Conditional Independence (CI) graphs are a type of Probabilistic Graphical Models that are primarily used to gain insights about feature relationships. Each edge represents the partial correlation between the connected features which gives information about their direct dependence. In this survey, we list different methods and study the advances in techniques developed to recover CI graphs. We cover traditional optimization methods as well as recently developed deep learning architectures along with their recommended implementations. To facilitate wider adoption, we include preliminaries that consolidate associated operations, for example techniques to obtain covariance matrix for mixed datatypes.

MOTIVATION: Reconstruction of genome-scale networks from gene expression data is an actively studied problem. A wide range of methods that differ between the types of interactions they uncover with varying trade-offs between sensitivity and specificity have been proposed. To leverage benefits of multiple such methods, ensemble network methods that combine predictions from resulting networks have been developed, promising results better than or as good as the individual networks. Perhaps owing to the difficulty in obtaining accurate training examples, these ensemble methods hitherto are unsupervised. RESULTS: In this article, we introduce EnGRaiN, the first supervised ensemble learning method to construct gene networks. The supervision for training is provided by small training datasets of true edge connections (positives) and edges known to be absent (negatives) among gene pairs. We demonstrate the effectiveness of EnGRaiN using simulated datasets as well as a curated collection of Arabidopsis thaliana datasets we created from microarray datasets available from public repositories. EnGRaiN shows better results not only in terms of receiver operating characteristic and PR characteristics for both real and simulated datasets compared with unsupervised methods for ensemble network construction, but also generates networks that can be mined for elucidating complex biological interactions. AVAILABILITY AND IMPLEMENTATION: EnGRaiN software and the datasets used in the study are publicly available at the github repository: https://github.com/AluruLab/EnGRaiN. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We propose automatic speech recognition (ASR) models inspired by echo state network (ESN) [1], in which a subset of recurrent neural networks (RNN) layers in the models are randomly initialized and untrained. Our study focuses on RNN-T and Conformer models, and we show that model quality does not drop even when the decoder is fully randomized. Furthermore, such models can be trained more efficiently as the decoders do not require to be updated. By contrast, randomizing encoders hurts model quality, indicating that optimizing encoders and learn proper representations for acoustic inputs are more vital for speech recognition. Overall, we challenge the common practice of training ASR models for all components, and demonstrate that ESN-based models can perform equally well but enable more efficient training and storage than fully-trainable counterparts.

We propose a new approach, called cooperative neural networks (CoNN), which use a set of cooperatively trained neural networks to capture latent representations that exploit prior given independence structure. The model is more flexible than traditional graphical models based on exponential family distributions, but incorporates more domain specific prior structure than traditional deep networks or variational autoencoders. The framework is very general and can be used to exploit the independence structure of any graphical model. We illustrate the technique by showing that we can transfer the independence structure of the popular Latent Dirichlet Allocation (LDA) model to a cooperative neural network, CoNN-sLDA. Empirical evaluation of CoNN-sLDA on supervised text classification tasks demonstrate that the theoretical advantages of prior independence structure can be realized in practice - we demonstrate a 23 percent reduction in error on the challenging MultiSent data set compared to state-of-the-art.

Determining mortality risk is important for critical decisions in Intensive Care Units (ICU). The need for machine learning models that provide accurate patient-specific prediction of mortality is well recognized. We present a new algorithm for ICU mortality prediction that is designed to address the problem of imbalance, which occurs, in the context of binary classification, when one of the two classes is significantly under--represented in the data. We take a fundamentally new approach in exploiting the class imbalance through a feature transformation such that the transformed features are easier to classify. Hypothesis testing is used for classification with a test statistic that follows the distribution of the difference of two chi-squared random variables, for which there are no analytic expressions and we derive an accurate approximation. Experiments on a benchmark dataset of 4000 ICU patients show that our algorithm surpasses the best competing methods for mortality prediction.

Binary classification based methods are commonly used for designing predictive models in healthcare. A common problem in many healthcare datasets is that of imbalance, where there are far more observations in one class than the other during training. In such conditions, most classifiers do not have good predictive accuracy with respect to the under-represented class. We design a new similarity-based classifier to learn from imbalanced datasets, wherein input features are transformed using similarity with respect to a chosen subset of training points. We empirically demonstrate the superiority of our algorithm over state-of-the-art methods for imbalanced data classification in real and synthetic datasets. We also illustrate the application of our classifier in predicting Acute Respiratory Failure (ARF), a critical complication in Intensive Care Units (ICU), using semi-structured text contained in nursing notes recorded during a patient's ICU stay. Our experiments, on more than 800 patient records show that using our new classifier to learn from text- based features can effectively be used to predict ARF and, potentially, other complications in ICUs.