Due to the potentially significant benefits for society, forecasting spatio-temporal societal events is currently attracting considerable attention from researchers. Beyond merely predicting the occurrence of future events, practitioners are now looking for information about specific subtypes of future events in order to allocate appropriate amounts and types of resources to manage such events and any associated social risks. However, forecasting event subtypes is far more complex than merely extending binary prediction to cover multiple classes, as 1) different locations require different models to handle their characteristic event subtype patterns due to spatial heterogeneity; 2) historically, many locations have only experienced a incomplete set of event subtypes, thus limiting the local model’s ability to predict previously “unseen” subtypes; and 3) the subtle discrepancy among different event subtypes requires more discriminative and profound representations of societal events. In order to address all these challenges concurrently, we propose a Spatial Incomplete Multi-task Deep leArning (SIMDA) framework that is capable of effectively forecasting the subtypes of future events. The new framework formulates spatial locations into tasks to handle spatial heterogeneity in event subtypes, and learns a joint deep representation of subtypes across tasks. Furthermore, based on the “first law of geography”, spatiallyclosed tasks sharemore »
Empowering Variational Inference with Predictive Features: Application to Disease Suptypying
Probabilistic topic models, have been widely deployed for various applications such as
learning disease or tissue subtypes. Yet, learning the parameters of such models is usually
an ill-posed problem and may result in losing valuable information about disease severity.
A common approach is to add a discriminative loss term to the generative model’s loss in
order to learn a representation that is also predictive of disease severity. However, finding
a balance between these two losses is not straightforward. We propose an alternative way
in this paper. We develop a framework which allows for incorporating external covariates
into the generative model’s approximate posterior. These covariates can have more discriminative power for disease severity compared to the representation that we extract from the posterior distribution. For instance, they can be features extracted from a neural network which predicts disease severity from CT images. Effectively, we enforce the generative model’s approximate posterior to reside in the subspace of these discriminative covariates. We illustrate our method’s application on a large-scale lung CT study of Chronic Obstructive Pulmonary Disease (COPD), a highly heterogeneous disease. We aim at identifying tissue subtypes by using a variant of topic model as a generative model. We quantitatively evaluate the predictive performance of the inferred subtypes and more »
- Award ID(s):
- 1839332
- Publication Date:
- NSF-PAR ID:
- 10299286
- Journal Name:
- Proceedings of Machine Learning Research
- Issue:
- 149
- Page Range or eLocation-ID:
- 1–19
- ISSN:
- 2640-3498
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Purpose: To develop and evaluate a deep learning (DL) approach to extract rich information from high-resolution computed tomography (HRCT) of patients with chronic obstructive pulmonary disease (COPD). Methods: We develop a DL-based model to learn a compact representation of a subject, which is predictive of COPD physiologic severity and other outcomes. Our DL model learned: (a) to extract informative regional image features from HRCT; (b) to adaptively weight these features and form an aggregate patient representation; and finally, (c) to predict several COPD outcomes. The adaptive weights correspond to the regional lung contribution to the disease. We evaluate the model on 10 300 participants from the COPDGene cohort. Results: Our model was strongly predictive of spirometric obstruction ( r2 = 0.67) and grouped 65.4% of subjects correctly and 89.1% within one stage of their GOLD severity stage. Our model achieved an accuracy of 41.7% and 52.8% in stratifying the population-based on centrilobular (5-grade) and paraseptal (3-grade) emphysema severity score, respectively. For predicting future exacerbation, combining subjects' representations from our model with their past exacerbation histories achieved an accuracy of 80.8% (area under the ROC curve of 0.73). For all-cause mortality, in Cox regression analysis, we outperformed the BODE index improvingmore »
-
Introduction: Computed tomography perfusion (CTP) imaging requires injection of an intravenous contrast agent and increased exposure to ionizing radiation. This process can be lengthy, costly, and potentially dangerous to patients, especially in emergency settings. We propose MAGIC, a multitask, generative adversarial network-based deep learning model to synthesize an entire CTP series from only a non-contrasted CT (NCCT) input. Materials and Methods: NCCT and CTP series were retrospectively retrieved from 493 patients at UF Health with IRB approval. The data were deidentified and all images were resized to 256x256 pixels. The collected perfusion data were analyzed using the RapidAI CT Perfusion analysis software (iSchemaView, Inc. CA) to generate each CTP map. For each subject, 10 CTP slices were selected. Each slice was paired with one NCCT slice at the same location and two NCCT slices at a predefined vertical offset, resulting in 4.3K CTP images and 12.9K NCCT images used for training. The incorporation of a spatial offset into the NCCT input allows MAGIC to more accurately synthesize cerebral perfusive structures, increasing the quality of the generated images. The studies included a variety of indications, including healthy tissue, mild infarction, and severe infarction. The proposed MAGIC model incorporates a novel multitaskmore »
-
Gorodkin, Jan (Ed.)Abstract Motivation When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks. Results In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variationalmore »
-
In many mechanistic medical, biological, physical, and engineered spatiotemporal dynamic models the numerical solution of partial differential equations (PDEs), especially for diffusion, fluid flow and mechanical relaxation, can make simulations impractically slow. Biological models of tissues and organs often require the simultaneous calculation of the spatial variation of concentration of dozens of diffusing chemical species. One clinical example where rapid calculation of a diffusing field is of use is the estimation of oxygen gradients in the retina, based on imaging of the retinal vasculature, to guide surgical interventions in diabetic retinopathy. Furthermore, the ability to predict blood perfusion and oxygenation may one day guide clinical interventions in diverse settings, i.e., from stent placement in treating heart disease to BOLD fMRI interpretation in evaluating cognitive function (Xie et al., 2019 ; Lee et al., 2020 ). Since the quasi-steady-state solutions required for fast-diffusing chemical species like oxygen are particularly computationally costly, we consider the use of a neural network to provide an approximate solution to the steady-state diffusion equation. Machine learning surrogates, neural networks trained to provide approximate solutions to such complicated numerical problems, can often provide speed-ups of several orders of magnitude compared to direct calculation. Surrogates of PDEs couldmore »
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Publisher's Version of Record
- The DOI is not currently available
