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Abstract INTRODUCTIONAlzheimer's disease (AD) initiates years prior to symptoms, underscoring the importance of early detection. While amyloid accumulation starts early, individuals with substantial amyloid burden may remain cognitively normal, implying that amyloid alone is not sufficient for early risk assessment. METHODSGiven the genetic susceptibility of AD, a multi‐factorial pseudotime approach was proposed to integrate amyloid imaging and genotype data for estimating a risk score. Validation involved association with cognitive decline and survival analysis across risk‐stratified groups, focusing on patients with mild cognitive impairment (MCI). RESULTSOur risk score outperformed amyloid composite standardized uptake value ratio in correlation with cognitive scores. MCI subjects with lower pseudotime risk score showed substantial delayed onset of AD and slower cognitive decline. Moreover, pseudotime risk score demonstrated strong capability in risk stratification within traditionally defined subgroups such as early MCI, apolipoprotein E (APOE) ε4+ MCI,APOEε4– MCI, and amyloid+ MCI. DISCUSSIONOur risk score holds great potential to improve the precision of early risk assessment. HighlightsAccurate early risk assessment is critical for the success of clinical trials.A new risk score was built from integrating amyloid imaging and genetic data.Our risk score demonstrated improved capability in early risk stratification. 

Background: There are various molecular hypotheses regarding Alzheimer’s disease (AD) like amyloid deposition, tau propagation, neuroinflammation, and synaptic dysfunction. However, detailed molecular mechanism underlying AD remains elusive. In addition, genetic contribution of these molecular hypothesis is not yet established despite the high heritability of AD. Objective: The study aims to enable the discovery of functionally connected multi-omic features through novel integration of multi-omic data and prior functional interactions. Methods: We propose a new deep learning model MoFNet with improved interpretability to investigate the AD molecular mechanism and its upstream genetic contributors. MoFNet integrates multi-omic data with prior functional interactions between SNPs, genes, and proteins, and for the first time models the dynamic information flow from DNA to RNA and proteins. Results: When evaluated using the ROS/MAP cohort, MoFNet outperformed other competing methods in prediction performance. It identified SNPs, genes, and proteins with significantly more prior functional interactions, resulting in three multi-omic subnetworks. SNP-gene pairs identified by MoFNet were mostly eQTLs specific to frontal cortex tissue where gene/protein data was collected. These molecular subnetworks are enriched in innate immune system, clearance of misfolded proteins, and neurotransmitter release respectively. We validated most findings in an independent dataset. One multi-omic subnetwork consists exclusively of core members of SNARE complex, a key mediator of synaptic vesicle fusion and neurotransmitter transportation. Conclusions: Our results suggest that MoFNet is effective in improving classification accuracy and in identifying multi-omic markers for AD with improved interpretability. Multi-omic subnetworks identified by MoFNet provided insights of AD molecular mechanism with improved details. 

SUMMARY Seismograms contain multiple sources of seismic waves, from distinct transient signals such as earthquakes to continuous ambient seismic vibrations such as microseism. Ambient vibrations contaminate the earthquake signals, while the earthquake signals pollute the ambient noise’s statistical properties necessary for ambient-noise seismology analysis. Separating ambient noise from earthquake signals would thus benefit multiple seismological analyses. This work develops a multitask encoder–decoder network named WaveDecompNet to separate transient signals from ambient signals directly in the time domain for 3-component seismograms. We choose the active-volcanic Big Island in Hawai’i as a natural laboratory given its richness in transients (tectonic and volcanic earthquakes) and diffuse ambient noise (strong microseism). The approach takes a noisy 3-component seismogram as input and independently predicts the 3-component earthquake and noise waveforms. The model is trained on earthquake and noise waveforms from the STandford EArthquake Dataset (STEAD) and on the local noise of seismic station IU.POHA. We estimate the network’s performance by using the explained variance metric on both earthquake and noise waveforms. We explore different neural network designs for WaveDecompNet and find that the model with long-short-term memory (LSTM) performs best over other structures. Overall, we find that WaveDecompNet provides satisfactory performance down to a signal-to-noise ratio (SNR) of 0.1. The potential of the method is (1) to improve broad-band SNR of transient (earthquake) waveforms and (2) to improve local ambient noise to monitor the Earth’s structure using ambient noise signals. To test this, we apply a short-time average to a long-time average filter and improve the number of detected events. We also measure single-station cross-correlation functions of the recovered ambient noise and establish their improved coherence through time and over different frequency bands. We conclude that WaveDecompNet is a promising tool for a broad range of seismological research. 

Abstract Background There is growing evidence indicating that a number of functional connectivity networks are disrupted at each stage of the full clinical Alzheimer’s disease spectrum. Such differences are also detectable in cognitive normal (CN) carrying mutations of AD risk genes, suggesting a substantial relationship between genetics and AD-altered functional brain networks. However, direct genetic effect on functional connectivity networks has not been measured. Methods Leveraging existing AD functional connectivity studies collected in NeuroSynth, we performed a meta-analysis to identify two sets of brain regions: ones with altered functional connectivity in resting state network and ones without. Then with the brain-wide gene expression data in the Allen Human Brain Atlas, we applied a new biclustering method to identify a set of genes with differential co-expression patterns between these two set of brain regions. Results Differential co-expression analysis using biclustering method led to a subset of 38 genes which showed distinctive co-expression patterns between AD-related and non AD-related brain regions in default mode network. More specifically, we observed 4 sub-clusters with noticeable co-expression difference, where the difference in correlations is above 0.5 on average. Conclusions This work applies a new biclustering method to search for a subset of genes with altered co-expression patterns in AD-related default mode network regions. Compared with traditional differential expression analysis, differential co-expression analysis yielded many more significant hits with extra insights into the wiring mechanism between genes. Particularly, the differential co-expression pattern was observed between two sets of genes, suggesting potential upstream genetic regulators in AD development. 

IntroductionBrain imaging genetics aims to explore the genetic architecture underlying brain structure and functions. Recent studies showed that the incorporation of prior knowledge, such as subject diagnosis information and brain regional correlation, can help identify significantly stronger imaging genetic associations. However, sometimes such information may be incomplete or even unavailable. MethodsIn this study, we explore a new data-driven prior knowledge that captures the subject-level similarity by fusing multi-modal similarity networks. It was incorporated into the sparse canonical correlation analysis (SCCA) model, which is aimed to identify a small set of brain imaging and genetic markers that explain the similarity matrix supported by both modalities. It was applied to amyloid and tau imaging data of the ADNI cohort, respectively. ResultsFused similarity matrix across imaging and genetic data was found to improve the association performance better or similarly well as diagnosis information, and therefore would be a potential substitute prior when the diagnosis information is not available (i.e., studies focused on healthy controls). DiscussionOur result confirmed the value of all types of prior knowledge in improving association identification. In addition, the fused network representing the subject relationship supported by multi-modal data showed consistently the best or equally best performance compared to the diagnosis network and the co-expression network.