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Pablo M. Olmos

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Published work

15 published item(s)

preprint2026arXiv

Order-Agnostic Autoregressive Modelling with Missing Data

Order-Agnostic autoregressive models have demonstrated strong performance in deep generative modeling, yet their use in settings with incomplete data remains largely unexplored. In this work, we reinterpret them through the lens of missing data. First, we show that their standard training procedure on fully observed data implicitly performs imputation under a missing completely at random mechanism, resulting in robust out-of-sample imputation performance in settings with high missingness. Second, we introduce the first principled framework for training them directly on incomplete datasets under general missingness mechanisms. Third, we leverage their amortized conditional density estimation to perform active information acquisition, i.e., sequentially selecting the most informative missing variables for downstream prediction or inference. Across a suite of real-world benchmarks, our Missingness-Aware Order-Agnostic Autoregressive Model (MO-ARM) consistently outperforms established imputation baselines.

preprint2022arXiv

Multi-task longitudinal forecasting with missing values on Alzheimer's Disease

Machine learning techniques typically applied to dementia forecasting lack in their capabilities to jointly learn several tasks, handle time dependent heterogeneous data and missing values. In this paper, we propose a framework using the recently presented SSHIBA model for jointly learning different tasks on longitudinal data with missing values. The method uses Bayesian variational inference to impute missing values and combine information of several views. This way, we can combine different data-views from different time-points in a common latent space and learn the relations between each time-point while simultaneously modelling and predicting several output variables. We apply this model to predict together diagnosis, ventricle volume, and clinical scores in dementia. The results demonstrate that SSHIBA is capable of learning a good imputation of the missing values and outperforming the baselines while simultaneously predicting three different tasks.

preprint2022arXiv

PyHHMM: A Python Library for Heterogeneous Hidden Markov Models

We introduce PyHHMM, an object-oriented open-source Python implementation of Heterogeneous-Hidden Markov Models (HHMMs). In addition to HMM's basic core functionalities, such as different initialization algorithms and classical observations models, i.e., continuous and multinoulli, PyHHMM distinctively emphasizes features not supported in similar available frameworks: a heterogeneous observation model, missing data inference, different model order selection criterias, and semi-supervised training. These characteristics result in a feature-rich implementation for researchers working with sequential data. PyHHMM relies on the numpy, scipy, scikit-learn, and seaborn Python packages, and is distributed under the Apache-2.0 License. PyHHMM's source code is publicly available on Github (https://github.com/fmorenopino/HeterogeneousHMM) to facilitate adoptions and future contributions. A detailed documentation (https://pyhhmm.readthedocs.io/en/latest), which covers examples of use and models' theoretical explanation, is available. The package can be installed through the Python Package Index (PyPI), via 'pip install pyhhmm'.

preprint2021arXiv

Bayesian Sparse Factor Analysis with Kernelized Observations

Multi-view problems can be faced with latent variable models since they are able to find low-dimensional projections that fairly capture the correlations among the multiple views that characterise each datum. On the other hand, high-dimensionality and non-linear issues are traditionally handled by kernel methods, inducing a (non)-linear function between the latent projection and the data itself. However, they usually come with scalability issues and exposition to overfitting. Here, we propose merging both approaches into single model so that we can exploit the best features of multi-view latent models and kernel methods and, moreover, overcome their limitations. In particular, we combine probabilistic factor analysis with what we refer to as kernelized observations, in which the model focuses on reconstructing not the data itself, but its relationship with other data points measured by a kernel function. This model can combine several types of views (kernelized or not), and it can handle heterogeneous data and work in semi-supervised settings. Additionally, by including adequate priors, it can provide compact solutions for the kernelized observations -- based in a automatic selection of Bayesian Relevance Vectors (RVs) -- and can include feature selection capabilities. Using several public databases, we demonstrate the potential of our approach (and its extensions) w.r.t. common multi-view learning models such as kernel canonical correlation analysis or manifold relevance determination.

preprint2020arXiv

Handling Incomplete Heterogeneous Data using VAEs

Variational autoencoders (VAEs), as well as other generative models, have been shown to be efficient and accurate for capturing the latent structure of vast amounts of complex high-dimensional data. However, existing VAEs can still not directly handle data that are heterogenous (mixed continuous and discrete) or incomplete (with missing data at random), which is indeed common in real-world applications. In this paper, we propose a general framework to design VAEs suitable for fitting incomplete heterogenous data. The proposed HI-VAE includes likelihood models for real-valued, positive real valued, interval, categorical, ordinal and count data, and allows accurate estimation (and potentially imputation) of missing data. Furthermore, HI-VAE presents competitive predictive performance in supervised tasks, outperforming supervised models when trained on incomplete data.

preprint2020arXiv

Improved BiGAN training with marginal likelihood equalization

We propose a novel training procedure for improving the performance of generative adversarial networks (GANs), especially to bidirectional GANs. First, we enforce that the empirical distribution of the inverse inference network matches the prior distribution, which favors the generator network reproducibility on the seen samples. Second, we have found that the marginal log-likelihood of the samples shows a severe overrepresentation of a certain type of samples. To address this issue, we propose to train the bidirectional GAN using a non-uniform sampling for the mini-batch selection, resulting in improved quality and variety in generated samples measured quantitatively and by visual inspection. We illustrate our new procedure with the well-known CIFAR10, Fashion MNIST and CelebA datasets.

preprint2020arXiv

Sparse Semi-supervised Heterogeneous Interbattery Bayesian Analysis

The Bayesian approach to feature extraction, known as factor analysis (FA), has been widely studied in machine learning to obtain a latent representation of the data. An adequate selection of the probabilities and priors of these bayesian models allows the model to better adapt to the data nature (i.e. heterogeneity, sparsity), obtaining a more representative latent space. The objective of this article is to propose a general FA framework capable of modelling any problem. To do so, we start from the Bayesian Inter-Battery Factor Analysis (BIBFA) model, enhancing it with new functionalities to be able to work with heterogeneous data, include feature selection, and handle missing values as well as semi-supervised problems. The performance of the proposed model, Sparse Semi-supervised Heterogeneous Interbattery Bayesian Analysis (SSHIBA) has been tested on 4 different scenarios to evaluate each one of its novelties, showing not only a great versatility and an interpretability gain, but also outperforming most of the state-of-the-art algorithms.

preprint2016arXiv

Finite-length scaling based on belief propagation for spatially coupled LDPC codes

The equivalence of peeling decoding (PD) and Belief Propagation (BP) for low-density parity-check (LDPC) codes over the binary erasure channel is analyzed. Modifying the scheduling for PD, it is shown that exactly the same variable nodes (VNs) are resolved in every iteration than with BP. The decrease of erased VNs during the decoding process is analyzed instead of resolvable equations. This quantity can also be derived with density evolution, resulting in a drastic decrease in complexity. Finally, a scaling law using this quantity is established for spatially coupled LDPC codes.

preprint2015arXiv

A Scaling Law to Predict the Finite-Length Performance of Spatially-Coupled LDPC Codes

Spatially-coupled LDPC codes are known to have excellent asymptotic properties. Much less is known regarding their finite-length performance. We propose a scaling law to predict the error probability of finite-length spatially-coupled ensembles when transmission takes place over the binary erasure channel. We discuss how the parameters of the scaling law are connected to fundamental quantities appearing in the asymptotic analysis of these ensembles and we verify that the predictions of the scaling law fit well to the data derived from simulations over a wide range of parameters. The ultimate goal of this line of research is to develop analytic tools for the design of spatially-coupled LDPC codes under practical constraints.

preprint2015arXiv

On Distributed Storage Allocations for Memory-Limited Systems

In this paper we consider distributed allocation problems with memory constraint limits. Firstly, we propose a tractable relaxation to the problem of optimal symmetric allocations from [1]. The approximated problem is based on the Q-error function, and its solution approaches the solution of the initial problem, as the number of storage nodes in the network grows. Secondly, exploiting this relaxation, we are able to formulate and to solve the problem for storage allocations for memory-limited DSS storing and arbitrary memory profiles. Finally, we discuss the extension to the case of multiple data objects, stored in the DSS.

preprint2014arXiv

Improving the Finite-Length Performance of Spatially Coupled LDPC Codes by Connecting Multiple Code Chains

In this paper, we analyze the finite-length performance of codes on graphs constructed by connecting spatially coupled low-density parity-check (SC-LDPC) code chains. Successive (peeling) decoding is considered for the binary erasure channel (BEC). The evolution of the undecoded portion of the bipartite graph remaining after each iteration is analyzed as a dynamical system. When connecting short SC-LDPC chains, we show that, in addition to superior iterative decoding thresholds, connected chain ensembles have better finite-length performance than single chain ensembles of the same rate and length. In addition, we present a novel encoding/transmission scheme to improve the performance of a system using long SC-LDPC chains, where, instead of transmitting codewords corresponding to a single SC-LDPC chain independently, we connect consecutive chains in a multi-layer format to form a connected chain ensemble. We refer to such a transmission scheme to as continuous chain (CC) transmission of SC-LDPC codes. We show that CC transmission can be implemented with no significant increase in encoding/decoding complexity or decoding delay with respect a system using a single SC-LDPC code chain for encoding.

preprint2012arXiv

Tree-Structure Expectation Propagation for LDPC Decoding in Erasure Channels

In this paper we present a new algorithm, denoted as TEP, to decode low-density parity-check (LDPC) codes over the Binary Erasure Channel (BEC). The TEP decoder is derived applying the expectation propagation (EP) algorithm with a tree- structured approximation. Expectation Propagation (EP) is a generalization to Belief Propagation (BP) in two ways. First, it can be used with any exponential family distribution over the cliques in the graph. Second, it can impose additional constraints on the marginal distributions. We use this second property to impose pair-wise marginal constraints in some check nodes of the LDPC code's Tanner graph. The algorithm has the same computational complexity than BP, but it can decode a higher fraction of errors when applied over the BEC. In this paper, we focus on the asymptotic performance of the TEP decoder, as the block size tends to infinity. We describe the TEP decoder by a set of differential equations that represents the residual graph evolution during the decoding process. The solution of these equations yields the capacity of this decoder for a given LDPC ensemble over the BEC. We show that the achieved capacity with the TEP is higher than the BP capacity, at the same computational complexity.

preprint2012arXiv

Tree-Structure Expectation Propagation for LDPC Decoding over the BEC

We present the tree-structure expectation propagation (Tree-EP) algorithm to decode low-density parity-check (LDPC) codes over discrete memoryless channels (DMCs). EP generalizes belief propagation (BP) in two ways. First, it can be used with any exponential family distribution over the cliques in the graph. Second, it can impose additional constraints on the marginal distributions. We use this second property to impose pair-wise marginal constraints over pairs of variables connected to a check node of the LDPC code's Tanner graph. Thanks to these additional constraints, the Tree-EP marginal estimates for each variable in the graph are more accurate than those provided by BP. We also reformulate the Tree-EP algorithm for the binary erasure channel (BEC) as a peeling-type algorithm (TEP) and we show that the algorithm has the same computational complexity as BP and it decodes a higher fraction of errors. We describe the TEP decoding process by a set of differential equations that represents the expected residual graph evolution as a function of the code parameters. The solution of these equations is used to predict the TEP decoder performance in both the asymptotic regime and the finite-length regime over the BEC. While the asymptotic threshold of the TEP decoder is the same as the BP decoder for regular and optimized codes, we propose a scaling law (SL) for finite-length LDPC codes, which accurately approximates the TEP improved performance and facilitates its optimization.

preprint2011arXiv

Scaling Behavior of Convolutional LDPC Ensembles over the BEC

We study the scaling behavior of coupled sparse graph codes over the binary erasure channel. In particular, let 2L+1 be the length of the coupled chain, let M be the number of variables in each of the 2L + 1 local copies, let l be the number of iterations, let Pb denote the bit error probability, and let ε denote the channel parameter. We are interested in how these quantities scale when we let the blocklength (2L + 1)M tend to infinity. Based on empirical evidence we show that the threshold saturation phenomenon is rather stable with respect to the scaling of the various parameters and we formulate some general rules of thumb which can serve as a guide for the design of coding systems based on coupled graphs.

preprint2010arXiv

Tree-structure Expectation Propagation for Decoding LDPC codes over Binary Erasure Channels

Expectation Propagation is a generalization to Belief Propagation (BP) in two ways. First, it can be used with any exponential family distribution over the cliques in the graph. Second, it can impose additional constraints on the marginal distributions. We use this second property to impose pair-wise marginal distribution constraints in some check nodes of the LDPC Tanner graph. These additional constraints allow decoding the received codeword when the BP decoder gets stuck. In this paper, we first present the new decoding algorithm, whose complexity is identical to the BP decoder, and we then prove that it is able to decode codewords with a larger fraction of erasures, as the block size tends to infinity. The proposed algorithm can be also understood as a simplification of the Maxwell decoder, but without its computational complexity. We also illustrate that the new algorithm outperforms the BP decoder for finite block-size