Stan is a probabilistic programming language that has been increasingly used for real-world scalable projects. However, to make practical inference possible, the language sacrifices some of its usability by adopting a block syntax, which lacks compositionality and flexible user-defined functions. Moreover, the semantics of the language has been mainly given in terms of intuition about implementation, and has not been formalised. This paper provides a formal treatment of the Stan language, and introduces the probabilistic programming language SlicStan --- a compositional, self-optimising version of Stan. Our main contributions are: (1) the formalisation of a core subset of Stan through an operational density-based semantics; (2) the design and semantics of the Stan-like language SlicStan, which facilities better code reuse and abstraction through its compositional syntax, more flexible functions, and information-flow type system; and (3) a formal, semantic-preserving procedure for translating SlicStan to Stan.

Such information includes: the database in modern hospital systems, usually known as Electronic Health Records (EHR), which store the patients' diagnosis, medication, laboratory test results, medical image data, etc.; information on various health behaviors tracked and stored by wearable devices, ubiquitous sensors and mobile applications, such as the smoking status, alcoholism history, exercise level, sleeping conditions, etc.; information collected by census or various surveys regarding sociodemographic factors of the target cohort; and information on people's mental health inferred from their social media activities or social networks such as Twitter, Facebook, etc. These health-related data come from heterogeneous sources, describe assorted aspects of the individual's health conditions. Such data is rich in structure and information which has great research potentials for revealing unknown medical knowledge about genomic epidemiology, disease developments and correlations, drug discoveries, medical diagnosis, mental illness prevention, health behavior adaption, etc. In real-world problems, the number of features relating to a certain health condition could grow exponentially with the development of new information techniques for collecting and measuring data. To reveal the causal influence between various factors and a certain disease or to discover the correlations among diseases from data at such a tremendous scale, requires the assistance of advanced information technology such as data mining, machine learning, text mining, etc. Machine learning technology not only provides a way for learning qualitative relationships among features and patients, but also the quantitative parameters regarding the strength of such correlations.

Identification of patterns from discrete data time-series for statistical inference, threat detection, social opinion dynamics, brain activity prediction has received recent momentum. In addition to the huge data size, the associated challenges are, for example, (i) missing data to construct a closed time-varying complex network, and (ii) contribution of unknown sources which are not probed. Towards this end, the current work focuses on statistical neuron system model with multi-covariates and unknown inputs. Previous research of neuron activity analysis is mainly limited with effects from the spiking history of target neuron and the interaction with other neurons in the system while ignoring the influence of unknown stimuli. We propose to use unknown unknowns, which describes the effect of unknown stimuli, undetected neuron activities and all other hidden sources of error. The maximum likelihood estimation with the fixed-point iteration method is implemented. The fixed-point iterations converge fast, and the proposed methods can be efficiently parallelized and offer computational advantage especially when the input spiking trains are over long time-horizon. The developed framework provides an intuition into the meaning of having extra degrees-of-freedom in the data to support the need for unknowns. The proposed algorithm is applied to simulated spike trains and on real-world experimental data of mouse somatosensory, mouse retina and cat retina. The model shows a successful increasing of system likelihood with respect to the conditional intensity function, and it also reveals the convergence with iterations. Results suggest that the neural connection model with unknown unknowns can efficiently estimate the statistical properties of the process by increasing the network likelihood.

We study the Automatic Relevance Determination procedure applied to deep neural networks. We show that ARD applied to Bayesian DNNs with Gaussian approximate posterior distributions leads to a variational bound similar to that of variational dropout, and in the case of a fixed dropout rate, objectives are exactly the same. Experimental results show that the two approaches yield comparable results in practice even when the dropout rates are trained. This leads to an alternative Bayesian interpretation of dropout and mitigates some of the theoretical issues that arise with the use of improper priors in the variational dropout model. Additionally, we explore the use of the hierarchical priors in ARD and show that it helps achieve higher sparsity for the same accuracy.

Electronic health records (EHR) are rich heterogeneous collection of patient health information, whose broad adoption provides great opportunities for systematic health data mining. However, heterogeneous EHR data types and biased ascertainment impose computational challenges. Here, we present mixEHR, an unsupervised generative model integrating collaborative filtering and latent topic models, which jointly models the discrete distributions of data observation bias and actual data using latent disease-topic distributions. We apply mixEHR on 12.8 million phenotypic observations from the MIMIC dataset, and use it to reveal latent disease topics, interpret EHR results, impute missing data, and predict mortality in intensive care units. Using both simulation and real data, we show that mixEHR outperforms previous methods and reveals meaningful multi-disease insights.

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.

Generalized linear models (GLMs) arise in high-dimensional machine learning, statistics, communications and signal processing. In this paper we analyze GLMs when the data matrix is random, as relevant in problems such as compressed sensing, error-correcting codes or benchmark models in neural networks. We evaluate the mutual information (or "free entropy") from which we deduce the Bayes-optimal estimation and generalization errors. Our analysis applies to the high-dimensional limit where both the number of samples and the dimension are large and their ratio is fixed. Non-rigorous predictions for the optimal errors existed for special cases of GLMs, e.g. for the perceptron, in the field of statistical physics based on the so-called replica method. Our present paper rigorously establishes those decades old conjectures and brings forward their algorithmic interpretation in terms of performance of the generalized approximate message-passing algorithm. Furthermore, we tightly characterize, for many learning problems, regions of parameters for which this algorithm achieves the optimal performance, and locate the associated sharp phase transitions separating learnable and non-learnable regions. We believe that this random version of GLMs can serve as a challenging benchmark for multi-purpose algorithms. This paper is divided in two parts that can be read independently: The first part (main part) presents the model and main results, discusses some applications and sketches the main ideas of the proof. The second part (supplementary informations) is much more detailed and provides more examples as well as all the proofs.

Abstract-- Beta Basis Function Neural Network (BBFNN) is a special kind of kernel basis neural networks. It is a feedforward network typified by the use of beta function as a hidden activation function. Beta is a flexible transfer function representing richer forms than the common existing functions. As in every network, the architecture setting as well as the learning method are two main gauntlets faced by BBFNN. In this paper, new architecture and training algorithm are proposed for the BBFNN. An Extreme Learning Machine (ELM) is used as a training approach of BBFNN with the aim of quickening the training process. The peculiarity of ELM is permitting a certain decrement of the computing time and complexity regarding the already used BBFNN learning algorithms such as backpropagation, OLS, etc. For the architectural design, a recurrent structure is added to the common BBFNN architecture in order to make it more able to deal with complex, nonlinear and time varying problems. Throughout this paper, the conceived recurrent ELMtrained BBFNN is tested on a number of tasks related to time series prediction, classification and regression. Experimental results show noticeable achievements of the proposed network compared to common feed-forward and recurrent networks trained by ELM and using hyperbolic tangent as activation function. These achievements are in terms of accuracy and robustness against data breakdowns such as noise signals. HE appeal to machine learning is resurged owing to reasons related to the high popularity of data mining and analysis. In fact, in a world full of available data varieties, computational processing seems to be very useful as it is cheap and powerful and it ensures affordable data handling [1] [2]. The automatic data treatment has provided quick and accurate models which are capable to manipulate much more complex data then deliver more precise results. They perform not only on small data but also on very large scale ones [3].

Pymc-learn is a Python package providing a variety of state-of-the-art probabilistic models for supervised and unsupervised machine learning. It is inspired by scikit-learn and focuses on bringing probabilistic machine learning to non-specialists. It uses a general-purpose high-level language that mimics scikit-learn. Emphasis is put on ease of use, productivity, flexibility, performance, documentation, and an API consistent with scikit-learn. It depends on scikit-learn and pymc3 and is distributed under the new BSD-3 license, encouraging its use in both academia and industry.

When analysing graph structure, it can be difficult to determine whether patterns found are due to chance, or due to structural aspects of the process that generated the data. Hypothesis tests are often used to support such analyses. These allow us to make statistical inferences about which null models are responsible for the data, and they can be used as a heuristic in searching for meaningful patterns. The minimum description length (MDL) principle [6, 4] allows us to build such hypothesis tests, based on efficient descriptions of the data. Broadly: we translate the regularity we are interested in into a code for the data, and if this code describes the data more efficiently than a code corresponding to the null model, by a sufficient margin, we may reject the null model. This is a frequentist approach to MDL, based on hypothesis testing. Bayesian approaches to MDL for model selection rather than model rejection are more common, but for the purposes of pattern analysis, a hypothesis testing approach provides a more natural fit with existing literature. 1 We provide a brief illustration of this principle based on the running example of analysing the size of the largest clique in a graph. We illustrate how a code can be constructed to efficiently represent graphs with large cliques, and how the description length of the data under this code can be compared to the description length under a code corresponding to a null model to show that the null model is highly unlikely to have generated the data.