arXiv subjects

Gregory F. Cooper

Publications and source records attributed to Gregory F. Cooper.

At least 19 recordsLinked to original sources

arXiv2026

Outlier detection for patient monitoring and alerting

We develop and evaluate a data-driven approach for detecting unusual (anomalous) patient-management decisions using past patient cases stored in electronic health records (EHRs). Our hypothesis is that a patient-management decision that is unusual with respect to past patient care may be due to an error and that it is worthwhile to generate an alert if such a decision is encountered. We evaluate this hypothesis using data obtained from EHRs of 4486 post-cardiac surgical patients and a subset of 222 alerts generated from the data. We base the evaluation on the opinions of a panel of experts. The results of the study support our hypothesis that the outlier-based alerting can lead to promising true alert rates. We observed true alert rates that ranged from 25\% to 66\% for a variety of patient-management actions, with 66\% corresponding to the strongest outliers.

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arXiv2026

Conditional anomaly detection using soft harmonic functions: An application to clinical alerting

Timely detection of concerning events is an important problem in clinical practice. In this paper, we consider the problem of conditional anomaly detection that aims to identify data instances with an unusual response, such as the omission of an important lab test. We develop a new non-parametric approach for conditional anomaly detection based on the soft harmonic solution, with which we estimate the confidence of the label to detect anomalous mislabeling. We further regularize the solution to avoid the detection of isolated examples and examples on the boundary of the distribution support. We demonstrate the efficacy of the proposed method in detecting unusual labels on a real-world electronic health record dataset and compare it to several baseline approaches.

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arXiv2026

Conditional anomaly detection with soft harmonic functions

In this paper, we consider the problem of conditional anomaly detection that aims to identify data instances with an unusual response or a class label. We develop a new non-parametric approach for conditional anomaly detection based on the soft harmonic solution, with which we estimate the confidence of the label to detect anomalous mislabeling. We further regularize the solution to avoid the detection of isolated examples and examples on the boundary of the distribution support. We demonstrate the efficacy of the proposed method on several synthetic and UCI ML datasets in detecting unusual labels when compared to several baseline approaches. We also evaluate the performance of our method on a real-world electronic health record dataset where we seek to identify unusual patient-management decisions.

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arXiv2025

Transportability without Graphs: A Bayesian Approach to Identifying s-Admissible Backdoor Sets

Transporting causal information across populations is a critical challenge in clinical decision-making. Causal modeling provides criteria for identifiability and transportability, but these require knowledge of the causal graph, which rarely holds in practice. We propose a Bayesian method that combines observational data from the target domain with experimental data from a different domain to identify s-admissible backdoor sets, which enable unbiased estimation of causal effects across populations, without requiring the causal graph. We prove that if such a set exists, we can always find one within the Markov boundary of the outcome, narrowing the search space, and we establish asymptotic convergence guarantees for our method. We develop a greedy algorithm that reframes transportability as a feature selection problem, selecting conditioning sets that maximize the marginal likelihood of experimental data given observational data. In simulated and semi-synthetic data, our method correctly identifies transportability bias, improves causal effect estimation, and performs favorably against alternatives.

stat.ML↗

arXiv2024

Online Transfer Learning for RSV Case Detection

Transfer learning has become a pivotal technique in machine learning and has proven to be effective in various real-world applications. However, utilizing this technique for classification tasks with sequential data often faces challenges, primarily attributed to the scarcity of class labels. To address this challenge, we introduce Multi-Source Adaptive Weighting (MSAW), an online multi-source transfer learning method. MSAW integrates a dynamic weighting mechanism into an ensemble framework, enabling automatic adjustment of weights based on the relevance and contribution of each source (representing historical knowledge) and target model (learning from newly acquired data). We demonstrate the effectiveness of MSAW by applying it to detect Respiratory Syncytial Virus cases within Emergency Department visits, utilizing multiple years of electronic health records from the University of Pittsburgh Medical Center. Our method demonstrates performance improvements over many baselines, including refining pre-trained models with online learning as well as three static weighting approaches, showing MSAW's capacity to integrate historical knowledge with progressively accumulated new data. This study indicates the potential of online transfer learning in healthcare, particularly for developing machine learning models that dynamically adapt to evolving situations where new data is incrementally accumulated.

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arXiv2022

The m-connecting imset and factorization for ADMG models

Directed acyclic graph (DAG) models have become widely studied and applied in statistics and machine learning -- indeed, their simplicity facilitates efficient procedures for learning and inference. Unfortunately, these models are not closed under marginalization, making them poorly equipped to handle systems with latent confounding. Acyclic directed mixed graph (ADMG) models characterize margins of DAG models, making them far better suited to handle such systems. However, ADMG models have not seen wide-spread use due to their complexity and a shortage of statistical tools for their analysis. In this paper, we introduce the m-connecting imset which provides an alternative representation for the independence models induced by ADMGs. Furthermore, we define the m-connecting factorization criterion for ADMG models, characterized by a single equation, and prove its equivalence to the global Markov property. The m-connecting imset and factorization criterion provide two new statistical tools for learning and inference with ADMG models. We demonstrate the usefulness of these tools by formulating and evaluating a consistent scoring criterion with a closed form solution.

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arXiv2020

Learning Latent Causal Structures with a Redundant Input Neural Network

Most causal discovery algorithms find causal structure among a set of observed variables. Learning the causal structure among latent variables remains an important open problem, particularly when using high-dimensional data. In this paper, we address a problem for which it is known that inputs cause outputs, and these causal relationships are encoded by a causal network among a set of an unknown number of latent variables. We developed a deep learning model, which we call a redundant input neural network (RINN), with a modified architecture and a regularized objective function to find causal relationships between input, hidden, and output variables. More specifically, our model allows input variables to directly interact with all latent variables in a neural network to influence what information the latent variables should encode in order to generate the output variables accurately. In this setting, the direct connections between input and latent variables makes the latent variables partially interpretable; furthermore, the connectivity among the latent variables in the neural network serves to model their potential causal relationships to each other and to the output variables. A series of simulation experiments provide support that the RINN method can successfully recover latent causal structure between input and output variables.

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arXiv2017

Obtaining Accurate Probabilistic Causal Inference by Post-Processing Calibration

Discovery of an accurate causal Bayesian network structure from observational data can be useful in many areas of science. Often the discoveries are made under uncertainty, which can be expressed as probabilities. To guide the use of such discoveries, including directing further investigation, it is important that those probabilities be well-calibrated. In this paper, we introduce a novel framework to derive calibrated probabilities of causal relationships from observational data. The framework consists of three components: (1) an approximate method for generating initial probability estimates of the edge types for each pair of variables, (2) the availability of a relatively small number of the causal relationships in the network for which the truth status is known, which we call a calibration training set, and (3) a calibration method for using the approximate probability estimates and the calibration training set to generate calibrated probabilities for the many remaining pairs of variables. We also introduce a new calibration method based on a shallow neural network. Our experiments on simulated data support that the proposed approach improves the calibration of causal edge predictions. The results also support that the approach often improves the precision and recall of predictions.

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arXiv2015

Binary Classifier Calibration using an Ensemble of Near Isotonic Regression Models

Learning accurate probabilistic models from data is crucial in many practical tasks in data mining. In this paper we present a new non-parametric calibration method called \textit{ensemble of near isotonic regression} (ENIR). The method can be considered as an extension of BBQ, a recently proposed calibration method, as well as the commonly used calibration method based on isotonic regression. ENIR is designed to address the key limitation of isotonic regression which is the monotonicity assumption of the predictions. Similar to BBQ, the method post-processes the output of a binary classifier to obtain calibrated probabilities. Thus it can be combined with many existing classification models. We demonstrate the performance of ENIR on synthetic and real datasets for the commonly used binary classification models. Experimental results show that the method outperforms several common binary classifier calibration methods. In particular on the real data, ENIR commonly performs statistically significantly better than the other methods, and never worse. It is able to improve the calibration power of classifiers, while retaining their discrimination power. The method is also computationally tractable for large scale datasets, as it is $O(N \log N)$ time, where $N$ is the number of samples.

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arXiv2014

Counting Markov Blanket Structures

Learning Markov blanket (MB) structures has proven useful in performing feature selection, learning Bayesian networks (BNs), and discovering causal relationships. We present a formula for efficiently determining the number of MB structures given a target variable and a set of other variables. As expected, the number of MB structures grows exponentially. However, we show quantitatively that there are many fewer MB structures that contain the target variable than there are BN structures that contain it. In particular, the ratio of BN structures to MB structures appears to increase exponentially in the number of variables.

stat.ML↗

arXiv2014

Binary Classifier Calibration: Non-parametric approach

Accurate calibration of probabilistic predictive models learned is critical for many practical prediction and decision-making tasks. There are two main categories of methods for building calibrated classifiers. One approach is to develop methods for learning probabilistic models that are well-calibrated, ab initio. The other approach is to use some post-processing methods for transforming the output of a classifier to be well calibrated, as for example histogram binning, Platt scaling, and isotonic regression. One advantage of the post-processing approach is that it can be applied to any existing probabilistic classification model that was constructed using any machine-learning method. In this paper, we first introduce two measures for evaluating how well a classifier is calibrated. We prove three theorems showing that using a simple histogram binning post-processing method, it is possible to make a classifier be well calibrated while retaining its discrimination capability. Also, by casting the histogram binning method as a density-based non-parametric binary classifier, we can extend it using two simple non-parametric density estimation methods. We demonstrate the performance of the proposed calibration methods on synthetic and real datasets. Experimental results show that the proposed methods either outperform or are comparable to existing calibration methods.

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arXiv2014

Binary Classifier Calibration: Bayesian Non-Parametric Approach

A set of probabilistic predictions is well calibrated if the events that are predicted to occur with probability p do in fact occur about p fraction of the time. Well calibrated predictions are particularly important when machine learning models are used in decision analysis. This paper presents two new non-parametric methods for calibrating outputs of binary classification models: a method based on the Bayes optimal selection and a method based on the Bayesian model averaging. The advantage of these methods is that they are independent of the algorithm used to learn a predictive model, and they can be applied in a post-processing step, after the model is learned. This makes them applicable to a wide variety of machine learning models and methods. These calibration methods, as well as other methods, are tested on a variety of datasets in terms of both discrimination and calibration performance. The results show the methods either outperform or are comparable in performance to the state-of-the-art calibration methods.

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arXiv2013

Kutato: An Entropy-Driven System for Construction of Probabilistic Expert Systems from Databases

Kutato is a system that takes as input a database of cases and produces a belief network that captures many of the dependence relations represented by those data. This system incorporates a module for determining the entropy of a belief network and a module for constructing belief networks based on entropy calculations. Kutato constructs an initial belief network in which all variables in the database are assumed to be marginally independent. The entropy of this belief network is calculated, and that arc is added that minimizes the entropy of the resulting belief network. Conditional probabilities for an arc are obtained directly from the database. This process continues until an entropy-based threshold is reached. We have tested the system by generating databases from networks using the probabilistic logic-sampling method, and then using those databases as input to Kutato. The system consistently reproduces the original belief networks with high fidelity.

cs.AI↗

arXiv2013

A Randomized Approximation Algorithm of Logic Sampling

In recent years, researchers in decision analysis and artificial intelligence (AI) have used Bayesian belief networks to build models of expert opinion. Using standard methods drawn from the theory of computational complexity, workers in the field have shown that the problem of exact probabilistic inference on belief networks almost certainly requires exponential computation in the worst ease [3]. We have previously described a randomized approximation scheme, called BN-RAS, for computation on belief networks [ 1, 2, 4]. We gave precise analytic bounds on the convergence of BN-RAS and showed how to trade running time for accuracy in the evaluation of posterior marginal probabilities. We now extend our previous results and demonstrate the generality of our framework by applying similar mathematical techniques to the analysis of convergence for logic sampling [7], an alternative simulation algorithm for probabilistic inference.

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arXiv2013

A Combination of Cutset Conditioning with Clique-Tree Propagation in the Pathfinder System

Cutset conditioning and clique-tree propagation are two popular methods for performing exact probabilistic inference in Bayesian belief networks. Cutset conditioning is based on decomposition of a subset of network nodes, whereas clique-tree propagation depends on aggregation of nodes. We describe a means to combine cutset conditioning and clique- tree propagation in an approach called aggregation after decomposition (AD). We discuss the application of the AD method in the Pathfinder system, a medical expert system that offers assistance with diagnosis in hematopathology.

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arXiv2013

An Empirical Analysis of Likelihood-Weighting Simulation on a Large, Multiply-Connected Belief Network

We analyzed the convergence properties of likelihood- weighting algorithms on a two-level, multiply connected, belief-network representation of the QMR knowledge base of internal medicine. Specifically, on two difficult diagnostic cases, we examined the effects of Markov blanket scoring, importance sampling, demonstrating that the Markov blanket scoring and self-importance sampling significantly improve the convergence of the simulation on our model.

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arXiv2013

An Empirical Evaluation of a Randomized Algorithm for Probabilistic Inference

In recent years, researchers in decision analysis and artificial intelligence (Al) have used Bayesian belief networks to build models of expert opinion. Using standard methods drawn from the theory of computational complexity, workers in the field have shown that the problem of probabilistic inference in belief networks is difficult and almost certainly intractable. K N ET, a software environment for constructing knowledge-based systems within the axiomatic framework of decision theory, contains a randomized approximation scheme for probabilistic inference. The algorithm can, in many circumstances, perform efficient approximate inference in large and richly interconnected models of medical diagnosis. Unlike previously described stochastic algorithms for probabilistic inference, the randomized approximation scheme computes a priori bounds on running time by analyzing the structure and contents of the belief network. In this article, we describe a randomized algorithm for probabilistic inference and analyze its performance mathematically. Then, we devote the major portion of the paper to a discussion of the algorithm's empirical behavior. The results indicate that the generation of good trials (that is, trials whose distribution closely matches the true distribution), rather than the computation of numerous mediocre trials, dominates the performance of stochastic simulation. Key words: probabilistic inference, belief networks, stochastic simulation, computational complexity theory, randomized algorithms.

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arXiv2013

Bounded Conditioning: Flexible Inference for Decisions under Scarce Resources

We introduce a graceful approach to probabilistic inference called bounded conditioning. Bounded conditioning monotonically refines the bounds on posterior probabilities in a belief network with computation, and converges on final probabilities of interest with the allocation of a complete resource fraction. The approach allows a reasoner to exchange arbitrary quantities of computational resource for incremental gains in inference quality. As such, bounded conditioning holds promise as a useful inference technique for reasoning under the general conditions of uncertain and varying reasoning resources. The algorithm solves a probabilistic bounding problem in complex belief networks by breaking the problem into a set of mutually exclusive, tractable subproblems and ordering their solution by the expected effect that each subproblem will have on the final answer. We introduce the algorithm, discuss its characterization, and present its performance on several belief networks, including a complex model for reasoning about problems in intensive-care medicine.

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