Challenge.AI
Patient subtyping based on temporal observations can lead to significantly nuanced subtyping that acknowledges the dynamic characteristics of diseases. Existing methods for subtyping trajectories treat the evolution of clinical observations as a homogeneous process or employ data available at regular intervals. In reality, diseases may have transient underlying states and a state-dependent observation pattern. In our paper, we present an approach to subtype irregular patient data while acknowledging the underlying progression of disease states. Our approach consists of two components: a probabilistic model to determine the likelihood of a patient’s observation trajectory and a mixture model to measure similarity between asynchronous patient trajectories. We demonstrate our model by discovering subtypes of progression to hemodynamic instability (requiring cardiovascular intervention) in a patient cohort from a multi-institution ICU dataset. We find three primary patterns: two of which show classic signs of decompensation (rising heart rate with dropping blood pressure), with one of these showing a faster course of decompensation than the other. The third pattern has transient period of low heart rate and blood pressure. We also show that our model results in a 13% reduction in average cross-entropy error compared to a model with no state progression when forecasting vital signs. …

Semantic Evaluation (SemEval)
SemEval (Semantic Evaluation) is an ongoing series of evaluations of computational semantic analysis systems; it evolved from the Senseval word sense evaluation series. The evaluations are intended to explore the nature of meaning in language. While meaning is intuitive to humans, transferring those intuitions to computational analysis has proved elusive. This series of evaluations is providing a mechanism to characterize in more precise terms exactly what is necessary to compute in meaning. As such, the evaluations provide an emergent mechanism to identify the problems and solutions for computations with meaning. These exercises have evolved to articulate more of the dimensions that are involved in our use of language. They began with apparently simple attempts to identify word senses computationally. They have evolved to investigate the interrelationships among the elements in a sentence (e.g., semantic role labeling), relations between sentences (e.g., coreference), and the nature of what we are saying (semantic relations and sentiment analysis). The purpose of the SemEval exercises and SENSEVAL is to evaluate semantic analysis systems. ‘Semantic Analysis’ refers to a formal analysis of meaning, and ‘computational’ refer to approaches that in principle support effective implementation. The first three evaluations, Senseval-1 through Senseval-3, were focused on word sense disambiguation, each time growing in the number of languages offered in the tasks and in the number of participating teams. Beginning with the fourth workshop, SemEval-2007 (SemEval-1), the nature of the tasks evolved to include semantic analysis tasks outside of word sense disambiguation. Triggered by the conception of the *SEM conference, the SemEval community had decided to hold the evaluation workshops yearly in association with the *SEM conference. It was also the decision that not every evaluation task will be run every year, e.g. none of the WSD tasks were running in the SemEval-2012 workshop. …

Generalized Entropy Agglomeration (GEA)
Entropy Agglomeration (EA) is a hierarchical clustering algorithm introduced in 2013. Here, we generalize it to define Generalized Entropy Agglomeration (GEA) that can work with multiset blocks and blocks with rational occurrence numbers. We also introduce a numerical categorization procedure to apply GEA to numerical datasets. The software REBUS 2.0 is published with these capabilities: http://…/rebus2 …

Dynamic Correlation Analysis (DCA)
In high-throughput data, dynamic correlation between genes, i.e. changing correlation patterns under different biological conditions, can reveal important regulatory mechanisms. Given the complex nature of dynamic correlation, and the underlying conditions for dynamic correlation may not manifest into clinical observations, it is difficult to recover such signal from the data. Current methods seek underlying conditions for dynamic correlation by using certain observed genes as surrogates, which may not faithfully represent true latent conditions. In this study we develop a new method that directly identifies strong latent signals that regulate the dynamic correlation of many pairs of genes, named DCA: Dynamic Correlation Analysis. At the center of the method is a new metric for the identification of gene pairs that are highly likely to be dynamically correlated, without knowing the underlying conditions of the dynamic correlation. We validate the performance of the method with extensive simulations. In real data analysis, the method reveals novel latent factors with clear biological meaning, bringing new insights into the data. …