Deep generative modeling for single-cell transcriptomics.

Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task

A common goodness-of-fit framework for neural population models using marked point process time-rescaling

A critical component of any statistical modeling procedure is the ability to assess the goodness-of-fit between a model and observed data. For spike train models of individual neurons, many goodness-of-fit measures rely on the time-rescaling theorem and assess model quality using rescaled spike times. Recently, there has been increasing interest in statistical models that describe the simultaneous spiking activity of neuron populations, either in a single brain region or across brain regions. Classically, such models have used spike sorted data to describe relationships between the identified neurons, but more recently clusterless modeling methods have been used to describe population activity using a single model. Here we develop a generalization of the time-rescaling theorem that enables comprehensive goodness-of-fit analysis for either of these classes of population models. We use the theory of marked point processes to model population spiking activity, and show that under the correct model, each spike can be rescaled individually to generate a uniformly distributed set of events in time and the space of spike marks. After rescaling, multiple well-established goodness-of-fit procedures and statistical tests are available. We demonstrate the application of these methods both to simulated data and real population spiking in rat hippocampus. We have made the MATLAB and Python code used for the analyses in this paper publicly available through our Github repository at https://github.com/Eden-Kramer-Lab/popTRT.This work was supported by grants from the NIH (MH105174, NS094288) and the Simons Foundation (542971). (MH105174 - NIH; NS094288 - NIH; 542971 - Simons Foundation)Published versio

Markovian Characterisation of H.264/SVC scalable video

In this paper, a multivariate Markovian traffic: model is proposed to characterise H.264/SVC scalable video traces. Parametrisation by a genetic algorithm results in models with a limited state space which accurately capture. both the temporal and the inter-layer correlation of the traces. A simulation study further shows that the model is capable of predicting performance of video streaming in various networking scenarios

The role of learning on industrial simulation design and analysis

The capability of modeling real-world system operations has turned simulation into an indispensable problemsolving methodology for business system design and analysis. Today, simulation supports decisions ranging from sourcing to operations to finance, starting at the strategic level and proceeding towards tactical and operational levels of decision-making. In such a dynamic setting, the practice of simulation goes beyond being a static problem-solving exercise and requires integration with learning. This article discusses the role of learning in simulation design and analysis motivated by the needs of industrial problems and describes how selected tools of statistical learning can be utilized for this purpose

Used-habitat calibration plots: a new procedure for validating species distribution, resource selection, and step-selection models

“Species distribution modeling” was recently ranked as one of the top five “research fronts” in ecology and the environmental sciences by ISI's Essential Science Indicators (Renner and Warton 2013), reflecting the importance of predicting how species distributions will respond to anthropogenic change. Unfortunately, species distribution models (SDMs) often perform poorly when applied to novel environments. Compounding on this problem is the shortage of methods for evaluating SDMs (hence, we may be getting our predictions wrong and not even know it). Traditional methods for validating SDMs quantify a model's ability to classify locations as used or unused. Instead, we propose to focus on how well SDMs can predict the characteristics of used locations. This subtle shift in viewpoint leads to a more natural and informative evaluation and validation of models across the entire spectrum of SDMs. Through a series of examples, we show how simple graphical methods can help with three fundamental challenges of habitat modeling: identifying missing covariates, non-linearity, and multicollinearity. Identifying habitat characteristics that are not well-predicted by the model can provide insights into variables affecting the distribution of species, suggest appropriate model modifications, and ultimately improve the reliability and generality of conservation and management recommendations

New topic detection in microblogs and topic model evaluation using topical alignment

textThis thesis deals with topic model evaluation and new topic detection in microblogs. Microblogs are short and thus may not carry any contextual clues. Hence it becomes challenging to apply traditional natural language processing algorithms on such data. Graphical models have been traditionally used for topic discovery and text clustering on sets of text-based documents. Their unsupervised nature allows topic models to be trained easily on datasets meant for specific domains. However the advantage of not requiring annotated data comes with a drawback with respect to evaluation difficulties. The problem aggravates when the data comprises microblogs which are unstructured and noisy. We demonstrate the application of three types of such models to microblogs - the Latent Dirichlet Allocation, the Author-Topic and the Author-Recipient-Topic model. We extensively evaluate these models under different settings, and our results show that the Author-Recipient-Topic model extracts the most coherent topics. We also addressed the problem of topic modeling on short text by using clustering techniques. This technique helps in boosting the performance of our models. Topical alignment is used for large scale assessment of topical relevance by comparing topics to manually generated domain specific concepts. In this thesis we use this idea to evaluate topic models by measuring misalignments between topics. Our study on comparing topic models reveals interesting traits about Twitter messages, users and their interactions and establishes that joint modeling on author-recipient pairs and on the content of tweet leads to qualitatively better topic discovery. This thesis gives a new direction to the well known problem of topic discovery in microblogs. Trend prediction or topic discovery for microblogs is an extensive research area. We propose the idea of using topical alignment to detect new topics by comparing topics from the current week to those of the previous week. We measure correspondence between a set of topics from the current week and a set of topics from the previous week to quantify five types of misalignments: \textit{junk, fused, missing} and \textit{repeated}. Our analysis compares three types of topic models under different settings and demonstrates how our framework can detect new topics from topical misalignments. In particular so-called \textit{junk} topics are more likely to be new topics and the \textit{missing} topics are likely to have died or die out. To get more insights into the nature of microblogs we apply topical alignment to hashtags. Comparing topics to hashtags enables us to make interesting inferences about Twitter messages and their content. Our study revealed that although a very small proportion of Twitter messages explicitly contain hashtags, the proportion of tweets that discuss topics related to hashtags is much higher.Computer Science

AutoDiscern: Rating the Quality of Online Health Information with Hierarchical Encoder Attention-based Neural Networks

Patients increasingly turn to search engines and online content before, or in place of, talking with a health professional. Low quality health information, which is common on the internet, presents risks to the patient in the form of misinformation and a possibly poorer relationship with their physician. To address this, the DISCERN criteria (developed at University of Oxford) are used to evaluate the quality of online health information. However, patients are unlikely to take the time to apply these criteria to the health websites they visit. We built an automated implementation of the DISCERN instrument (Brief version) using machine learning models. We compared the performance of a traditional model (Random Forest) with that of a hierarchical encoder attention-based neural network (HEA) model using two language embeddings, BERT and BioBERT. The HEA BERT and BioBERT models achieved average F1-macro scores across all criteria of 0.75 and 0.74, respectively, outperforming the Random Forest model (average F1-macro = 0.69). Overall, the neural network based models achieved 81% and 86% average accuracy at 100% and 80% coverage, respectively, compared to 94% manual rating accuracy. The attention mechanism implemented in the HEA architectures not only provided 'model explainability' by identifying reasonable supporting sentences for the documents fulfilling the Brief DISCERN criteria, but also boosted F1 performance by 0.05 compared to the same architecture without an attention mechanism. Our research suggests that it is feasible to automate online health information quality assessment, which is an important step towards empowering patients to become informed partners in the healthcare process

Constructing a no-reference H.264/AVC bitstream-based video quality metric using genetic programming-based symbolic regression

In order to ensure optimal quality of experience toward end users during video streaming, automatic video quality assessment becomes an important field-of-interest to video service providers. Objective video quality metrics try to estimate perceived quality with high accuracy and in an automated manner. In traditional approaches, these metrics model the complex properties of the human visual system. More recently, however, it has been shown that machine learning approaches can also yield competitive results. In this paper, we present a novel no-reference bitstream-based objective video quality metric that is constructed by genetic programming-based symbolic regression. A key benefit of this approach is that it calculates reliable white-box models that allow us to determine the importance of the parameters. Additionally, these models can provide human insight into the underlying principles of subjective video quality assessment. Numerical results show that perceived quality can be modeled with high accuracy using only parameters extracted from the received video bitstream