Detecting drought regulators using stochastic inference in Bayesian networks

Drought is a natural hazard that affects crops by inducing water stress. Water stress, induced by drought accounts for more loss in crop yield than all the other causes combined. With the increasing frequency and intensity of droughts worldwide, it is essential to develop drought-resistant crops to ensure food security. In this paper, we model multiple drought signaling pathways in Arabidopsis using Bayesian networks to identify potential regulators of drought-responsive reporter genes. Genetically intervening at these regulators can help develop drought-resistant crops. We create the Bayesian network model from the biological literature and determine its parameters from publicly available data. We conduct inference on this model using a stochastic simulation technique known as likelihood weighting to determine the best regulators of drought-responsive reporter genes. Our analysis reveals that activating MYC2 or inhibiting ATAF1 are the best single node intervention strategies to regulate the drought-responsive reporter genes. Additionally, we observe simultaneously activating MYC2 and inhibiting ATAF1 is a better strategy. The Bayesian network model indicated that MYC2 and ATAF1 are possible regulators of the drought response. Validation experiments showed that ATAF1 negatively regulated the drought response. Thus intervening at ATAF1 has the potential to create drought-resistant crops.

scvi-tools: a library for deep probabilistic analysis of single-cell omics data

Probabilistic models have provided the underpinnings for state-of-the-art performance in many single-cell omics data analysis tasks, including dimensionality reduction, clustering, differential expression, annotation, removal of unwanted variation, and integration across modalities. Many of the models being deployed are amenable to scalable stochastic inference techniques, and accordingly they are able to process single-cell datasets of realistic and growing sizes. However, the community-wide adoption of probabilistic approaches is hindered by a fractured software ecosystem resulting in an array of packages with distinct, and often complex interfaces. To address this issue, we developed scvi-tools (https://scvi-tools.org), a Python package that implements a variety of leading probabilistic methods. These methods, which cover many fundamental analysis tasks, are accessible through a standardized, easy-to-use interface with direct links to Scanpy, Seurat, and Bioconductor workflows. By standardizing the implementations, we were able to develop and reuse novel functionalities across different models, such as support for complex study designs through nonlinear removal of unwanted variation due to multiple covariates and reference-query integration via scArches. The extensible software building blocks that underlie scvi-tools also enable a developer environment in which new probabilistic models for single cell omics can be efficiently developed, benchmarked, and deployed. We demonstrate this through a code-efficient reimplementation of Stereoscope for deconvolution of spatial transcriptomics profiles. By catering to both the end user and developer audiences, we expect scvi-tools to become an essential software dependency and serve to formulate a community standard for probabilistic modeling of single cell omics.

Detecting Drought Regulators using Stochastic Inference in Bayesian Networks

Drought is a natural hazard that affects crops by inducing water stress. Water stress, induced by drought, accounts for more loss in crop yield than all the other causes combined. With the increasing frequency and intensity of droughts worldwide, it is essential to develop drought-resistant crops to ensure food security. In this paper, we model multiple drought signaling pathways in Arabidopsis using Bayesian networks to identify potential regulators of drought-responsive reporter genes. Genetically intervening at these regulators can help develop drought-resistant crops. We create the Bayesian network model from the biological literature and determine its parameters from publicly available data. We conduct inference on this model using a stochastic simulation technique known as likelihood weighting to determine the best regulators of drought-responsive reporter genes. Our analysis reveals that activating MYC2 or inhibiting ATAF1 are the best single node intervention strategies to regulate the drought-responsive reporter genes. Additionally, we observe simultaneously activating MYC2 and inhibiting ATAF1 is a better strategy. The Bayesian network model indicated that MYC2 and ATAF1 are possible regulators of the drought response. Validation experiments showed that ATAF1 negatively regulated the drought response. Thus intervening at ATAF1 has the potential to create drought-resistant crops.

Precise Event-level Prediction of Urban Crime Reveals Signature of Enforcement Bias

Policing efforts to thwart urban crime often rely on detailed reports of criminal infractions. However, crime rates do not document the distribution of crime in isolation, but rather its complex relationship with policing and society. Several results attempting to predict future crime now exist, with varying degrees of predictive efficacy. However, the very idea of predictive policing has stirred controversy, with the algorithms being largely black boxes producing little to no insight into the social system of crime, and its rules of organization. The issue of how enforcement interacts with, modulates, and reinforces crime has been rarely addressed in the context of precise event predictions. In this study, we demonstrate that predictive tools are not purely an instrument enhacing state power, but may be effectively used to seek out systemic biases in urban enforcement. We introduce a novel stochastic inference algorithm as a new forecasting approach that learns spatio-temporal dependencies from individual event reports with demonstrated performance far surpassing past results (e.g., average AUC of ~90% in the City of Chicago for property and violent crimes predicted a week in advance within spatial tiles ~1000ft across). These precise predictions enable equally precise evaluation of inequities in law enforcement, discovering that response to increased crime rates is biased by the socio-economic status of neighborhoods, draining policy resources to wealthy areas with disproportionately negative impacts for the inner city, as demonstrated in Chicago and six other major U.S. metropolitan areas. While the emergence of powerful predictive tools raise concerns regarding the unprecedented power they place in the hands of over-zealous states in the name of civilian protection, our approach demonstrates how sophisticated algorithms enable us to audit enforcement biases, and hold states accountable in ways previously inconceivable.

Update-Based Machine Learning Classification of Hierarchical Symbols in a Slowly Varying Two-Way Relay Channel

This paper presents a stochastic inference problem suited to a classification approach in a time-varying observation model with continuous-valued unknown parameterization. The utilization of an artificial neural network (ANN)-based classifier is considered, and the concept of a training process via the backpropagation algorithm is used. The main objective is the minimization of resources required for the training of the classifier in the parametric observation model. To reach this, it is proposed that the weights of the ANN classifier vary continuously with the change of the observation model parameters. This behavior is then used in an update-based backpropagation algorithm. This proposed idea is demonstrated on several procedures, which re-use previously trained weights as prior information when updating the classifier after a channel phase change. This approach successfully saves resources needed for re-training the ANN. The new approach is verified via a simulation on an example communication system with the two-way relay slowly fading channel.

Detecting Drought Regulators using Stochastic Inference in Bayesian Networks

Background: Drought is a natural hazard that affects crops by inducing water stress. Water stress, induced by drought, accounts for more loss in crop yield than all the other causes combined. With the increasing frequency and intensity of droughts worldwide, it is essential to develop drought-resistant crops to ensure food security. In this paper, we model multiple drought signaling pathways in Arabidopsis using Bayesian networks to identify potential regulators of drought-responsive reporter genes. Genetically intervening at these regulators can help develop drought-resistant crops.Result: We create the Bayesian network model from the biological literature and determine its parameters from publicly available data. We conduct inference on this model using a stochastic simulation technique known as likelihood weighting to determine the best regulators of drought-responsive reporter genes. Our analysis reveals that activating MYC2 or inhibiting ATAF1 are the best single node intervention strategies to regulate the drought-responsive reporter genes. Additionally, we observe simultaneously activating MYC2 and inhibiting ATAF1 is a better strategy.Conclusion: The Bayesian network model indicated that MYC2 and ATAF1 are possible regulators of the drought response. Validation experiments showed that ATAF1 negatively regulated the drought response. Thus intervening at ATAF1 has the potential to create drought-resistant crops.