arXiv subjects

Shekhar S. Chandra

Publications and source records attributed to Shekhar S. Chandra.

At least 37 records · Page 2Linked to original sources

arXiv2023

Towards Trustable Skin Cancer Diagnosis via Rewriting Model's Decision

Deep neural networks have demonstrated promising performance on image recognition tasks. However, they may heavily rely on confounding factors, using irrelevant artifacts or bias within the dataset as the cue to improve performance. When a model performs decision-making based on these spurious correlations, it can become untrustable and lead to catastrophic outcomes when deployed in the real-world scene. In this paper, we explore and try to solve this problem in the context of skin cancer diagnosis. We introduce a human-in-the-loop framework in the model training process such that users can observe and correct the model's decision logic when confounding behaviors happen. Specifically, our method can automatically discover confounding factors by analyzing the co-occurrence behavior of the samples. It is capable of learning confounding concepts using easily obtained concept exemplars. By mapping the black-box model's feature representation onto an explainable concept space, human users can interpret the concept and intervene via first order-logic instruction. We systematically evaluate our method on our newly crafted, well-controlled skin lesion dataset and several public skin lesion datasets. Experiments show that our method can effectively detect and remove confounding factors from datasets without any prior knowledge about the category distribution and does not require fully annotated concept labels. We also show that our method enables the model to focus on clinical-related concepts, improving the model's performance and trustworthiness during model inference.

cs.CV↗

arXiv2022

NBC-Softmax : Darkweb Author fingerprinting and migration tracking

Metric learning aims to learn distances from the data, which enhances the performance of similarity-based algorithms. An author style detection task is a metric learning problem, where learning style features with small intra-class variations and larger inter-class differences is of great importance to achieve better performance. Recently, metric learning based on softmax loss has been used successfully for style detection. While softmax loss can produce separable representations, its discriminative power is relatively poor. In this work, we propose NBC-Softmax, a contrastive loss based clustering technique for softmax loss, which is more intuitive and able to achieve superior performance. Our technique meets the criterion for larger number of samples, thus achieving block contrastiveness, which is proven to outperform pair-wise losses. It uses mini-batch sampling effectively and is scalable. Experiments on 4 darkweb social forums, with NBCSAuthor that uses the proposed NBC-Softmax for author and sybil detection, shows that our negative block contrastive approach constantly outperforms state-of-the-art methods using the same network architecture. Our code is publicly available at : https://github.com/gayanku/NBC-Softmax

cs.LG↗

arXiv2022

Automated anomaly-aware 3D segmentation of bones and cartilages in knee MR images from the Osteoarthritis Initiative

In medical image analysis, automated segmentation of multi-component anatomical structures, which often have a spectrum of potential anomalies and pathologies, is a challenging task. In this work, we develop a multi-step approach using U-Net-based neural networks to initially detect anomalies (bone marrow lesions, bone cysts) in the distal femur, proximal tibia and patella from 3D magnetic resonance (MR) images of the knee in individuals with varying grades of osteoarthritis. Subsequently, the extracted data are used for downstream tasks involving semantic segmentation of individual bone and cartilage volumes as well as bone anomalies. For anomaly detection, the U-Net-based models were developed to reconstruct the bone profiles of the femur and tibia in images via inpainting so anomalous bone regions could be replaced with close to normal appearances. The reconstruction error was used to detect bone anomalies. A second anomaly-aware network, which was compared to anomaly-naïve segmentation networks, was used to provide a final automated segmentation of the femoral, tibial and patellar bones and cartilages from the knee MR images containing a spectrum of bone anomalies. The anomaly-aware segmentation approach provided up to 58% reduction in Hausdorff distances for bone segmentations compared to the results from the anomaly-naïve segmentation networks. In addition, the anomaly-aware networks were able to detect bone lesions in the MR images with greater sensitivity and specificity (area under the receiver operating characteristic curve [AUC] up to 0.896) compared to the anomaly-naïve segmentation networks (AUC up to 0.874).

eess.IV↗

arXiv2022

Generalisable 3D Fabric Architecture for Streamlined Universal Multi-Dataset Medical Image Segmentation

Data scarcity is common in deep learning models for medical image segmentation. Previous works proposed multi-dataset learning, either simultaneously or via transfer learning to expand training sets. However, medical image datasets have diverse-sized images and features, and developing a model simultaneously for multiple datasets is challenging. This work proposes Fabric Image Representation Encoding Network (FIRENet), a universal architecture for simultaneous multi-dataset segmentation and transfer learning involving arbitrary numbers of dataset(s). To handle different-sized image and feature, a 3D fabric module is used to encapsulate many multi-scale sub-architectures. An optimal combination of these sub-architectures can be implicitly learnt to best suit the target dataset(s). For diverse-scale feature extraction, a 3D extension of atrous spatial pyramid pooling (ASPP3D) is used in each fabric node for a fine-grained coverage of rich-scale image features. In the first experiment, FIRENet performed 3D universal bone segmentation of multiple musculoskeletal datasets of the human knee, shoulder and hip joints and exhibited excellent simultaneous multi-dataset segmentation performance. When tested for transfer learning, FIRENet further exhibited excellent single dataset performance (when pre-training on a prostate dataset), as well as significantly improved universal bone segmentation performance. The following experiment involves the simultaneous segmentation of the 10 Medical Segmentation Decathlon (MSD) challenge datasets. FIRENet demonstrated good multi-dataset segmentation results and inter-dataset adaptability of highly diverse image sizes. In both experiments, FIRENet's streamlined multi-dataset learning with one unified network that requires no hyper-parameter tuning.

eess.IV↗

arXiv2022

Efficient block contrastive learning via parameter-free meta-node approximation

Contrastive learning has recently achieved remarkable success in many domains including graphs. However contrastive loss, especially for graphs, requires a large number of negative samples which is unscalable and computationally prohibitive with a quadratic time complexity. Sub-sampling is not optimal and incorrect negative sampling leads to sampling bias. In this work, we propose a meta-node based approximation technique that can (a) proxy all negative combinations (b) in quadratic cluster size time complexity, (c) at graph level, not node level, and (d) exploit graph sparsity. By replacing node-pairs with additive cluster-pairs, we compute the negatives in cluster-time at graph level. The resulting Proxy approximated meta-node Contrastive (PamC) loss, based on simple optimized GPU operations, captures the full set of negatives, yet is efficient with a linear time complexity. By avoiding sampling, we effectively eliminate sample bias. We meet the criterion for larger number of samples, thus achieving block-contrastiveness, which is proven to outperform pair-wise losses. We use learnt soft cluster assignments for the meta-node constriction, and avoid possible heterophily and noise added during edge creation. Theoretically, we show that real world graphs easily satisfy conditions necessary for our approximation. Empirically, we show promising accuracy gains over state-of-the-art graph clustering on 6 benchmarks. Importantly, we gain substantially in efficiency; up to 3x in training time, 1.8x in inference time and over 5x in GPU memory reduction.

cs.LG↗

arXiv2022

Skin Lesion Recognition with Class-Hierarchy Regularized Hyperbolic Embeddings

In practice, many medical datasets have an underlying taxonomy defined over the disease label space. However, existing classification algorithms for medical diagnoses often assume semantically independent labels. In this study, we aim to leverage class hierarchy with deep learning algorithms for more accurate and reliable skin lesion recognition. We propose a hyperbolic network to learn image embeddings and class prototypes jointly. The hyperbola provably provides a space for modeling hierarchical relations better than Euclidean geometry. Meanwhile, we restrict the distribution of hyperbolic prototypes with a distance matrix that is encoded from the class hierarchy. Accordingly, the learned prototypes preserve the semantic class relations in the embedding space and we can predict the label of an image by assigning its feature to the nearest hyperbolic class prototype. We use an in-house skin lesion dataset which consists of around 230k dermoscopic images on 65 skin diseases to verify our method. Extensive experiments provide evidence that our model can achieve higher accuracy with less severe classification errors than models without considering class relations.

cs.CV↗

arXiv2022

Transformer Compressed Sensing via Global Image Tokens

Convolutional neural networks (CNN) have demonstrated outstanding Compressed Sensing (CS) performance compared to traditional, hand-crafted methods. However, they are broadly limited in terms of generalisability, inductive bias and difficulty to model long distance relationships. Transformer neural networks (TNN) overcome such issues by implementing an attention mechanism designed to capture dependencies between inputs. However, high-resolution tasks typically require vision Transformers (ViT) to decompose an image into patch-based tokens, limiting inputs to inherently local contexts. We propose a novel image decomposition that naturally embeds images into low-resolution inputs. These Kaleidoscope tokens (KD) provide a mechanism for global attention, at the same computational cost as a patch-based approach. To showcase this development, we replace CNN components in a well-known CS-MRI neural network with TNN blocks and demonstrate the improvements afforded by KD. We also propose an ensemble of image tokens, which enhance overall image quality and reduces model size. Supplementary material is available: https://github.com/uqmarlonbran/TCS.git

cs.CV↗

arXiv2022

SCGC : Self-Supervised Contrastive Graph Clustering

Graph clustering discovers groups or communities within networks. Deep learning methods such as autoencoders (AE) extract effective clustering and downstream representations but cannot incorporate rich structural information. While Graph Neural Networks (GNN) have shown great success in encoding graph structure, typical GNNs based on convolution or attention variants suffer from over-smoothing, noise, heterophily, are computationally expensive and typically require the complete graph being present. Instead, we propose Self-Supervised Contrastive Graph Clustering (SCGC), which imposes graph-structure via contrastive loss signals to learn discriminative node representations and iteratively refined soft cluster labels. We also propose SCGC*, with a more effective, novel, Influence Augmented Contrastive (IAC) loss to fuse richer structural information, and half the original model parameters. SCGC(*) is faster with simple linear units, completely eliminate convolutions and attention of traditional GNNs, yet efficiently incorporates structure. It is impervious to layer depth and robust to over-smoothing, incorrect edges and heterophily. It is scalable by batching, a limitation in many prior GNN models, and trivially parallelizable. We obtain significant improvements over state-of-the-art on a wide range of benchmark graph datasets, including images, sensor data, text, and citation networks efficiently. Specifically, 20% on ARI and 18% on NMI for DBLP; overall 55% reduction in training time and overall, 81% reduction on inference time. Our code is available at : https://github.com/gayanku/SCGC

cs.LG↗

arXiv2022

Undersampled MRI Reconstruction with Side Information-Guided Normalisation

Magnetic resonance (MR) images exhibit various contrasts and appearances based on factors such as different acquisition protocols, views, manufacturers, scanning parameters, etc. This generally accessible appearance-related side information affects deep learning-based undersampled magnetic resonance imaging (MRI) reconstruction frameworks, but has been overlooked in the majority of current works. In this paper, we investigate the use of such side information as normalisation parameters in a convolutional neural network (CNN) to improve undersampled MRI reconstruction. Specifically, a Side Information-Guided Normalisation (SIGN) module, containing only few layers, is proposed to efficiently encode the side information and output the normalisation parameters. We examine the effectiveness of such a module on two popular reconstruction architectures, D5C5 and OUCR. The experimental results on both brain and knee images under various acceleration rates demonstrate that the proposed method improves on its corresponding baseline architectures with a significant margin.

eess.IV↗

arXiv2021

Automated volumetric and statistical shape assessment of cam-type morphology of the femoral head-neck region from 3D magnetic resonance images

Femoroacetabular impingement (FAI) cam morphology is routinely assessed using two-dimensional alpha angles which do not provide specific data on cam size characteristics. The purpose of this study is to implement a novel, automated three-dimensional (3D) pipeline, CamMorph, for segmentation and measurement of cam volume, surface area and height from magnetic resonance (MR) images in patients with FAI. The CamMorph pipeline involves two processes: i) proximal femur segmentation using an approach integrating 3D U-net with focused shape modelling (FSM); ii) use of patient-specific anatomical information from 3D FSM to simulate healthy femoral bone models and pathological region constraints to identify cam bone mass. Agreement between manual and automated segmentation of the proximal femur was evaluated with the Dice similarity index (DSI) and surface distance measures. Independent t-tests or Mann-Whitney U rank tests were used to compare the femoral head volume, cam volume, surface area and height data between female and male patients with FAI. There was a mean DSI value of 0.964 between manual and automated segmentation of proximal femur volume. Compared to female FAI patients, male patients had a significantly larger mean femoral head volume (66.12cm3 v 46.02cm3, p<0.001). Compared to female FAI patients, male patients had a significantly larger mean cam volume (1136.87mm3 v 337.86mm3, p<0.001), surface area (657.36mm2 v 306.93mm2 , p<0.001), maximum-height (3.89mm v 2.23mm, p<0.001) and average-height (1.94mm v 1.00mm, p<0.001). Automated analyses of 3D MR images from patients with FAI using the CamMorph pipeline showed that, in comparison with female patients, male patients had significantly greater cam volume, surface area and height.

eess.IV↗

arXiv2021

FDGATII : Fast Dynamic Graph Attention with Initial Residual and Identity Mapping

While Graph Neural Networks have gained popularity in multiple domains, graph-structured input remains a major challenge due to (a) over-smoothing, (b) noisy neighbours (heterophily), and (c) the suspended animation problem. To address all these problems simultaneously, we propose a novel graph neural network FDGATII, inspired by attention mechanism's ability to focus on selective information supplemented with two feature preserving mechanisms. FDGATII combines Initial Residuals and Identity Mapping with the more expressive dynamic self-attention to handle noise prevalent from the neighbourhoods in heterophilic data sets. By using sparse dynamic attention, FDGATII is inherently parallelizable in design, whist efficient in operation; thus theoretically able to scale to arbitrary graphs with ease. Our approach has been extensively evaluated on 7 datasets. We show that FDGATII outperforms GAT and GCN based benchmarks in accuracy and performance on fully supervised tasks, obtaining state-of-the-art results on Chameleon and Cornell datasets with zero domain-specific graph pre-processing, and demonstrate its versatility and fairness.

cs.LG↗

arXiv2021

CAN3D: Fast 3D Medical Image Segmentation via Compact Context Aggregation

Direct automatic segmentation of objects from 3D medical imaging, such as magnetic resonance (MR) imaging, is challenging as it often involves accurately identifying a number of individual objects with complex geometries within a large volume under investigation. To address these challenges, most deep learning approaches typically enhance their learning capability by substantially increasing the complexity or the number of trainable parameters within their models. Consequently, these models generally require long inference time on standard workstations operating clinical MR systems and are restricted to high-performance computing hardware due to their large memory requirement. Further, to fit 3D dataset through these large models using limited computer memory, trade-off techniques such as patch-wise training are often used which sacrifice the fine-scale geometric information from input images which could be clinically significant for diagnostic purposes. To address these challenges, we present a compact convolutional neural network with a shallow memory footprint to efficiently reduce the number of model parameters required for state-of-art performance. This is critical for practical employment as most clinical environments only have low-end hardware with limited computing power and memory. The proposed network can maintain data integrity by directly processing large full-size 3D input volumes with no patches required and significantly reduces the computational time required for both training and inference. We also propose a novel loss function with extra shape constraint to improve the accuracy for imbalanced classes in 3D MR images.

eess.IV↗

arXiv2021

Bespoke Fractal Sampling Patterns for Discrete Fourier Space via the Kaleidoscope Transform

Sampling strategies are important for sparse imaging methodologies, especially those employing the discrete Fourier transform (DFT). Chaotic sensing is one such methodology that employs deterministic, fractal sampling in conjunction with finite, iterative reconstruction schemes to form an image from limited samples. Using a sampling pattern constructed entirely from periodic lines in DFT space, chaotic sensing was found to outperform traditional compressed sensing for magnetic resonance imaging; however, only one such sampling pattern was presented and the reason for its fractal nature was not proven. Through the introduction of a novel image transform known as the kaleidoscope transform, which formalises and extends upon the concept of downsampling and concatenating an image with itself, this paper: (1) demonstrates a fundamental relationship between multiplication in modular arithmetic and downsampling; (2) provides a rigorous mathematical explanation for the fractal nature of the sampling pattern in the DFT; and (3) leverages this understanding to develop a collection of novel fractal sampling patterns for the 2D DFT with customisable properties. The ability to design tailor-made fractal sampling patterns expands the utility of the DFT in chaotic imaging and may form the basis for a bespoke chaotic sensing methodology, in which the fractal sampling matches the imaging task for improved reconstruction.

eess.IV↗

arXiv2021

Deep Simultaneous Optimisation of Sampling and Reconstruction for Multi-contrast MRI

MRI images of the same subject in different contrasts contain shared information, such as the anatomical structure. Utilizing the redundant information amongst the contrasts to sub-sample and faithfully reconstruct multi-contrast images could greatly accelerate the imaging speed, improve image quality and shorten scanning protocols. We propose an algorithm that generates the optimised sampling pattern and reconstruction scheme of one contrast (e.g. T2-weighted image) when images with different contrast (e.g. T1-weighted image) have been acquired. The proposed algorithm achieves increased PSNR and SSIM with the resulting optimal sampling pattern compared to other acquisition patterns and single contrast methods.

cs.CV↗

arXiv2020

Manipulating Medical Image Translation with Manifold Disentanglement

Medical image translation (e.g. CT to MR) is a challenging task as it requires I) faithful translation of domain-invariant features (e.g. shape information of anatomical structures) and II) realistic synthesis of target-domain features (e.g. tissue appearance in MR). In this work, we propose Manifold Disentanglement Generative Adversarial Network (MDGAN), a novel image translation framework that explicitly models these two types of features. It employs a fully convolutional generator to model domain-invariant features, and it uses style codes to separately model target-domain features as a manifold. This design aims to explicitly disentangle domain-invariant features and domain-specific features while gaining individual control of both. The image translation process is formulated as a stylisation task, where the input is "stylised" (translated) into diverse target-domain images based on style codes sampled from the learnt manifold. We test MDGAN for multi-modal medical image translation, where we create two domain-specific manifold clusters on the manifold to translate segmentation maps into pseudo-CT and pseudo-MR images, respectively. We show that by traversing a path across the MR manifold cluster, the target output can be manipulated while still retaining the shape information from the input.

cs.CV↗

arXiv2020

Automatic lesion detection, segmentation and characterization via 3D multiscale morphological sifting in breast MRI

Previous studies on computer aided detection/diagnosis (CAD) in 4D breast magnetic resonance imaging (MRI) regard lesion detection, segmentation and characterization as separate tasks, and typically require users to manually select 2D MRI slices or regions of interest as the input. In this work, we present a breast MRI CAD system that can handle 4D multimodal breast MRI data, and integrate lesion detection, segmentation and characterization with no user intervention. The proposed CAD system consists of three major stages: region candidate generation, feature extraction and region candidate classification. Breast lesions are firstly extracted as region candidates using the novel 3D multiscale morphological sifting (MMS). The 3D MMS, which uses linear structuring elements to extract lesion-like patterns, can segment lesions from breast images accurately and efficiently. Analytical features are then extracted from all available 4D multimodal breast MRI sequences, including T1-, T2-weighted and DCE sequences, to represent the signal intensity, texture, morphological and enhancement kinetic characteristics of the region candidates. The region candidates are lastly classified as lesion or normal tissue by the random under-sampling boost (RUSboost), and as malignant or benign lesion by the random forest. Evaluated on a breast MRI dataset which contains a total of 117 cases with 95 malignant and 46 benign lesions, the proposed system achieves a true positive rate (TPR) of 0.90 at 3.19 false positives per patient (FPP) for lesion detection and a TPR of 0.91 at a FPP of 2.95 for identifying malignant lesions without any user intervention. The average dice similarity index (DSI) is 0.72 for lesion segmentation. Compared with previously proposed systems evaluated on the same breast MRI dataset, the proposed CAD system achieves a favourable performance in breast lesion detection and characterization.

eess.IV↗

arXiv2019

Fully automatic computer-aided mass detection and segmentation via pseudo-color mammograms and Mask R-CNN

Mammographic mass detection and segmentation are usually performed as serial and separate tasks, with segmentation often only performed on manually confirmed true positive detections in previous studies. We propose a fully-integrated computer-aided detection (CAD) system for simultaneous mammographic mass detection and segmentation without user intervention. The proposed CAD only consists of a pseudo-color image generation and a mass detection-segmentation stage based on Mask R-CNN. Grayscale mammograms are transformed into pseudo-color images based on multi-scale morphological sifting where mass-like patterns are enhanced to improve the performance of Mask R-CNN. Transfer learning with the Mask R-CNN is then adopted to simultaneously detect and segment masses on the pseudo-color images. Evaluated on the public dataset INbreast, the method outperforms the state-of-the-art methods by achieving an average true positive rate of 0.90 at 0.9 false positive per image and an average Dice similarity index of 0.88 for mass segmentation.

cs.CV↗

arXiv2010

Fast Mojette Transform for Discrete Tomography

A new algorithm for reconstructing a two dimensional object from a set of one dimensional projected views is presented that is both computationally exact and experimentally practical. The algorithm has a computational complexity of O(n log2 n) with n = N^2 for an NxN image, is robust in the presence of noise and produces no artefacts in the reconstruction process, as is the case with conventional tomographic methods. The reconstruction process is approximation free because the object is assumed to be discrete and utilizes fully discrete Radon transforms. Noise in the projection data can be suppressed further by introducing redundancy in the reconstruction. The number of projections required for exact reconstruction and the response to noise can be controlled without comprising the digital nature of the algorithm. The digital projections are those of the Mojette Transform, a form of discrete linogram. A simple analytical mapping is developed that compacts these projections exactly into symmetric periodic slices within the Discrete Fourier Transform. A new digital angle set is constructed that allows the periodic slices to completely fill all of the objects Discrete Fourier space. Techniques are proposed to acquire these digital projections experimentally to enable fast and robust two dimensional reconstructions.

physics.med-ph↗