arXiv subjects

Archana Venkataraman

Publications and source records attributed to Archana Venkataraman.

27 records · Page 2Linked to original sources

arXiv2021

G-MIND: An End-to-End Multimodal Imaging-Genetics Framework for Biomarker Identification and Disease Classification

We propose a novel deep neural network architecture to integrate imaging and genetics data, as guided by diagnosis, that provides interpretable biomarkers. Our model consists of an encoder, a decoder and a classifier. The encoder learns a non-linear subspace shared between the input data modalities. The classifier and the decoder act as regularizers to ensure that the low-dimensional encoding captures predictive differences between patients and controls. We use a learnable dropout layer to extract interpretable biomarkers from the data, and our unique training strategy can easily accommodate missing data modalities across subjects. We have evaluated our model on a population study of schizophrenia that includes two functional MRI (fMRI) paradigms and Single Nucleotide Polymorphism (SNP) data. Using 10-fold cross validation, we demonstrate that our model achieves better classification accuracy than baseline methods, and that this performance generalizes to a second dataset collected at a different site. In an exploratory analysis we further show that the biomarkers identified by our model are closely associated with the well-documented deficits in schizophrenia.

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arXiv2020

Neuropsychiatric Disease Classification Using Functional Connectomics -- Results of the Connectomics in NeuroImaging Transfer Learning Challenge

Large, open-source consortium datasets have spurred the development of new and increasingly powerful machine learning approaches in brain connectomics. However, one key question remains: are we capturing biologically relevant and generalizable information about the brain, or are we simply overfitting to the data? To answer this, we organized a scientific challenge, the Connectomics in NeuroImaging Transfer Learning Challenge (CNI-TLC), held in conjunction with MICCAI 2019. CNI-TLC included two classification tasks: (1) diagnosis of Attention-Deficit/Hyperactivity Disorder (ADHD) within a pre-adolescent cohort; and (2) transference of the ADHD model to a related cohort of Autism Spectrum Disorder (ASD) patients with an ADHD comorbidity. In total, 240 resting-state fMRI time series averaged according to three standard parcellation atlases, along with clinical diagnosis, were released for training and validation (120 neurotypical controls and 120 ADHD). We also provided demographic information of age, sex, IQ, and handedness. A second set of 100 subjects (50 neurotypical controls, 25 ADHD, and 25 ASD with ADHD comorbidity) was used for testing. Models were submitted in a standardized format as Docker images through ChRIS, an open-source image analysis platform. Utilizing an inclusive approach, we ranked the methods based on 16 different metrics. The final rank was calculated using the rank product for each participant across all measures. Furthermore, we assessed the calibration curves of each method. Five participants submitted their model for evaluation, with one outperforming all other methods in both ADHD and ASD classification. However, further improvements are needed to reach the clinical translation of functional connectomics. We are keeping the CNI-TLC open as a publicly available resource for developing and validating new classification methodologies in the field of connectomics.

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arXiv2020

A Multi-Task Deep Learning Framework to Localize the Eloquent Cortex in Brain Tumor Patients Using Dynamic Functional Connectivity

We present a novel deep learning framework that uses dynamic functional connectivity to simultaneously localize the language and motor areas of the eloquent cortex in brain tumor patients. Our method leverages convolutional layers to extract graph-based features from the dynamic connectivity matrices and a long-short term memory (LSTM) attention network to weight the relevant time points during classification. The final stage of our model employs multi-task learning to identify different eloquent subsystems. Our unique training strategy finds a shared representation between the cognitive networks of interest, which enables us to handle missing patient data. We evaluate our method on resting-state fMRI data from 56 brain tumor patients while using task fMRI activations as surrogate ground-truth labels for training and testing. Our model achieves higher localization accuracies than conventional deep learning approaches and can identify bilateral language areas even when trained on left-hemisphere lateralized cases. Hence, our method may ultimately be useful for preoperative mapping in tumor patients.

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arXiv2020

Non-parallel Emotion Conversion using a Deep-Generative Hybrid Network and an Adversarial Pair Discriminator

We introduce a novel method for emotion conversion in speech that does not require parallel training data. Our approach loosely relies on a cycle-GAN schema to minimize the reconstruction error from converting back and forth between emotion pairs. However, unlike the conventional cycle-GAN, our discriminator classifies whether a pair of input real and generated samples corresponds to the desired emotion conversion (e.g., A to B) or to its inverse (B to A). We will show that this setup, which we refer to as a variational cycle-GAN (VC-GAN), is equivalent to minimizing the empirical KL divergence between the source features and their cyclic counterpart. In addition, our generator combines a trainable deep network with a fixed generative block to implement a smooth and invertible transformation on the input features, in our case, the fundamental frequency (F0) contour. This hybrid architecture regularizes our adversarial training procedure. We use crowd sourcing to evaluate both the emotional saliency and the quality of synthesized speech. Finally, we show that our model generalizes to new speakers by modifying speech produced by Wavenet.

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arXiv2020

Multi-speaker Emotion Conversion via Latent Variable Regularization and a Chained Encoder-Decoder-Predictor Network

We propose a novel method for emotion conversion in speech based on a chained encoder-decoder-predictor neural network architecture. The encoder constructs a latent embedding of the fundamental frequency (F0) contour and the spectrum, which we regularize using the Large Diffeomorphic Metric Mapping (LDDMM) registration framework. The decoder uses this embedding to predict the modified F0 contour in a target emotional class. Finally, the predictor uses the original spectrum and the modified F0 contour to generate a corresponding target spectrum. Our joint objective function simultaneously optimizes the parameters of three model blocks. We show that our method outperforms the existing state-of-the-art approaches on both, the saliency of emotion conversion and the quality of resynthesized speech. In addition, the LDDMM regularization allows our model to convert phrases that were not present in training, thus providing evidence for out-of-sample generalization.

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arXiv2020

A Coupled Manifold Optimization Framework to Jointly Model the Functional Connectomics and Behavioral Data Spaces

The problem of linking functional connectomics to behavior is extremely challenging due to the complex interactions between the two distinct, but related, data domains. We propose a coupled manifold optimization framework which projects fMRI data onto a low dimensional matrix manifold common to the cohort. The patient specific loadings simultaneously map onto a behavioral measure of interest via a second, non-linear, manifold. By leveraging the kernel trick, we can optimize over a potentially infinite dimensional space without explicitly computing the embeddings. As opposed to conventional manifold learning, which assumes a fixed input representation, our framework directly optimizes for embedding directions that predict behavior. Our optimization algorithm combines proximal gradient descent with the trust region method, which has good convergence guarantees. We validate our framework on resting state fMRI from fifty-eight patients with Autism Spectrum Disorder using three distinct measures of clinical severity. Our method outperforms traditional representation learning techniques in a cross validated setting, thus demonstrating the predictive power of our coupled objective.

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arXiv2018

A Novel Method for Epileptic Seizure Detection Using Coupled Hidden Markov Models

We propose a novel Coupled Hidden Markov Model to detect epileptic seizures in multichannel electroencephalography (EEG) data. Our model defines a network of seizure propagation paths to capture both the temporal and spatial evolution of epileptic activity. To address the intractability introduced by the coupled interactions, we derive a variational inference procedure to efficiently infer the seizure evolution from spectral patterns in the EEG data. We validate our model on EEG aquired under clinical conditions in the Epilepsy Monitoring Unit of the Johns Hopkins Hospital. Using 5-fold cross validation, we demonstrate that our model outperforms three baseline approaches which rely on a classical detection framework. Our model also demonstrates the potential to localize seizure onset zones in focal epilepsy.

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arXiv2018

A Generative-Discriminative Basis Learning Framework to Predict Clinical Severity from Resting State Functional MRI Data

We propose a matrix factorization technique that decomposes the resting state fMRI (rs-fMRI) correlation matrices for a patient population into a sparse set of representative subnetworks, as modeled by rank one outer products. The subnetworks are combined using patient specific non-negative coefficients; these coefficients are also used to model, and subsequently predict the clinical severity of a given patient via a linear regression. Our generative-discriminative framework is able to exploit the structure of rs-fMRI correlation matrices to capture group level effects, while simultaneously accounting for patient variability. We employ ten fold cross validation to demonstrate the predictive power of our model on a cohort of fifty eight patients diagnosed with Autism Spectrum Disorder. Our method outperforms classical semi-supervised frameworks, which perform dimensionality reduction on the correlation features followed by non-linear regression to predict the clinical scores.

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arXiv2018

Prediction of Autism Treatment Response from Baseline fMRI using Random Forests and Tree Bagging

Treating children with autism spectrum disorders (ASD) with behavioral interventions, such as Pivotal Response Treatment (PRT), has shown promise in recent studies. However, deciding which therapy is best for a given patient is largely by trial and error, and choosing an ineffective intervention results in loss of valuable treatment time. We propose predicting patient response to PRT from baseline task-based fMRI by the novel application of a random forest and tree bagging strategy. Our proposed learning pipeline uses random forest regression to determine candidate brain voxels that may be informative in predicting treatment response. The candidate voxels are then tested stepwise for inclusion in a bagged tree ensemble. After the predictive model is constructed, bias correction is performed to further increase prediction accuracy. Using data from 19 ASD children who underwent a 16 week trial of PRT and a leave-one-out cross-validation framework, the presented learning pipeline was tested against several standard methods and variations of the pipeline and resulted in the highest prediction accuracy.

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