Data-driven prediction of a multi-scale Lorenz 96 chaotic system using deep learning methods: Reservoir computing, ANN, and RNN-LSTM

In this paper, the performance of three deep learning methods for predicting short-term evolution and for reproducing the long-term statistics of a multi-scale spatio-temporal Lorenz 96 system is examined. The methods are: echo state network (a type of reservoir computing, RC-ESN), deep feed-forward artificial neural network (ANN), and recurrent neural network with long short-term memory (RNN-LSTM). This Lorenz 96 system has three tiers of nonlinearly interacting variables representing slow/large-scale ($X$), intermediate ($Y$), and fast/small-scale ($Z$) processes. For training or testing, only $X$ is available; $Y$ and $Z$ are never known or used. We show that RC-ESN substantially outperforms ANN and RNN-LSTM for short-term prediction, e.g., accurately forecasting the chaotic trajectories for hundreds of numerical solver's time steps, equivalent to several Lyapunov timescales. The RNN-LSTM and ANN show some prediction skills as well; RNN-LSTM bests ANN. Furthermore, even after losing the trajectory, data predicted by RC-ESN and RNN-LSTM have probability density functions (PDFs) that closely match the true PDF, even at the tails. The PDF of the data predicted using ANN, however, deviates from the true PDF. Implications, caveats, and applications to data-driven and data-assisted surrogate modeling of complex nonlinear dynamical systems such as weather/climate are discussed.Comment: Some changes, in Figures, addition of an appendix etc has been don

Dense attentive GAN-based one-class model for detection of autism and ADHD

We investigate two neuro-developmental disorders in children– Autism Spectrum Disorder (ASD) and Attention-deficit/hyperactivity disorder (ADHD). Most works in literature have examined these disorders separately, e.g., ASD or ADHD subjects vs healthy subjects. We base our framework on the approach adopted by a paediatrician. We propose a one-class model for characterizing healthy subjects. Any subject with ASD/ADHD is considered an outlier by this one-class model. We adopt a Dense GAN architecture with self-attention modules as our one-class model. Our system uses T1-weighted longitudinal structural magnetic resonance images (sMRI) as input modalities. Further, we train our framework using longitudinal data (two scans per subject over time) only, instead of the traditional approaches using cross-sectional data (one scan per subject). Our approach is similar to paediatricians diagnosing the subject over multiple sessions to confirm the disorder. Comprehensive experiments show that our proposed approach performs better than competing ASD and ADHD works

The Common Order-Theoretic Structure of Version Spaces and ATMS\u27s

This paper exposes the common order-theoretic properties of the structures manipulated by the version space algorithm [Mit78]and the assumption-based truth maintenance systems (ATMS) [dk86a,dk86b] by recasting them in the framework of convex spaces. Our analysis of version spaces in this framework reveals necessary and sufficient conditions for ensuring the preservation of an essential finite representability property in version space merging. This analysis is used to formulate several sufficient conditions for when a language will allow version spaces to be represented by finite sets of concepts (even when the universe of concepts may be infinite). We provide a new convex space based formulation of computation performs by an ATMS which extends the expressiveness of disjunctions in the systems. This approach obviates the need for hyper-resolution in dealing with disjunction and results in simpler label-update algorithms

Improving Pharmacovigilance Signal Detection from Clinical Notes with Locality Sensitive Neural Concept Embeddings

Although pharmaceutical products undergo clinical trials to profile efficacy and safety, some adverse drug reactions (ADRs) are only discovered after release to market. Post-market drug safety surveillance - pharmacovigilance - leverages information from various sources to proactively identify such ADRs. Clinical notes are one source of observational data that could assist this process, but their inherent complexity can obfuscate possible ADR signals. In previous research, embeddings trained on observational reports have improved detection of such signals over commonly used statistical measures. Moreover, neural embedding methods which further encode juxtapositional information have shown promise on analogical retrieval tasks, suggesting proximity-based alternatives to document-level modeling for signal detection. This work uses natural language processing and locality sensitive neural embeddings to increase ADR signal recovery from clinical notes, with AUCs of ~0.63-0.71. Constituting a ~50% increase over baselines, our method sets the state-of-the-art for these reference standards when solely leveraging clinical notes

New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data

<p>Abstract</p> <p>Background</p> <p>Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining the data is not a trivial task. Algorithms that infer Bayesian networks from expression data are powerful tools for learning complex genetic networks, since they can incorporate prior knowledge and uncover higher-order dependencies among genes. However, these algorithms are computationally demanding, so novel techniques that allow targeted exploration for discovering new members of known pathways are essential.</p> <p>Results</p> <p>Here we describe a Bayesian network approach that addresses a specific network within a large dataset to discover new components. Our algorithm draws individual genes from a large gene-expression repository, and ranks them as potential members of a known pathway. We apply this method to discover new components of the cAMP-dependent protein kinase (PKA) pathway, a central regulator of <it>Dictyostelium discoideum </it>development. The PKA network is well studied in <it>D. discoideum </it>but the transcriptional networks that regulate PKA activity and the transcriptional outcomes of PKA function are largely unknown. Most of the genes highly ranked by our method encode either known components of the PKA pathway or are good candidates. We tested 5 uncharacterized highly ranked genes by creating mutant strains and identified a candidate cAMP-response element-binding protein, yet undiscovered in <it>D. discoideum</it>, and a histidine kinase, a candidate upstream regulator of PKA activity.</p> <p>Conclusions</p> <p>The single-gene expansion method is useful in identifying new components of known pathways. The method takes advantage of the Bayesian framework to incorporate prior biological knowledge and discovers higher-order dependencies among genes while greatly reducing the computational resources required to process high-throughput datasets.</p