arXiv subjects

Sergey Plis

Publications and source records attributed to Sergey Plis.

35 records · Page 2Linked to original sources

arXiv2023

SalientGrads: Sparse Models for Communication Efficient and Data Aware Distributed Federated Training

Federated learning (FL) enables the training of a model leveraging decentralized data in client sites while preserving privacy by not collecting data. However, one of the significant challenges of FL is limited computation and low communication bandwidth in resource limited edge client nodes. To address this, several solutions have been proposed in recent times including transmitting sparse models and learning dynamic masks iteratively, among others. However, many of these methods rely on transmitting the model weights throughout the entire training process as they are based on ad-hoc or random pruning criteria. In this work, we propose Salient Grads, which simplifies the process of sparse training by choosing a data aware subnetwork before training, based on the model-parameter's saliency scores, which is calculated from the local client data. Moreover only highly sparse gradients are transmitted between the server and client models during the training process unlike most methods that rely on sharing the entire dense model in each round. We also demonstrate the efficacy of our method in a real world federated learning application and report improvement in wall-clock communication time.

cs.LG↗

arXiv2022

Self-Supervised Mental Disorder Classifiers via Time Reversal

Data scarcity is a notable problem, especially in the medical domain, due to patient data laws. Therefore, efficient Pre-Training techniques could help in combating this problem. In this paper, we demonstrate that a model trained on the time direction of functional neuro-imaging data could help in any downstream task, for example, classifying diseases from healthy controls in fMRI data. We train a Deep Neural Network on Independent components derived from fMRI data using the Independent component analysis (ICA) technique. It learns time direction in the ICA-based data. This pre-trained model is further trained to classify brain disorders in different datasets. Through various experiments, we have shown that learning time direction helps a model learn some causal relation in fMRI data that helps in faster convergence, and consequently, the model generalizes well in downstream classification tasks even with fewer data records.

cs.LG↗

arXiv2022

Geometrically Guided Integrated Gradients

Interpretability methods for deep neural networks mainly focus on the sensitivity of the class score with respect to the original or perturbed input, usually measured using actual or modified gradients. Some methods also use a model-agnostic approach to understanding the rationale behind every prediction. In this paper, we argue and demonstrate that local geometry of the model parameter space relative to the input can also be beneficial for improved post-hoc explanations. To achieve this goal, we introduce an interpretability method called "geometrically-guided integrated gradients" that builds on top of the gradient calculation along a linear path as traditionally used in integrated gradient methods. However, instead of integrating gradient information, our method explores the model's dynamic behavior from multiple scaled versions of the input and captures the best possible attribution for each input. We demonstrate through extensive experiments that the proposed approach outperforms vanilla and integrated gradients in subjective and quantitative assessment. We also propose a "model perturbation" sanity check to complement the traditionally used "model randomization" test.

cs.CV↗

arXiv2022

Deep Dynamic Effective Connectivity Estimation from Multivariate Time Series

Recently, methods that represent data as a graph, such as graph neural networks (GNNs) have been successfully used to learn data representations and structures to solve classification and link prediction problems. The applications of such methods are vast and diverse, but most of the current work relies on the assumption of a static graph. This assumption does not hold for many highly dynamic systems, where the underlying connectivity structure is non-stationary and is mostly unobserved. Using a static model in these situations may result in sub-optimal performance. In contrast, modeling changes in graph structure with time can provide information about the system whose applications go beyond classification. Most work of this type does not learn effective connectivity and focuses on cross-correlation between nodes to generate undirected graphs. An undirected graph is unable to capture direction of an interaction which is vital in many fields, including neuroscience. To bridge this gap, we developed dynamic effective connectivity estimation via neural network training (DECENNT), a novel model to learn an interpretable directed and dynamic graph induced by the downstream classification/prediction task. DECENNT outperforms state-of-the-art (SOTA) methods on five different tasks and infers interpretable task-specific dynamic graphs. The dynamic graphs inferred from functional neuroimaging data align well with the existing literature and provide additional information. Additionally, the temporal attention module of DECENNT identifies time-intervals crucial for predictive downstream task from multivariate time series data.

cs.LG↗

arXiv2022

Brain dynamics via Cumulative Auto-Regressive Self-Attention

Multivariate dynamical processes can often be intuitively described by a weighted connectivity graph between components representing each individual time-series. Even a simple representation of this graph as a Pearson correlation matrix may be informative and predictive as demonstrated in the brain imaging literature. However, there is a consensus expectation that powerful graph neural networks (GNNs) should perform better in similar settings. In this work, we present a model that is considerably shallow than deep GNNs, yet outperforms them in predictive accuracy in a brain imaging application. Our model learns the autoregressive structure of individual time series and estimates directed connectivity graphs between the learned representations via a self-attention mechanism in an end-to-end fashion. The supervised training of the model as a classifier between patients and controls results in a model that generates directed connectivity graphs and highlights the components of the time-series that are predictive for each subject. We demonstrate our results on a functional neuroimaging dataset classifying schizophrenia patients and controls.

cs.LG↗

arXiv2022

Multi network InfoMax: A pre-training method involving graph convolutional networks

Discovering distinct features and their relations from data can help us uncover valuable knowledge crucial for various tasks, e.g., classification. In neuroimaging, these features could help to understand, classify, and possibly prevent brain disorders. Model introspection of highly performant overparameterized deep learning (DL) models could help find these features and relations. However, to achieve high-performance level DL models require numerous labeled training samples ($n$) rarely available in many fields. This paper presents a pre-training method involving graph convolutional/neural networks (GCNs/GNNs), based on maximizing mutual information between two high-level embeddings of an input sample. Many of the recently proposed pre-training methods pre-train one of many possible networks of an architecture. Since almost every DL model is an ensemble of multiple networks, we take our high-level embeddings from two different networks of a model --a convolutional and a graph network--. The learned high-level graph latent representations help increase performance for downstream graph classification tasks and bypass the need for a high number of labeled data samples. We apply our method to a neuroimaging dataset for classifying subjects into healthy control (HC) and schizophrenia (SZ) groups. Our experiments show that the pre-trained model significantly outperforms the non-pre-trained model and requires $50\%$ less data for similar performance.

cs.LG↗

arXiv2021

Single-Shot Pruning for Offline Reinforcement Learning

Deep Reinforcement Learning (RL) is a powerful framework for solving complex real-world problems. Large neural networks employed in the framework are traditionally associated with better generalization capabilities, but their increased size entails the drawbacks of extensive training duration, substantial hardware resources, and longer inference times. One way to tackle this problem is to prune neural networks leaving only the necessary parameters. State-of-the-art concurrent pruning techniques for imposing sparsity perform demonstrably well in applications where data distributions are fixed. However, they have not yet been substantially explored in the context of RL. We close the gap between RL and single-shot pruning techniques and present a general pruning approach to the Offline RL. We leverage a fixed dataset to prune neural networks before the start of RL training. We then run experiments varying the network sparsity level and evaluating the validity of pruning at initialization techniques in continuous control tasks. Our results show that with 95% of the network weights pruned, Offline-RL algorithms can still retain performance in the majority of our experiments. To the best of our knowledge, no prior work utilizing pruning in RL retained performance at such high levels of sparsity. Moreover, pruning at initialization techniques can be easily integrated into any existing Offline-RL algorithms without changing the learning objective.

cs.LG↗

arXiv2021

A deep learning model for data-driven discovery of functional connectivity

Functional connectivity (FC) studies have demonstrated the overarching value of studying the brain and its disorders through the undirected weighted graph of fMRI correlation matrix. Most of the work with the FC, however, depends on the way the connectivity is computed, and further depends on the manual post-hoc analysis of the FC matrices. In this work we propose a deep learning architecture BrainGNN that learns the connectivity structure as part of learning to classify subjects. It simultaneously applies a graphical neural network to this learned graph and learns to select a sparse subset of brain regions important to the prediction task. We demonstrate the model's state-of-the-art classification performance on a schizophrenia fMRI dataset and demonstrate how introspection leads to disorder relevant findings. The graphs learned by the model exhibit strong class discrimination and the sparse subset of relevant regions are consistent with the schizophrenia literature.

q-bio.NC↗

arXiv2021

Fusing multimodal neuroimaging data with a variational autoencoder

Neuroimaging studies often involve the collection of multiple data modalities. These modalities contain both shared and mutually exclusive information about the brain. This work aims at finding a scalable and interpretable method to fuse the information of multiple neuroimaging modalities using a variational autoencoder (VAE). To provide an initial assessment, this work evaluates the representations that are learned using a schizophrenia classification task. A support vector machine trained on the representations achieves an area under the curve for the classifier's receiver operating characteristic (ROC-AUC) of 0.8610.

cs.LG↗

arXiv2020

Meta-modal Information Flow: A Method for Capturing Multimodal Modular Disconnectivity in Schizophrenia

Objective: Multimodal measurements of the same phenomena provide complementary information and highlight different perspectives, albeit each with their own limitations. A focus on a single modality may lead to incorrect inferences, which is especially important when a studied phenomenon is a disease. In this paper, we introduce a method that takes advantage of multimodal data in addressing the hypotheses of disconnectivity and dysfunction within schizophrenia (SZ). Methods: We start with estimating and visualizing links within and among extracted multimodal data features using a Gaussian graphical model (GGM). We then propose a modularity-based method that can be applied to the GGM to identify links that are associated with mental illness across a multimodal data set. Through simulation and real data, we show our approach reveals important information about disease-related network disruptions that are missed with a focus on a single modality. We use functional MRI (fMRI), diffusion MRI (dMRI), and structural MRI (sMRI) to compute the fractional amplitude of low frequency fluctuations (fALFF), fractional anisotropy (FA), and gray matter (GM) concentration maps. These three modalities are analyzed using our modularity method. Results: Our results show missing links that are only captured by the cross-modal information that may play an important role in disconnectivity between the components. Conclusion: We identified multimodal (fALFF, FA and GM) disconnectivity in the default mode network area in patients with SZ, which would not have been detectable in a single modality. Significance: The proposed approach provides an important new tool for capturing information that is distributed among multiple imaging modalities.

cs.LG↗

arXiv2019

Transfer Learning of fMRI Dynamics

As a mental disorder progresses, it may affect brain structure, but brain function expressed in brain dynamics is affected much earlier. Capturing the moment when brain dynamics express the disorder is crucial for early diagnosis. The traditional approach to this problem via training classifiers either proceeds from handcrafted features or requires large datasets to combat the $m>>n$ problem when a high dimensional fMRI volume only has a single label that carries learning signal. Large datasets may not be available for a study of each disorder, or rare disorder types or sub-populations may not warrant for them. In this paper, we demonstrate a self-supervised pre-training method that enables us to pre-train directly on fMRI dynamics of healthy control subjects and transfer the learning to much smaller datasets of schizophrenia. Not only we enable classification of disorder directly based on fMRI dynamics in small data but also significantly speed up the learning when possible. This is encouraging evidence of informative transfer learning across datasets and diagnostic categories.

eess.IV↗

arXiv2019

Prediction of Progression to Alzheimer's disease with Deep InfoMax

Arguably, unsupervised learning plays a crucial role in the majority of algorithms for processing brain imaging. A recently introduced unsupervised approach Deep InfoMax (DIM) is a promising tool for exploring brain structure in a flexible non-linear way. In this paper, we investigate the use of variants of DIM in a setting of progression to Alzheimer's disease in comparison with supervised AlexNet and ResNet inspired convolutional neural networks. As a benchmark, we use a classification task between four groups: patients with stable, and progressive mild cognitive impairment (MCI), with Alzheimer's disease, and healthy controls. Our dataset is comprised of 828 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Our experiments highlight encouraging evidence of the high potential utility of DIM in future neuroimaging studies.

cs.LG↗

arXiv2018

Improving Classification Rate of Schizophrenia Using a Multimodal Multi-Layer Perceptron Model with Structural and Functional MR

The wide variety of brain imaging technologies allows us to exploit information inherent to different data modalities. The richness of multimodal datasets may increase predictive power and reveal latent variables that otherwise would have not been found. However, the analysis of multimodal data is often conducted by assuming linear interactions which impact the accuracy of the results. We propose the use of a multimodal multi-layer perceptron model to enhance the predictive power of structural and functional magnetic resonance imaging (sMRI and fMRI) combined. We also use a synthetic data generator to pre-train each modality input layers, alleviating the effects of the small sample size that is often the case for brain imaging modalities. The proposed model improved the average and uncertainty of the area under the ROC curve to 0.850+-0.051 compared to the best results on individual modalities (0.741+-0.075 for sMRI, and 0.833+-0.050 for fMRI).

cs.CV↗

arXiv2018

Learning to Run challenge solutions: Adapting reinforcement learning methods for neuromusculoskeletal environments

In the NIPS 2017 Learning to Run challenge, participants were tasked with building a controller for a musculoskeletal model to make it run as fast as possible through an obstacle course. Top participants were invited to describe their algorithms. In this work, we present eight solutions that used deep reinforcement learning approaches, based on algorithms such as Deep Deterministic Policy Gradient, Proximal Policy Optimization, and Trust Region Policy Optimization. Many solutions use similar relaxations and heuristics, such as reward shaping, frame skipping, discretization of the action space, symmetry, and policy blending. However, each of the eight teams implemented different modifications of the known algorithms.

cs.LG↗

arXiv2017

Almost instant brain atlas segmentation for large-scale studies

Large scale studies of group differences in healthy controls and patients and screenings for early stage disease prevention programs require processing and analysis of extensive multisubject datasets. Complexity of the task increases even further when segmenting structural MRI of the brain into an atlas with more than 50 regions. Current automatic approaches are time-consuming and hardly scalable; they often involve many error prone intermediate steps and don't utilize other available modalities. To alleviate these problems, we propose a feedforward fully convolutional neural network trained on the output produced by the state of the art models. Incredible speed due to available powerful GPUs neural network makes this analysis much easier and faster (from $>10$ hours to a minute). The proposed model is more than two orders of magnitudes faster than the state of the art and yet as accurate. We have evaluated the network's performance by comparing it with the state of the art in the task of differentiating region volumes of healthy controls and patients with schizophrenia on a dataset with 311 subjects. This comparison provides a strong evidence that speed did not harm the accuracy. The overall quality may also be increased by utilizing multi-modal datasets (not an easy task for other models) by simple adding more modalities as an input. Our model will be useful in large-scale studies as well as in clinical care solutions, where it can significantly reduce delay between the patient screening and the result.

cs.CV↗

arXiv2017

End-to-end learning of brain tissue segmentation from imperfect labeling

Segmenting a structural magnetic resonance imaging (MRI) scan is an important pre-processing step for analytic procedures and subsequent inferences about longitudinal tissue changes. Manual segmentation defines the current gold standard in quality but is prohibitively expensive. Automatic approaches are computationally intensive, incredibly slow at scale, and error prone due to usually involving many potentially faulty intermediate steps. In order to streamline the segmentation, we introduce a deep learning model that is based on volumetric dilated convolutions, subsequently reducing both processing time and errors. Compared to its competitors, the model has a reduced set of parameters and thus is easier to train and much faster to execute. The contrast in performance between the dilated network and its competitors becomes obvious when both are tested on a large dataset of unprocessed human brain volumes. The dilated network consistently outperforms not only another state-of-the-art deep learning approach, the up convolutional network, but also the ground truth on which it was trained. Not only can the incredible speed of our model make large scale analyses much easier but we also believe it has great potential in a clinical setting where, with little to no substantial delay, a patient and provider can go over test results.

cs.CV↗

arXiv2016

Causal Discovery from Subsampled Time Series Data by Constraint Optimization

This paper focuses on causal structure estimation from time series data in which measurements are obtained at a coarser timescale than the causal timescale of the underlying system. Previous work has shown that such subsampling can lead to significant errors about the system's causal structure if not properly taken into account. In this paper, we first consider the search for the system timescale causal structures that correspond to a given measurement timescale structure. We provide a constraint satisfaction procedure whose computational performance is several orders of magnitude better than previous approaches. We then consider finite-sample data as input, and propose the first constraint optimization approach for recovering the system timescale causal structure. This algorithm optimally recovers from possible conflicts due to statistical errors. More generally, these advances allow for a robust and non-parametric estimation of system timescale causal structures from subsampled time series data.

cs.AI↗