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Genomics and Machine Learning

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Using SNP profiles of over 10k individuals from the Alzheimer's Disease Sequencing Project (ADSP) we have developed a computational framework for making diagnostic predictions regarding the likelihood that someone will develop Alzheimer's Disease (AD). A key feature of this framework is a neural network algorithm that, through machine learning, has been trained to predict AD patients or non-AD controls with high accuracy. Importantly, these predictions were made on individuals never seen by the classifier, suggesting high accuracy diagnoses could transfer to the general population. In fact, only a few hundred genomic loci are needed, and have been identified by the learning algorithms. The neural net outputs a ‘confidence’ level for each prediction; for individuals registering high-confidence predictions, the classifier is over 90% accurate. Since network weights have already been trained, and only a relatively small number of key variant loci are needed, this system could aid in clinical diagnostics; and as new genomes and clinical status are added, the system will continue to improve performance over time.

Here I provide a step-by-step analysis-walkthrough towards the goal of developing a platform for Alzheimer's Disease diagnosis based on machine learning techniques. Here are some entry pages: Intro, More Neural Nets, PCA, t-SNE.

Brownian Motion

Over the last year my main interest has been the study of synaptic potentiation from an animated, quantitative perspective (read: MCMC methods and simulation). Currently, I'm examining the membrane diffusion of neurotransmitter receptors and modeling how these particles swarm and potentiate synapses. It has been an interesting transition into these topics - prior to these projects I worked primarily with brain tissue and mice, but now I find myself spending most of my day programming, running simulations, and working with equations. I'm not sure why, but I find diffusion quite interesting. Stochastic diffusion, like that in Brownian motion, is a pure actuation of the basic properties of statistics - probability distributions in particular. Given that synaptic potentiation is directly mediated by stochastic diffusion and synaptic capture of receptors, it seem that neurons have evolved into innate statistical computers. The result of 100 billion of these statistical computers making 100 trillion connections is the human brain.

• MY NOTES ON MODELING DIFFUSION

Synaptic Plasticity

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It is now generally accepted that many forms of adaptive behavior, including learning and memory, engender lasting physiological changes in the brain; reciprocally, neural plasticity among the brain’s synaptic connections provides the capacity for learning and memory. Whenever I have to summarize my primary research focus using just a few words, they always include: "synaptic plasticity". Indeed, I feel that the key to fully understanding cognitive processes like memory formation is through studying neural dynamics at the cellular-network, synaptic, and molecular levels.

Actin Modeling

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Machine Learning Tutorial

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I have developed a machine learning tutorial, focusing on supervised learning, but it also touches on techniques like t-SNE. It makes heavy use of Tensorflow Playground to visualize what is happening in multilayer neural networks during training. It also provides learners with an opportunity to try and solve problems classification problems live right on the web app.

Brain Functional Connectome Project

A connectome is a comprehensive map of the neural networks within the brain. It details the efferent and afferent pathways within and between brain regions. Functional Connectivity refers to the function of a particular brain region and its information processing role within a distributed neural network. The goal of this project is to create a platform where users can jump into the connectome at any given brain region and visually navigate to upstream and downstream regions; along the way, users can learn about the functional role of each brain region. All information has been collected from empirical sources and scientific databases, in particular, the Allan Brain Atlas. Error creating thumbnail: File missing

Brain Molecular Pathways Project

This project aims to provide annotated sets of molecular pathways involved in neural plasticity underlying learning and memory systems. In general, biological pathways display the series of interactions among molecules resulting in functional changes within cells and neural networks. Currently there are large scale projects dedicated to amassing pathway evidence via high-throughput methods. The goal is to translate this unwieldy biopathway data from several empirical databases into visually digestible material, by characterizing the features of molecular cascades most sensitive to an event of interest (e.g. fear conditioning or amphetamine addiction).

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Welcome to the official wiki of Brad Monk

Hello and welcome to my wiki. This is where I stash random information and have every intention of linking it all together someday. If you are so inclined, recent additions to this wiki can be found in the box on the right. For a non-curated glimpse of my activity you can check out the latest wiki updates. Older wiki content can be accessed using the [search box] or perusing all pages. If you would like to contact me, you can find this info on my home page.

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