-sample further from the initial sampling set, allowing a very small set of data points to largely reconstruct the contamination dynamics over real and artificial WDNs. Various sources of the contamination are tested and we obtain high accuracy reconstruction using around 5-10% of the sample set. This general approach of compression and under-sampled recovery via neural networks can be applied to a wide range of networked infrastructures to enable digital twins.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Observational-Interventional Priors for Dose-Response Learning

Controlled interventions provide the most direct source of information for learning causal effects. In particular, a dose-response curve can be learned by varying the treatment level and observing the corresponding outcomes. However, interventions can be expensive and time-consuming. Observational data, where the treatment is not controlled by a known mechanism, is sometimes available. Under some strong assumptions, observational data allows for the estimation of dose-response curves. Estimating such curves nonparametrically is hard: sample sizes for controlled interventions may be small, while in the observational case a large number of measured confounders may need to be marginalized. In this paper, we introduce a hierarchical Gaussian process prior that constructs a distribution over the dose-response curve by learning from observational data, and reshapes the distribution with a nonparametric affine transform learned from controlled interventions. This function composition from different sources is shown to speed-up learning, which we demonstrate with a thorough sensitivity analysis and an application to modeling the effect of therapy on cognitive skills of premature infants.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Scaling Factorial Hidden Markov Models: Stochastic Variational Inference without Messages

Factorial Hidden Markov Models (FHMMs) are powerful models for sequential data but they do not scale well with long sequences. We propose a scalable inference and learning algorithm for FHMMs that draws on ideas from the stochastic variational inference, neural network and copula literatures. Unlike existing approaches, the proposed algorithm requires no message passing procedure among latent variables and can be distributed to a network of computers to speed up learning. Our experiments corroborate that the proposed algorithm does not introduce further approximation bias compared to the proven structured mean-field algorithm, and achieves better performance with long sequences and large FHMMs.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Bayesian Inference in Cumulative Distribution Fields

One approach for constructing copula functions is by multiplication. Given that products of cumulative distribution functions (CDFs) are also CDFs, an adjustment to this multiplication will result in a copula model, as discussed by Liebscher (J Mult Analysis, 2008). Parameterizing models via products of CDFs has some advantages, both from the copula perspective (e.g., it is well-defined for any dimensionality) and from general multivariate analysis (e.g., it provides models where small dimensional marginal distributions can be easily read-off from the parameters). Independently, Huang and Frey (J Mach Learn Res, 2011) showed the connection between certain sparse graphical models and products of CDFs, as well as message-passing (dynamic programming) schemes for computing the likelihood function of such models. Such schemes allows models to be estimated with likelihood-based methods. We discuss and demonstrate MCMC approaches for estimating such models in a Bayesian context, their application in copula modeling, and how message-passing can be strongly simplified. Importantly, our view of message-passing opens up possibilities to scaling up such methods, given that even dynamic programming is not a scalable solution for calculating likelihood functions in many models.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Learning Instrumental Variables with Non-Gaussianity Assumptions: Theoretical Limitations and Practical Algorithms

Learning a causal effect from observational data is not straightforward, as this is not possible without further assumptions. If hidden common causes between treatment $X$ and outcome $Y$ cannot be blocked by other measurements, one possibility is to use an instrumental variable. In principle, it is possible under some assumptions to discover whether a variable is structurally instrumental to a target causal effect $X \rightarrow Y$, but current frameworks are somewhat lacking on how general these assumptions can be. A instrumental variable discovery problem is challenging, as no variable can be tested as an instrument in isolation but only in groups, but different variables might require different conditions to be considered an instrument. Moreover, identification constraints might be hard to detect statistically. In this paper, we give a theoretical characterization of instrumental variable discovery, highlighting identifiability problems and solutions, the need for non-Gaussianity assumptions, and how they fit within existing methods.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Causal Inference through a Witness Protection Program

One of the most fundamental problems in causal inference is the estimation of a causal effect when variables are confounded. This is difficult in an observational study, because one has no direct evidence that all confounders have been adjusted for. We introduce a novel approach for estimating causal effects that exploits observational conditional independencies to suggest "weak" paths in a unknown causal graph. The widely used faithfulness condition of Spirtes et al. is relaxed to allow for varying degrees of "path cancellations" that imply conditional independencies but do not rule out the existence of confounding causal paths. The outcome is a posterior distribution over bounds on the average causal effect via a linear programming approach and Bayesian inference. We claim this approach should be used in regular practice along with other default tools in observational studies.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Gaussian Process Structural Equation Models with Latent Variables

In a variety of disciplines such as social sciences, psychology, medicine and economics, the recorded data are considered to be noisy measurements of latent variables connected by some causal structure. This corresponds to a family of graphical models known as the structural equation model with latent variables. While linear non-Gaussian variants have been well-studied, inference in nonparametric structural equation models is still underdeveloped. We introduce a sparse Gaussian process parameterization that defines a non-linear structure connecting latent variables, unlike common formulations of Gaussian process latent variable models. The sparse parameterization is given a full Bayesian treatment without compromising Markov chain Monte Carlo efficiency. We compare the stability of the sampling procedure and the predictive ability of the model against the current practice.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Flexible sampling of discrete data correlations without the marginal distributions

Learning the joint dependence of discrete variables is a fundamental problem in machine learning, with many applications including prediction, clustering and dimensionality reduction. More recently, the framework of copula modeling has gained popularity due to its modular parametrization of joint distributions. Among other properties, copulas provide a recipe for combining flexible models for univariate marginal distributions with parametric families suitable for potentially high dimensional dependence structures. More radically, the extended rank likelihood approach of Hoff (2007) bypasses learning marginal models completely when such information is ancillary to the learning task at hand as in, e.g., standard dimensionality reduction problems or copula parameter estimation. The main idea is to represent data by their observable rank statistics, ignoring any other information from the marginals. Inference is typically done in a Bayesian framework with Gaussian copulas, and it is complicated by the fact this implies sampling within a space where the number of constraints increases quadratically with the number of data points. The result is slow mixing when using off-the-shelf Gibbs sampling. We present an efficient algorithm based on recent advances on constrained Hamiltonian Markov chain Monte Carlo that is simple to implement and does not require paying for a quadratic cost in sample size.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Ranking relations using analogies in biological and information networks

Analogical reasoning depends fundamentally on the ability to learn and generalize about relations between objects. We develop an approach to relational learning which, given a set of pairs of objects $\mathbf{S}=\{A^{(1)}:B^{(1)},A^{(2)}:B^{(2)},\ldots,A^{(N)}:B ^{(N)}\}$, measures how well other pairs A:B fit in with the set $\mathbf{S}$. Our work addresses the following question: is the relation between objects A and B analogous to those relations found in $\mathbf{S}$? Such questions are particularly relevant in information retrieval, where an investigator might want to search for analogous pairs of objects that match the query set of interest. There are many ways in which objects can be related, making the task of measuring analogies very challenging. Our approach combines a similarity measure on function spaces with Bayesian analysis to produce a ranking. It requires data containing features of the objects of interest and a link matrix specifying which relationships exist; no further attributes of such relationships are necessary. We illustrate the potential of our method on text analysis and information networks. An application on discovering functional interactions between pairs of proteins is discussed in detail, where we show that our approach can work in practice even if a small set of protein pairs is provided.

0 citations0 reviewsNo code linkedOpen access
preprint2012arXiv

Bayesian Inference for Gaussian Mixed Graph Models

We introduce priors and algorithms to perform Bayesian inference in Gaussian models defined by acyclic directed mixed graphs. Such a class of graphs, composed of directed and bi-directed edges, is a representation of conditional independencies that is closed under marginalization and arises naturally from causal models which allow for unmeasured confounding. Monte Carlo methods and a variational approximation for such models are presented. Our algorithms for Bayesian inference allow the evaluation of posterior distributions for several quantities of interest, including causal effects that are not identifiable from data alone but could otherwise be inferred where informative prior knowledge about confounding is available.

0 citations0 reviewsNo code linkedOpen access
preprint2012arXiv

Latent Composite Likelihood Learning for the Structured Canonical Correlation Model

Latent variable models are used to estimate variables of interest quantities which are observable only up to some measurement error. In many studies, such variables are known but not precisely quantifiable (such as "job satisfaction" in social sciences and marketing, "analytical ability" in educational testing, or "inflation" in economics). This leads to the development of measurement instruments to record noisy indirect evidence for such unobserved variables such as surveys, tests and price indexes. In such problems, there are postulated latent variables and a given measurement model. At the same time, other unantecipated latent variables can add further unmeasured confounding to the observed variables. The problem is how to deal with unantecipated latents variables. In this paper, we provide a method loosely inspired by canonical correlation that makes use of background information concerning the "known" latent variables. Given a partially specified structure, it provides a structure learning approach to detect "unknown unknowns," the confounding effect of potentially infinitely many other latent variables. This is done without explicitly modeling such extra latent factors. Because of the special structure of the problem, we are able to exploit a new variation of composite likelihood fitting to efficiently learn this structure. Validation is provided with experiments in synthetic data and the analysis of a large survey done with a sample of over 100,000 staff members of the National Health Service of the United Kingdom.

0 citations0 reviewsNo code linkedOpen access
preprint2012arXiv

Learning Measurement Models for Unobserved Variables

Observed associations in a database may be due in whole or part to variations in unrecorded (latent) variables. Identifying such variables and their causal relationships with one another is a principal goal in many scientific and practical domains. Previous work shows that, given a partition of observed variables such that members of a class share only a single latent common cause, standard search algorithms for causal Bayes nets can infer structural relations between latent variables. We introduce an algorithm for discovering such partitions when they exist. Uniquely among available procedures, the algorithm is (asymptotically) correct under standard assumptions in causal Bayes net search algorithms, requires no prior knowledge of the number of latent variables, and does not depend on the mathematical form of the relationships among the latent variables. We evaluate the algorithm on a variety of simulated data sets.

0 citations0 reviewsNo code linkedOpen access
preprint2010arXiv

Gaussian Process Structural Equation Models with Latent Variables

In a variety of disciplines such as social sciences, psychology, medicine and economics, the recorded data are considered to be noisy measurements of latent variables connected by some causal structure. This corresponds to a family of graphical models known as the structural equation model with latent variables. While linear non-Gaussian variants have been well-studied, inference in nonparametric structural equation models is still underdeveloped. We introduce a sparse Gaussian process parameterization that defines a non-linear structure connecting latent variables, unlike common formulations of Gaussian process latent variable models. The sparse parameterization is given a full Bayesian treatment without compromising Markov chain Monte Carlo efficiency. We compare the stability of the sampling procedure and the predictive ability of the model against the current practice.

0 citations0 reviewsNo code linkedOpen access
preprint2010arXiv

Measuring Latent Causal Structure

Discovering latent representations of the observed world has become increasingly more relevant in data analysis. Much of the effort concentrates on building latent variables which can be used in prediction problems, such as classification and regression. A related goal of learning latent structure from data is that of identifying which hidden common causes generate the observations, such as in applications that require predicting the effect of policies. This will be the main problem tackled in our contribution: given a dataset of indicators assumed to be generated by unknown and unmeasured common causes, we wish to discover which hidden common causes are those, and how they generate our data. This is possible under the assumption that observed variables are linear functions of the latent causes with additive noise. Previous results in the literature present solutions for the case where each observed variable is a noisy function of a single latent variable. We show how to extend the existing results for some cases where observed variables measure more than one latent variable.

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preprint2010arXiv

Mixed Cumulative Distribution Networks

Directed acyclic graphs (DAGs) are a popular framework to express multivariate probability distributions. Acyclic directed mixed graphs (ADMGs) are generalizations of DAGs that can succinctly capture much richer sets of conditional independencies, and are especially useful in modeling the effects of latent variables implicitly. Unfortunately there are currently no good parameterizations of general ADMGs. In this paper, we apply recent work on cumulative distribution networks and copulas to propose one one general construction for ADMG models. We consider a simple parameter estimation approach, and report some encouraging experimental results.

0 citations0 reviewsNo code linkedOpen access