arXiv subjects

Neelam Sinha

Publications and source records attributed to Neelam Sinha.

31 records · Page 2Linked to original sources

arXiv2024

Multi-scale fMRI time series analysis for understanding neurodegeneration in MCI

In this study, we present a technique that spans multi-scale views (global scale -- meaning brain network-level and local scale -- examining each individual ROI that constitutes the network) applied to resting-state fMRI volumes. Deep learning based classification is utilized in understanding neurodegeneration. The novelty of the proposed approach lies in utilizing two extreme scales of analysis. One branch considers the entire network within graph-analysis framework. Concurrently, the second branch scrutinizes each ROI within a network independently, focusing on evolution of dynamics. For each subject, graph-based approach employs partial correlation to profile the subject in a single graph where each ROI is a node, providing insights into differences in levels of participation. In contrast, non-linear analysis employs recurrence plots to profile a subject as a multichannel 2D image, revealing distinctions in underlying dynamics. The proposed approach is employed for classification of a cohort of 50 healthy control (HC) and 50 Mild Cognitive Impairment (MCI), sourced from ADNI dataset. Results point to: (1) reduced activity in ROIs such as PCC in MCI (2) greater activity in occipital in MCI, which is not seen in HC (3) when analysed for dynamics, all ROIs in MCI show greater predictability in time-series.

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arXiv2023

Localizing and Assessing Node Significance in Default Mode Network using Sub-Community Detection in Mild Cognitive Impairment

Our study aims to utilize fMRI to identify the affected brain regions within the Default Mode Network (DMN) in subjects with Mild Cognitive Impairment (MCI), using a novel Node Significance Score (NSS). We construct subject-specific DMN graphs by employing partial correlation of Regions of Interest (ROIs) that make-up the DMN. For the DMN graph, ROIs are the nodes and edges are determined based on partial correlation. Four popular community detection algorithms (Clique Percolation Method (CPM), Louvain algorithm, Greedy Modularity and Leading Eigenvectors) are applied to determine the largest sub-community. NSS ratings are derived for each node, considering (I) frequency in the largest sub-community within a class across all subjects and (II) occurrence in the largest sub-community according to all four methods. After computing the NSS of each ROI in both healthy and MCI subjects, we quantify the score disparity to identify nodes most impacted by MCI. The results reveal a disparity exceeding 20% for 10 DMN nodes, maximally for PCC and Fusiform, showing 45.69% and 43.08% disparity. This aligns with existing medical literature, additionally providing a quantitative measure that enables the ordering of the affected ROIs. These findings offer valuable insights and could lead to treatment strategies aggressively targeting the affected nodes.

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arXiv2023

MCI Detection using fMRI time series embeddings of Recurrence plots

The human brain can be conceptualized as a dynamical system. Utilizing resting state fMRI time series imaging, we can study the underlying dynamics at ear-marked Regions of Interest (ROIs) to understand structure or lack thereof. This differential behavior could be key to understanding the neurodegeneration and also to classify between healthy and Mild Cognitive Impairment (MCI) subjects. In this study, we consider 6 brain networks spanning over 160 ROIs derived from Dosenbach template, where each network consists of 25-30 ROIs. Recurrence plot, extensively used to understand evolution of time series, is employed. Representative time series at each ROI is converted to its corresponding recurrence plot visualization, which is subsequently condensed to low-dimensional feature embeddings through Autoencoders. The performance of the proposed method is shown on fMRI volumes of 100 subjects (balanced data), taken from publicly available ADNI dataset. Results obtained show peak classification accuracy of 93% among the 6 brain networks, mean accuracy of 89.3% thereby illustrating promise in the proposed approach.

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arXiv2023

Image complexity based fMRI-BOLD visual network categorization across visual datasets using topological descriptors and deep-hybrid learning

This study proposes a new approach that investigates differences in topological characteristics of visual networks, which are constructed using fMRI BOLD time-series corresponding to visual datasets of COCO, ImageNet, and SUN. A publicly available BOLD5000 dataset is utilized that contains fMRI scans while viewing 5254 images of diverse complexities. The objective of this study is to examine how network topology differs in response to distinct visual stimuli from these visual datasets. To achieve this, 0- and 1-dimensional persistence diagrams are computed for each visual network representing COCO, ImageNet, and SUN. For extracting suitable features from topological persistence diagrams, K-means clustering is executed. The extracted K-means cluster features are fed to a novel deep-hybrid model that yields accuracy in the range of 90%-95% in classifying these visual networks. To understand vision, this type of visual network categorization across visual datasets is important as it captures differences in BOLD signals while perceiving images with different contexts and complexities. Furthermore, distinctive topological patterns of visual network associated with each dataset, as revealed from this study, could potentially lead to the development of future neuroimaging biomarkers for diagnosing visual processing disorders like visual agnosia or prosopagnosia, and tracking changes in visual cognition over time.

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arXiv2023

Investigating the changes in BOLD responses during viewing of images with varied complexity: An fMRI time-series based analysis on human vision

Functional MRI (fMRI) is widely used to examine brain functionality by detecting alteration in oxygenated blood flow that arises with brain activity. This work aims to investigate the neurological variation of human brain responses during viewing of images with varied complexity using fMRI time series (TS) analysis. Publicly available BOLD5000 dataset is used for this purpose which contains fMRI scans while viewing 5254 distinct images of diverse categories, drawn from three standard computer vision datasets: COCO, Imagenet and SUN. To understand vision, it is important to study how brain functions while looking at images of diverse complexities. Our first study employs classical machine learning and deep learning strategies to classify image complexity-specific fMRI TS, represents instances when images from COCO, Imagenet and SUN datasets are seen. The implementation of this classification across visual datasets holds great significance, as it provides valuable insights into the fluctuations in BOLD signals when perceiving images of varying complexities. Subsequently, temporal semantic segmentation is also performed on whole fMRI TS to segment these time instances. The obtained result of this analysis has established a baseline in studying how differently human brain functions while looking into images of diverse complexities. Therefore, accurate identification and distinguishing of variations in BOLD signals from fMRI TS data serves as a critical initial step in vision studies, providing insightful explanations for how static images with diverse complexities are perceived.

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arXiv2023

Spatial encoding of BOLD fMRI time series for categorizing static images across visual datasets: A pilot study on human vision

Functional MRI (fMRI) is widely used to examine brain functionality by detecting alteration in oxygenated blood flow that arises with brain activity. In this study, complexity specific image categorization across different visual datasets is performed using fMRI time series (TS) to understand differences in neuronal activities related to vision. Publicly available BOLD5000 dataset is used for this purpose, containing fMRI scans while viewing 5254 images of diverse categories, drawn from three standard computer vision datasets: COCO, ImageNet and SUN. To understand vision, it is important to study how brain functions while looking at different images. To achieve this, spatial encoding of fMRI BOLD TS has been performed that uses classical Gramian Angular Field (GAF) and Markov Transition Field (MTF) to obtain 2D BOLD TS, representing images of COCO, Imagenet and SUN. For classification, individual GAF and MTF features are fed into regular CNN. Subsequently, parallel CNN model is employed that uses combined 2D features for classifying images across COCO, Imagenet and SUN. The result of 2D CNN models is also compared with 1D LSTM and Bi-LSTM that utilizes raw fMRI BOLD signal for classification. It is seen that parallel CNN model outperforms other network models with an improvement of 7% for multi-class classification. Clinical relevance- The obtained result of this analysis establishes a baseline in studying how differently human brain functions while looking at images of diverse complexities.

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arXiv2023

Identification of Stochasticity by Matrix-decomposition: Applied on Black Hole Data

Timeseries classification as stochastic (noise-like) or non-stochastic (structured), helps understand the underlying dynamics, in several domains. Here we propose a two-legged matrix decomposition-based algorithm utilizing two complementary techniques for classification. In Singular Value Decomposition (SVD) based analysis leg, we perform topological analysis (Betti numbers) on singular vectors containing temporal information, leading to SVD-label. Parallely, temporal-ordering agnostic Principal Component Analysis (PCA) is performed, and the proposed PCA-derived features are computed. These features, extracted from synthetic timeseries of the two labels, are observed to map the timeseries to a linearly separable feature space. Support Vector Machine (SVM) is used to produce PCA-label. The proposed methods have been applied to synthetic data, comprising 41 realisations of white-noise, pink-noise (stochastic), Logistic-map at growth-rate 4 and Lorentz-system (non-stochastic), as proof-of-concept. Proposed algorithm is applied on astronomical data: 12 temporal-classes of timeseries of black hole GRS 1915+105, obtained from RXTE satellite with average length 25000. For a given timeseries, if SVD-label and PCA-label concur, then the label is retained; else deemed "Uncertain". Comparison of obtained results with those in literature are presented. It's found that out of 12 temporal classes of GRS 1915+105, concurrence between SVD-label and PCA-label is obtained on 11 of them.

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arXiv2023

Interpretable simultaneous localization of MRI corpus callosum and classification of atypical Parkinsonian disorders using YOLOv5

Structural MRI(S-MRI) is one of the most versatile imaging modality that revolutionized the anatomical study of brain in past decades. The corpus callosum (CC) is the principal white matter fibre tract, enabling all kinds of inter-hemispheric communication. Thus, subtle changes in CC might be associated with various neurological disorders. The present work proposes the potential of YOLOv5-based CC detection framework to differentiate atypical Parkinsonian disorders (PD) from healthy controls (HC). With 3 rounds of hold-out validation, mean classification accuracy of 92% is obtained using the proposed method on a proprietary dataset consisting of 20 healthy subjects and 20 cases of APDs, with an improvement of 5% over SOTA methods (CC morphometry and visual texture analysis) that used the same dataset. Subsequently, in order to incorporate the explainability of YOLO predictions, Eigen CAM based heatmap is generated for identifying the most important sub-region in CC that leads to the classification. The result of Eigen CAM showed CC mid-body as the most distinguishable sub-region in classifying APDs and HC, which is in-line with SOTA methodologies and the current prevalent understanding in medicine.

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arXiv2023

Identifying Stochasticity in Time-Series with Autoencoder-Based Content-aware 2D Representation: Application to Black Hole Data

In this work, we report an autoencoder-based 2D representation to classify a time-series as stochastic or non-stochastic, to understand the underlying physical process. Content-aware conversion of 1D time-series to 2D representation, that simultaneously utilizes time- and frequency-domain characteristics, is proposed. An autoencoder is trained with a loss function to learn latent space (using both time- and frequency domains) representation, that is designed to be, time-invariant. Every element of the time-series is represented as a tuple with two components, one each, from latent space representation in time- and frequency-domains, forming a binary image. In this binary image, those tuples that represent the points in the time-series, together form the ``Latent Space Signature" (LSS) of the input time-series. The obtained binary LSS images are fed to a classification network. The EfficientNetv2-S classifier is trained using 421 synthetic time-series, with fair representation from both categories. The proposed methodology is evaluated on publicly available astronomical data which are 12 distinct temporal classes of time-series pertaining to the black hole GRS 1915 + 105, obtained from RXTE satellite. Results obtained using the proposed methodology are compared with existing techniques. Concurrence in labels obtained across the classes, illustrates the efficacy of the proposed 2D representation using the latent space co-ordinates. The proposed methodology also outputs the confidence in the classification label.

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arXiv2021

SSEGEP: Small SEGment Emphasized Performance evaluation metric for medical image segmentation

Automatic image segmentation is a critical component of medical image analysis, and hence quantifying segmentation performance is crucial. Challenges in medical image segmentation are mainly due to spatial variations of regions to be segmented and imbalance in distribution of classes. Commonly used metrics treat all detected pixels, indiscriminately. However, pixels in smaller segments must be treated differently from pixels in larger segments, as detection of smaller ones aid in early treatment of associated disease and are also easier to miss. To address this, we propose a novel evaluation metric for segmentation performance, emphasizing smaller segments, by assigning higher weightage to smaller segment pixels. Weighted false positives are also considered in deriving the new metric named, "SSEGEP"(Small SEGment Emphasized Performance evaluation metric), (range : 0(Bad) to 1(Good)). The experiments were performed on diverse anatomies(eye, liver, pancreas and breast) from publicly available datasets to show applicability of the proposed metric across different imaging techniques. Mean opinion score (MOS) and statistical significance testing is used to quantify the relevance of proposed approach. Across 33 fundus images, where the largest exudate is 1.41%, and the smallest is 0.0002% of the image, the proposed metric is 30% closer to MOS, as compared to Dice Similarity Coefficient (DSC). Statistical significance testing resulted in promising p-value of order 10^{-18} with SSEGEP for hepatic tumor compared to DSC. The proposed metric is found to perform better for the images having multiple segments for a single label.

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arXiv2021

Using Topological Framework for the Design of Activation Function and Model Pruning in Deep Neural Networks

Success of deep neural networks in diverse tasks across domains of computer vision, speech recognition and natural language processing, has necessitated understanding the dynamics of training process and also working of trained models. Two independent contributions of this paper are 1) Novel activation function for faster training convergence 2) Systematic pruning of filters of models trained irrespective of activation function. We analyze the topological transformation of the space of training samples as it gets transformed by each successive layer during training, by changing the activation function. The impact of changing activation function on the convergence during training is reported for the task of binary classification. A novel activation function aimed at faster convergence for classification tasks is proposed. Here, Betti numbers are used to quantify topological complexity of data. Results of experiments on popular synthetic binary classification datasets with large Betti numbers(>150) using MLPs are reported. Results show that the proposed activation function results in faster convergence requiring fewer epochs by a factor of 1.5 to 2, since Betti numbers reduce faster across layers with the proposed activation function. The proposed methodology was verified on benchmark image datasets: fashion MNIST, CIFAR-10 and cat-vs-dog images, using CNNs. Based on empirical results, we propose a novel method for pruning a trained model. The trained model was pruned by eliminating filters that transform data to a topological space with large Betti numbers. All filters with Betti numbers greater than 300 were removed from each layer without significant reduction in accuracy. This resulted in faster prediction time and reduced memory size of the model.

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arXiv2021

Towards Learning a Vocabulary of Visual Concepts and Operators using Deep Neural Networks

Deep neural networks have become the default choice for many applications like image and video recognition, segmentation and other image and video related tasks.However, a critical challenge with these models is the lack of explainability.This requirement of generating explainable predictions has motivated the research community to perform various analysis on trained models.In this study, we analyze the learned feature maps of trained models using MNIST images for achieving more explainable predictions.Our study is focused on deriving a set of primitive elements, here called visual concepts, that can be used to generate any arbitrary sample from the data generating distribution.We derive the primitive elements from the feature maps learned by the model.We illustrate the idea by generating visual concepts from a Variational Autoencoder trained using MNIST images.We augment the training data of MNIST dataset by adding about 60,000 new images generated with visual concepts chosen at random.With this we were able to reduce the reconstruction loss (mean square error) from an initial value of 120 without augmentation to 60 with augmentation.Our approach is a first step towards the final goal of achieving trained deep neural network models whose predictions, features in hidden layers and the learned filters can be well explained.Such a model when deployed in production can easily be modified to adapt to new data, whereas existing deep learning models need a re training or fine tuning. This process again needs a huge number of data samples that are not easy to generate unless the model has good explainability.

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arXiv2016

Cognitive state classification using transformed fMRI data

One approach, for understanding human brain functioning, is to analyze the changes in the brain while performing cognitive tasks. Towards this, Functional Magnetic Resonance (fMR) images of subjects performing well-defined tasks are widely utilized for task-specific analyses. In this work, we propose a procedure to enable classification between two chosen cognitive tasks, using their respective fMR image sequences. The time series of expert-marked anatomically-mapped relevant voxels are processed and fed as input to the classical Naive Bayesian and SVM classifiers. The processing involves use of random sieve function, phase information in the data transformed using Fourier and Hilbert transformations. This processing results in improved classification, as against using the voxel intensities directly, as illustrated. The novelty of the proposed method lies in utilizing the phase information in the transformed domain, for classifying between the cognitive tasks along with random sieve function chosen with a particular probability distribution. The proposed classification procedure is applied on a publicly available dataset, StarPlus data, with 6 subjects performing the two distinct cognitive tasks of watching either a picture or a sentence. The classification accuracy stands at an average of 65.6%(using Naive Bayes classifier) and 76.4%(using SVM classifier) for raw data. The corresponding classification accuracy stands at 96.8% and 97.5% for Fourier transformed data. For Hilbert transformed data, it is 93.7% and 99%, for 6 subjects, on 2 cognitive tasks.

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