Predicting onset of disease progression using temporal disease occurrence networks.

OBJECTIVE: Early recognition and prevention are crucial for reducing the risk of disease progression. This study aimed to develop a novel technique based on a temporal disease occurrence network to analyze and predict disease progression. METHODS: This study used a total of 3.9 million patient records. Patient health records were transformed into temporal disease occurrence networks, and a supervised depth first search was used to find frequent disease sequences to predict the onset of disease progression. The diseases represented nodes in the network and paths between nodes represented edges that co-occurred in a patient cohort with temporal order. The node and edge level attributes contained meta-information about patients' gender, age group, and identity as labels where the disease occurred. The node and edge level attributes guided the depth first search to identify frequent disease occurrences in specific genders and age groups. The patient history was used to match the most frequent disease occurrences and then the obtained sequences were merged together to generate a ranked list of diseases with their conditional probability and relative risk. RESULTS: The study found that the proposed method had improved performance compared to other methods. Specifically, when predicting a single disease, the method achieved an area under the receiver operating characteristic curve (AUC) of 0.65 and an F1-score of 0.11. When predicting a set of diseases relative to ground truth, the method achieved an AUC of 0.68 and an F1-score of 0.13. CONCLUSION: The ranked list generated by the proposed method, which includes the probability of occurrence and relative risk score, can provide physicians with valuable information about the sequential development of diseases in patients. This information can help physicians to take preventive measures in a timely manner, based on the best available information.

Minimizing stochastic complexity using local search and GLA with applications to classification of bacteria.

In this paper, we compare the performance of two iterative clustering methods when applied to an extensive data set describing strains of the bacterial family Enterobacteriaceae. In both methods, the classification (i.e. the number of classes and the partitioning) is determined by minimizing stochastic complexity. The first method performs the minimization by repeated application of the generalized Lloyd algorithm (GLA). The second method uses an optimization technique known as local search (LS). The method modifies the current solution by making global changes to the class structure and it, then, performs local fine-tuning to find a local optimum. It is observed that if we fix the number of classes, the LS finds a classification with a lower stochastic complexity value than GLA. In addition, the variance of the solutions is much smaller for the LS due to its more systematic method of searching. Overall, the two algorithms produce similar classifications but they merge certain natural classes with microbiological relevance in different ways.

Fast and memory efficient implementation of the exact PNN.

Straightforward implementation of the exact pairwise nearest neighbor (PNN) algorithm takes O(N3) time, where N is the number of training vectors. This is rather slow in practical situations. Fortunately, much faster implementation can be obtained with rather simple modifications to the basic algorithm. In this paper, we propose a fast O(tauN2) time implementation of the exact PNN, where tau is shown to be significantly smaller than N, We give all necessary data structures and implementation details, and give the time complexity of the algorithm both in the best case and in the worst case. The proposed implementation achieves the results of the exact PNN with the same O(N) memory requirement.

A fast exact GLA based on code vector activity detection.

This paper introduces a new method for reducing the number of distance calculations in the generalized Lloyd algorithm (GLA), which is a widely used method to construct a codebook in vector quantization. Reduced comparison search detects the activity of the code vectors and utilizes it on the classification of the training vectors. For training vectors whose current code vector has not been modified, we calculate distances only to the active code vectors. A large proportion of the distance calculations can be omitted without sacrificing the optimality of the partition. The new method is included in several fast GLA variants reducing their running times over 50% on average.