Browsing by Subject "graph neural network"

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    Deep trans-omic network fusion reveals altered synaptic network in Alzheimer’s Disease
    (CSH, 2023-02-21) Xie, Linhui; Raj, Yash; Varathan, Pradeep; He, Bing; Nho, Kwangsik; Risacher, Shannon L.; Salama, Paul; Saykin, Andrew J.; Yan, Jingwen; Electrical and Computer Engineering, School of Engineering and Technology
    Multi-omic data spanning from genotype, gene expression to protein expression have been increasingly explored to interpret findings from genome wide association studies of Alzheimer’s disease (AD) and to gain more insight of the disease mechanism. However, each -omics data type is usually examined individually and the functional interactions between genetic variations, genes and proteins are only used after discovery to interpret the findings, but not beforehand. In this case, multi-omic findings are likely not functionally related and therefore give rise to challenges in interpretation. To address this problem, we propose a new interpretable deep neural network model MoFNet to jointly model the prior knowledge of functional interactions and multi-omic data set. It aims to identify a subnetwork of functional interactions predictive of AD evidenced by multi-omic measures. Particularly, prior functional interaction network was embedded into the architecture of MoFNet in a way that it resembles the information flow from DNA to gene and protein. The proposed model MoFNet significantly outperformed all other state-of-art classifiers when evaluated using multi-omic data from the ROS/MAP cohort. Instead of individual markers, MoFNet yielded multi-omic sub-networks related to innate immune system, clearance of misfolded proteins, and neurotransmitter release respectively. Around 50% of these findings were replicated in another independent cohort. Our identified gene/proteins are highly related to synaptic vesicle function. Altered regulation or expression of these genes/proteins could cause disruption in neuron-neuron or neuron-glia cross talk and further lead to neuronal and synapse loss in AD. Further investigation of these identified genes/proteins could possibly help decipher the mechanisms underlying synaptic dysfunction in AD, and ultimately inform therapeutic strategies to modify AD progression in the early stage.
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    Solving Prediction Problems from Temporal Event Data on Networks
    (2021-08) Sha, Hao; Mohler, George; Hasan, Mohammad; Dundar, Murat; Mukhopadhyay, Snehasis
    Many complex processes can be viewed as sequential events on a network. In this thesis, we study the interplay between a network and the event sequences on it. We first focus on predicting events on a known network. Examples of such include: modeling retweet cascades, forecasting earthquakes, and tracing the source of a pandemic. In specific, given the network structure, we solve two types of problems - (1) forecasting future events based on the historical events, and (2) identifying the initial event(s) based on some later observations of the dynamics. The inverse problem of inferring the unknown network topology or links, based on the events, is also of great important. Examples along this line include: constructing influence networks among Twitter users from their tweets, soliciting new members to join an event based on their participation history, and recommending positions for job seekers according to their work experience. Following this direction, we study two types of problems - (1) recovering influence networks, and (2) predicting links between a node and a group of nodes, from event sequences.