Recent research has revealed that many machine-learning models and the datasets they are trained on suffer from various forms of bias, and a large number of different fairness metrics have been created to measure this bias. However, determining which metrics to use, as well as interpreting their results, is difficult for a non-expert due to a lack of clear guidance and issues of ambiguity or alternate naming schemes between different research papers. To address this knowledge gap, we present the Fairness Metrics Ontology (FMO), a comprehensive and extensible knowledge resource that defines each fairness metric, describes their use cases, and details the relationships between them. We include additional concepts related to fairness and machine learning models, enabling the representation of specific fairness information within a resource description framework (RDF) knowledge graph. We evaluate the ontology by examining the process of how reasoning-based queries to the ontology were used to guide the fairness metric-based evaluation of a synthetic data model.

Temporal graph regression is a frequently encountered research problem in many studies of graph analytics. A temporal graph is a sequence of attributed graphs where node features and target variables change over time, but network structure stays constant. The task of temporal graph regression is to predict the target variables associated with nodes at future time-points given historical snapshots of the graph. Existing methods tackle this problem mostly by conducting structured regression for all target variables. However, those methods have limited performance due to redundant information. Although several techniques have been proposed recently to learn lower dimensional embedding for the target space, the problem of how to effectively exploit the structure of the temporal graph in such embeddings is still unsolved. Other recent works only study node embedding of the stationary graphs only, and this is not applicable to temporal attributed graphs. In this paper, we introduced a Structure-Aware Intrinsic Representation Learning model (SAIRL) to jointly learn lower dimensional embeddings of the target space and feature space via structure-aware graph abstraction and feature-aware target embedding learning. To solve this problem, we have developed a derivative-free block coordinate descent algorithm with closed-form solutions. To characterize the quality of embedding-based learned with SAIRL, we conducted extensive experiments on a variety of different real-world temporal graphs. The results indicate that the proposed method can be more accurate than the state-of-the-art embedding learning methods, regardless of regressors.

The proliferation of Electronic Health Records (EHRs) challenges data miners to discover potential and previously unknown patterns from a large collection of medical data. One of the tasks that we address in this paper is to reveal previously unknown effects of drugs on laboratory test results. We propose a method that leverages drug information to find a meaningful list of drugs that have an effect on the laboratory result. We formulate the problem as a convex non smooth function and develop a proximal gradient method to optimize it. The model has been evaluated on two important use cases: lowering low-density lipoproteins and glycated hemoglobin test results. The experimental results provide evidence that the proposed method is more accurate than the state-of-the-art method, rediscover drugs that are known to lower the levels of laboratory test results, and most importantly, discover additional potential drugs that may also lower these levels.

BACKGROUND: Feature selection, aiming to identify a subset of features among a possibly large set of features that are relevant for predicting a response, is an important preprocessing step in machine learning. In gene expression studies this is not a trivial task for several reasons, including potential temporal character of data. However, most feature selection approaches developed for microarray data cannot handle multivariate temporal data without previous data flattening, which results in loss of temporal information. We propose a temporal minimum redundancy - maximum relevance (TMRMR) feature selection approach, which is able to handle multivariate temporal data without previous data flattening. In the proposed approach we compute relevance of a gene by averaging F-statistic values calculated across individual time steps, and we compute redundancy between genes by using a dynamical time warping approach. RESULTS: The proposed method is evaluated on three temporal gene expression datasets from human viral challenge studies. Obtained results show that the proposed method outperforms alternatives widely used in gene expression studies. In particular, the proposed method achieved improvement in accuracy in 34 out of 54 experiments, while the other methods outperformed it in no more than 4 experiments. CONCLUSION: We developed a filter-based feature selection method for temporal gene expression data based on maximum relevance and minimum redundancy criteria. The proposed method incorporates temporal information by combining relevance, which is calculated as an average F-statistic value across different time steps, with redundancy, which is calculated by employing dynamical time warping approach. As evident in our experiments, incorporating the temporal information into the feature selection process leads to selection of more discriminative features.

Gaussian Conditional Random Fields (GCRF) are atype of structured regression model that incorporatesmultiple predictors and multiple graphs. This isachieved by defining quadratic term feature functions inGaussian canonical form which makes the conditionallog-likelihood function convex and hence allows findingthe optimal parameters by learning from data. In thiswork, the parameter space for the GCRF model is extendedto facilitate joint modelling of positive and negativeinfluences. This is achieved by restricting the modelto a single graph and formulating linear bounds on convexitywith respect to the models parameters. In addition,our formulation for the model using one networkallows calculating gradients much faster than alternativeimplementations. Lastly, we extend the model onestep farther and incorporate a bias term into our linkweight. This bias is solved as part of the convex optimization.Benefits of the proposed model in terms ofimproved accuracy and speed are characterized on severalsynthetic graphs with 2 million links as well as on ahospital admissions prediction task represented as a humandisease-symptom similarity network correspondingto more than 35 million hospitalization records inCalifornia over 9 years.

Structured regression has been successfully used in many applications where explanatory and response variables are inter-correlated, such as in weighted attributed networks. One of structured models, Gaussian Conditional Random Fields (GCRF), utilizing multiple unstructured models to learn the non-linear relationships between node attributes and the structured response variable, achieves high prediction accuracy. However, it does not scale well with large networks. We propose a novel model, called Scalable Approximate GCRF (SA-GCRF), which integrates weighted attributed network compression with GCRF, with the aim of making GCRF applicable to large networks. The model consists of three steps: first, it compresses a network into a smaller one by generalizing nodes into supernodes and edges into superedges; then, it applies GCRF to the reduced network; and finally, it unfolds the predicted response variables into the original nodes. Our hypothesis is that the reduced network maintains most information of the original network such that the loss in prediction accuracy obtained by GCRF on the reduced network is minor. The comprehensive experimental results indicate that SA-GCRF was 150-520 times faster than standard GCRF and 11-29 times faster than state-of-the-art UmGCRF on large networks, and provided regression results where GCRF and UmGCRF were not applicable. Furthermore, SA-GCRF achieved a similar regression accuracy, 0.76, to the one obtained from the original real-world weighted attributed citation network, even after compressing the network to 10% of its size.

In many applications, including climate science, power systems, and remote sensing, multiple input variables are observed for each output variable and the output variables are dependent. Several methods have been proposed to improve prediction by learning the conditional distribution of the output variables. However, when the relationship between the raw features and the outputs is nonlinear, the existing methods cannot capture both the nonlinearity and the underlying structure well. In this study, we propose a structured model containing hidden variables, which are nonlinear functions of inputs and which are linearly related with the output variables. The parameters modeling the relationships between the input and hidden variables, between the hidden and output variables, as well as among the output variables are learned simultaneously. To demonstrate the effectiveness of our proposed method, we conducted extensive experiments on eight synthetic datasets and three real-world challenging datasets: forecasting wind power, forecasting solar energy, and forecasting precipitation over U.S. The proposed method was more accurate than state-of-the-art structured regression methods.

BACKGROUND: Existing feature selection methods typically do not consider prior knowledge in the form of structural relationships among features. In this study, the features are structured based on prior knowledge into groups. The problem addressed in this article is how to select one representative feature from each group such that the selected features are jointly discriminating the classes. The problem is formulated as a binary constrained optimization and the combinatorial optimization is relaxed as a convex-concave problem, which is then transformed into a sequence of convex optimization problems so that the problem can be solved by any standard optimization algorithm. Moreover, a block coordinate gradient descent optimization algorithm is proposed for high dimensional feature selection, which in our experiments was four times faster than using a standard optimization algorithm. RESULTS: In order to test the effectiveness of the proposed formulation, we used microarray analysis as a case study, where genes with similar expressions or similar molecular functions were grouped together. In particular, the proposed block coordinate gradient descent feature selection method is evaluated on five benchmark microarray gene expression datasets and evidence is provided that the proposed method gives more accurate results than the state-of-the-art gene selection methods. Out of 25 experiments, the proposed method achieved the highest average AUC in 13 experiments while the other methods achieved higher average AUC in no more than 6 experiments. CONCLUSION: A method is developed to select a feature from each group. When the features are grouped based on similarity in gene expression, we showed that the proposed algorithm is more accurate than state-of-the-art gene selection methods that are particularly developed to select highly discriminative and less redundant genes. In addition, the proposed method can exploit any grouping structure among features, while alternative methods are restricted to using similarity based grouping.

High false alarm rates in intensive care units (ICUs) cause desensitization among care providers, thus risking patients' lives. Providing early detection of true and false cardiac arrhythmia alarms can alert hospital personnel and avoid alarm fatigue, so that they can act only on true life-threatening alarms, hence improving efficiency in ICUs. However, suppressing false alarms cannot be an excuse to suppress true alarm detection rates. In this study, we investigate a cost-sensitive approach for false alarm suppression while keeping near perfect true alarm detection rates. Our experiments on two life threatening cardiac arrhythmia datasets from Physionet's MIMIC II repository provide evidence that the proposed method is capable of identifying patterns that can distinguish false and true alarms using on average 60% of the available time series' length. Using temporal uncertainty estimates of time series predictions, we were able to estimate the confidence in our early classification predictions, therefore providing a cost-sensitive prediction model for ECG signal classification. The results from the proposed method are interpretable, providing medical personnel a visual verification of the predicted results. In conducted experiments, moderate false alarm suppression rates were achieved (34.29% for Asystole and 20.32% for Ventricular Tachycardia) while keeping near 100% true alarm detection, outperforming the state-of-the-art methods, which compromise true alarm detection rate for higher false alarm suppression rate, on these challenging applications.

Early classification of time series is prevalent in many time-sensitive applications such as, but not limited to, early warning of disease outcome and early warning of crisis in stock market. \textcolor{black}{ For example,} early diagnosis allows physicians to design appropriate therapeutic strategies at early stages of diseases. However, practical adaptation of early classification of time series requires an easy to understand explanation (interpretability) and a measure of confidence of the prediction results (uncertainty estimates). These two aspects were not jointly addressed in previous time series early classification studies, such that a difficult choice of selecting one of these aspects is required. In this study, we propose a simple and yet effective method to provide uncertainty estimates for an interpretable early classification method. The question we address here is "how to provide estimates of uncertainty in regard to interpretable early prediction." In our extensive evaluation on twenty time series datasets we showed that the proposed method has several advantages over the state-of-the-art method that provides reliability estimates in early classification. Namely, the proposed method is more effective than the state-of-the-art method, is simple to implement, and provides interpretable results.

Leveraging temporal observations to predict a patient's health state at a future period is a very challenging task. Providing such a prediction early and accurately allows for designing a more successful treatment that starts before a disease completely develops. Information for this kind of early diagnosis could be extracted by use of temporal data mining methods for handling complex multivariate time series. However, physicians usually prefer to use interpretable models that can be easily explained, rather than relying on more complex black-box approaches. In this study, a temporal data mining method is proposed for extracting interpretable patterns from multivariate time series data, which can be used to assist in providing interpretable early diagnosis. The problem is formulated as an optimization based binary classification task addressed in three steps. First, the time series data is transformed into a binary matrix representation suitable for application of classification methods. Second, a novel convex-concave optimization problem is defined to extract multivariate patterns from the constructed binary matrix. Then, a mixed integer discrete optimization formulation is provided to reduce the dimensionality and extract interpretable multivariate patterns. Finally, those interpretable multivariate patterns are used for early classification in challenging clinical applications. In the conducted experiments on two human viral infection datasets and a larger myocardial infarction dataset, the proposed method was more accurate and provided classifications earlier than three alternative state-of-the-art methods.

Early classification of time series has been receiving a lot of attention as of late, particularly in the context of gene expression. In the biomédical realm, early classification can be of tremendous help, by identifying the onset of a disease before it has time to fully take hold, or determining that a treatment has done its job and can be discontinued. In this paper we present a state-of-the-art model, which we call the Early Classification Model (ECM), that allows for early, accurate, and patient-specific classification of multivariate time series. The model is comprised of an integration of the widely-used HMM and SVM models, which, while not a new technique per se, has not been used for early classification of multivariate time series classification until now. It attained very promising results on the datasets we tested it on: in our experiments based on a published dataset of response to drug therapy in Multiple Sclerosis patients, ECM used only an average of 40% of a time series and was able to outperform some of the baseline models, which needed the full time series for classification.

BACKGROUND: Early classification of time series is beneficial for biomedical informatics problems such including, but not limited to, disease change detection. Early classification can be of tremendous help by identifying the onset of a disease before it has time to fully take hold. In addition, extracting patterns from the original time series helps domain experts to gain insights into the classification results. This problem has been studied recently using time series segments called shapelets. In this paper, we present a method, which we call Multivariate Shapelets Detection (MSD), that allows for early and patient-specific classification of multivariate time series. The method extracts time series patterns, called multivariate shapelets, from all dimensions of the time series that distinctly manifest the target class locally. The time series were classified by searching for the earliest closest patterns. RESULTS: The proposed early classification method for multivariate time series has been evaluated on eight gene expression datasets from viral infection and drug response studies in humans. In our experiments, the MSD method outperformed the baseline methods, achieving highly accurate classification by using as little as 40%-64% of the time series. The obtained results provide evidence that using conventional classification methods on short time series is not as accurate as using the proposed methods specialized for early classification. CONCLUSION: For the early classification task, we proposed a method called Multivariate Shapelets Detection (MSD), which extracts patterns from all dimensions of the time series. We showed that the MSD method can classify the time series early by using as little as 40%-64% of the time series' length.