arXiv subjects

Binod Bhattarai

Publications and source records attributed to Binod Bhattarai.

At least 55 records · Page 3Linked to original sources

arXiv2024

Input Invex Neural Network

Connected decision boundaries are useful in several tasks like image segmentation, clustering, alpha-shape or defining a region in nD-space. However, the machine learning literature lacks methods for generating connected decision boundaries using neural networks. Thresholding an invex function, a generalization of a convex function, generates such decision boundaries. This paper presents two methods for constructing invex functions using neural networks. The first approach is based on constraining a neural network with Gradient Clipped-Gradient Penality (GCGP), where we clip and penalise the gradients. In contrast, the second one is based on the relationship of the invex function to the composition of invertible and convex functions. We employ connectedness as a basic interpretation method and create connected region-based classifiers. We show that multiple connected set based classifiers can approximate any classification function. In the experiments section, we use our methods for classification tasks using an ensemble of 1-vs-all models as well as using a single multiclass model on small-scale datasets. The experiments show that connected set-based classifiers do not pose any disadvantage over ordinary neural network classifiers, but rather, enhance their interpretability. We also did an extensive study on the properties of invex function and connected sets for interpretability and network morphism with experiments on toy and real-world data sets. Our study suggests that invex function is fundamental to understanding and applying locality and connectedness of input space which is useful for various downstream tasks.

cs.LG↗

arXiv2024

Cross-Task Data Augmentation by Pseudo-label Generation for Region Based Coronary Artery Instance Segmentation

Coronary Artery Diseases (CADs) although preventable, are one of the leading causes of death and disability. Diagnosis of these diseases is often difficult and resource intensive. Angiographic imaging segmentation of the arteries has evolved as a tool of assistance that helps clinicians make an accurate diagnosis. However, due to the limited amount of data and the difficulty in curating a dataset, the task of segmentation has proven challenging. In this study, we introduce the use of pseudo-labels to address the issue of limited data in the angiographic dataset to enhance the performance of the baseline YOLO model. Unlike existing data augmentation techniques that improve the model constrained to a fixed dataset, we introduce the use of pseudo-labels generated on a dataset of separate related task to diversify and improve model performance. This method increases the baseline F1 score by 9% in the validation data set and by 3% in the test data set.

eess.IV↗

arXiv2024

TTA-OOD: Test-time Augmentation for Improving Out-of-Distribution Detection in Gastrointestinal Vision

Deep learning has significantly advanced the field of gastrointestinal vision, enhancing disease diagnosis capabilities. One major challenge in automating diagnosis within gastrointestinal settings is the detection of abnormal cases in endoscopic images. Due to the sparsity of data, this process of distinguishing normal from abnormal cases has faced significant challenges, particularly with rare and unseen conditions. To address this issue, we frame abnormality detection as an out-of-distribution (OOD) detection problem. In this setup, a model trained on In-Distribution (ID) data, which represents a healthy GI tract, can accurately identify healthy cases, while abnormalities are detected as OOD, regardless of their class. We introduce a test-time augmentation segment into the OOD detection pipeline, which enhances the distinction between ID and OOD examples, thereby improving the effectiveness of existing OOD methods with the same model. This augmentation shifts the pixel space, which translates into a more distinct semantic representation for OOD examples compared to ID examples. We evaluated our method against existing state-of-the-art OOD scores, showing improvements with test-time augmentation over the baseline approach.

cs.CV↗

arXiv2024

CAR-MFL: Cross-Modal Augmentation by Retrieval for Multimodal Federated Learning with Missing Modalities

Multimodal AI has demonstrated superior performance over unimodal approaches by leveraging diverse data sources for more comprehensive analysis. However, applying this effectiveness in healthcare is challenging due to the limited availability of public datasets. Federated learning presents an exciting solution, allowing the use of extensive databases from hospitals and health centers without centralizing sensitive data, thus maintaining privacy and security. Yet, research in multimodal federated learning, particularly in scenarios with missing modalities a common issue in healthcare datasets remains scarce, highlighting a critical area for future exploration. Toward this, we propose a novel method for multimodal federated learning with missing modalities. Our contribution lies in a novel cross-modal data augmentation by retrieval, leveraging the small publicly available dataset to fill the missing modalities in the clients. Our method learns the parameters in a federated manner, ensuring privacy protection and improving performance in multiple challenging multimodal benchmarks in the medical domain, surpassing several competitive baselines. Code Available: https://github.com/bhattarailab/CAR-MFL

cs.CV↗

arXiv2024

TE-SSL: Time and Event-aware Self Supervised Learning for Alzheimer's Disease Progression Analysis

Alzheimer's Dementia (AD) represents one of the most pressing challenges in the field of neurodegenerative disorders, with its progression analysis being crucial for understanding disease dynamics and developing targeted interventions. Recent advancements in deep learning and various representation learning strategies, including self-supervised learning (SSL), have shown significant promise in enhancing medical image analysis, providing innovative ways to extract meaningful patterns from complex data. Notably, the computer vision literature has demonstrated that incorporating supervisory signals into SSL can further augment model performance by guiding the learning process with additional relevant information. However, the application of such supervisory signals in the context of disease progression analysis remains largely unexplored. This gap is particularly pronounced given the inherent challenges of incorporating both event and time-to-event information into the learning paradigm. Addressing this, we propose a novel framework, Time and Even-aware SSL (TE-SSL), which integrates time-to-event and event data as supervisory signals to refine the learning process. Our comparative analysis with existing SSL-based methods in the downstream task of survival analysis shows superior performance across standard metrics.

cs.CV↗

arXiv2024

Multimodal Federated Learning in Healthcare: a Review

Recent advancements in multimodal machine learning have empowered the development of accurate and robust AI systems in the medical domain, especially within centralized database systems. Simultaneously, Federated Learning (FL) has progressed, providing a decentralized mechanism where data need not be consolidated, thereby enhancing the privacy and security of sensitive healthcare data. The integration of these two concepts supports the ongoing progress of multimodal learning in healthcare while ensuring the security and privacy of patient records within local data-holding agencies. This paper offers a concise overview of the significance of FL in healthcare and outlines the current state-of-the-art approaches to Multimodal Federated Learning (MMFL) within the healthcare domain. It comprehensively examines the existing challenges in the field, shedding light on the limitations of present models. Finally, the paper outlines potential directions for future advancements in the field, aiming to bridge the gap between cutting-edge AI technology and the imperative need for patient data privacy in healthcare applications.

cs.LG↗

arXiv2024

Investigating the Robustness of Vision Transformers against Label Noise in Medical Image Classification

Label noise in medical image classification datasets significantly hampers the training of supervised deep learning methods, undermining their generalizability. The test performance of a model tends to decrease as the label noise rate increases. Over recent years, several methods have been proposed to mitigate the impact of label noise in medical image classification and enhance the robustness of the model. Predominantly, these works have employed CNN-based architectures as the backbone of their classifiers for feature extraction. However, in recent years, Vision Transformer (ViT)-based backbones have replaced CNNs, demonstrating improved performance and a greater ability to learn more generalizable features, especially when the dataset is large. Nevertheless, no prior work has rigorously investigated how transformer-based backbones handle the impact of label noise in medical image classification. In this paper, we investigate the architectural robustness of ViT against label noise and compare it to that of CNNs. We use two medical image classification datasets -- COVID-DU-Ex, and NCT-CRC-HE-100K -- both corrupted by injecting label noise at various rates. Additionally, we show that pretraining is crucial for ensuring ViT's improved robustness against label noise in supervised training.

eess.IV↗

arXiv2024

Investigation of Federated Learning Algorithms for Retinal Optical Coherence Tomography Image Classification with Statistical Heterogeneity

Purpose: We apply federated learning to train an OCT image classifier simulating a realistic scenario with multiple clients and statistical heterogeneous data distribution where data in the clients lack samples of some categories entirely. Methods: We investigate the effectiveness of FedAvg and FedProx to train an OCT image classification model in a decentralized fashion, addressing privacy concerns associated with centralizing data. We partitioned a publicly available OCT dataset across multiple clients under IID and Non-IID settings and conducted local training on the subsets for each client. We evaluated two federated learning methods, FedAvg and FedProx for these settings. Results: Our experiments on the dataset suggest that under IID settings, both methods perform on par with training on a central data pool. However, the performance of both algorithms declines as we increase the statistical heterogeneity across the client data, while FedProx consistently performs better than FedAvg in the increased heterogeneity settings. Conclusion: Despite the effectiveness of federated learning in the utilization of private data across multiple medical institutions, the large number of clients and heterogeneous distribution of labels deteriorate the performance of both algorithms. Notably, FedProx appears to be more robust to the increased heterogeneity.

cs.CV↗

arXiv2024

How does self-supervised pretraining improve robustness against noisy labels across various medical image classification datasets?

Noisy labels can significantly impact medical image classification, particularly in deep learning, by corrupting learned features. Self-supervised pretraining, which doesn't rely on labeled data, can enhance robustness against noisy labels. However, this robustness varies based on factors like the number of classes, dataset complexity, and training size. In medical images, subtle inter-class differences and modality-specific characteristics add complexity. Previous research hasn't comprehensively explored the interplay between self-supervised learning and robustness against noisy labels in medical image classification, considering all these factors. In this study, we address three key questions: i) How does label noise impact various medical image classification datasets? ii) Which types of medical image datasets are more challenging to learn and more affected by label noise? iii) How do different self-supervised pretraining methods enhance robustness across various medical image datasets? Our results show that DermNet, among five datasets (Fetal plane, DermNet, COVID-DU-Ex, MURA, NCT-CRC-HE-100K), is the most challenging but exhibits greater robustness against noisy labels. Additionally, contrastive learning stands out among the eight self-supervised methods as the most effective approach to enhance robustness against noisy labels.

eess.IV↗

arXiv2023

Bimodal Camera Pose Prediction for Endoscopy

Deducing the 3D structure of endoscopic scenes from images is exceedingly challenging. In addition to deformation and view-dependent lighting, tubular structures like the colon present problems stemming from their self-occluding and repetitive anatomical structure. In this paper, we propose SimCol, a synthetic dataset for camera pose estimation in colonoscopy, and a novel method that explicitly learns a bimodal distribution to predict the endoscope pose. Our dataset replicates real colonoscope motion and highlights the drawbacks of existing methods. We publish 18k RGB images from simulated colonoscopy with corresponding depth and camera poses and make our data generation environment in Unity publicly available. We evaluate different camera pose prediction methods and demonstrate that, when trained on our data, they generalize to real colonoscopy sequences, and our bimodal approach outperforms prior unimodal work.

cs.CV↗

arXiv2023

Medical Vision Language Pretraining: A survey

Medical Vision Language Pretraining (VLP) has recently emerged as a promising solution to the scarcity of labeled data in the medical domain. By leveraging paired/unpaired vision and text datasets through self-supervised learning, models can be trained to acquire vast knowledge and learn robust feature representations. Such pretrained models have the potential to enhance multiple downstream medical tasks simultaneously, reducing the dependency on labeled data. However, despite recent progress and its potential, there is no such comprehensive survey paper that has explored the various aspects and advancements in medical VLP. In this paper, we specifically review existing works through the lens of different pretraining objectives, architectures, downstream evaluation tasks, and datasets utilized for pretraining and downstream tasks. Subsequently, we delve into current challenges in medical VLP, discussing existing and potential solutions, and conclude by highlighting future directions. To the best of our knowledge, this is the first survey focused on medical VLP.

cs.CV↗

arXiv2023

TextAug: Test time Text Augmentation for Multimodal Person Re-identification

Multimodal Person Reidentification is gaining popularity in the research community due to its effectiveness compared to counter-part unimodal frameworks. However, the bottleneck for multimodal deep learning is the need for a large volume of multimodal training examples. Data augmentation techniques such as cropping, flipping, rotation, etc. are often employed in the image domain to improve the generalization of deep learning models. Augmenting in other modalities than images, such as text, is challenging and requires significant computational resources and external data sources. In this study, we investigate the effectiveness of two computer vision data augmentation techniques: cutout and cutmix, for text augmentation in multi-modal person re-identification. Our approach merges these two augmentation strategies into one strategy called CutMixOut which involves randomly removing words or sub-phrases from a sentence (Cutout) and blending parts of two or more sentences to create diverse examples (CutMix) with a certain probability assigned to each operation. This augmentation was implemented at inference time without any prior training. Our results demonstrate that the proposed technique is simple and effective in improving the performance on multiple multimodal person re-identification benchmarks.

cs.CV↗

arXiv2023

Federated Active Learning for Target Domain Generalisation

In this paper, we introduce Active Learning framework in Federated Learning for Target Domain Generalisation, harnessing the strength from both learning paradigms. Our framework, FEDALV, composed of Active Learning (AL) and Federated Domain Generalisation (FDG), enables generalisation of an image classification model trained from limited source domain client's data without sharing images to an unseen target domain. To this end, our FDG, FEDA, consists of two optimisation updates during training, one at the client and another at the server level. For the client, the introduced losses aim to reduce feature complexity and condition alignment, while in the server, the regularisation limits free energy biases between source and target obtained by the global model. The remaining component of FEDAL is AL with variable budgets, which queries the server to retrieve and sample the most informative local data for the targeted client. We performed multiple experiments on FDG w/ and w/o AL and compared with both conventional FDG baselines and Federated Active Learning baselines. Our extensive quantitative experiments demonstrate the superiority of our method in accuracy and efficiency compared to the multiple contemporary methods. FEDALV manages to obtain the performance of the full training target accuracy while sampling as little as 5% of the source client's data.

cs.LG↗

arXiv2023

Importance Estimation with Random Gradient for Neural Network Pruning

Global Neuron Importance Estimation is used to prune neural networks for efficiency reasons. To determine the global importance of each neuron or convolutional kernel, most of the existing methods either use activation or gradient information or both, which demands abundant labelled examples. In this work, we use heuristics to derive importance estimation similar to Taylor First Order (TaylorFO) approximation based methods. We name our methods TaylorFO-abs and TaylorFO-sq. We propose two additional methods to improve these importance estimation methods. Firstly, we propagate random gradients from the last layer of a network, thus avoiding the need for labelled examples. Secondly, we normalize the gradient magnitude of the last layer output before propagating, which allows all examples to contribute similarly to the importance score. Our methods with additional techniques perform better than previous methods when tested on ResNet and VGG architectures on CIFAR-100 and STL-10 datasets. Furthermore, our method also complements the existing methods and improves their performances when combined with them.

cs.LG↗

arXiv2023

ConvNeXtv2 Fusion with Mask R-CNN for Automatic Region Based Coronary Artery Stenosis Detection for Disease Diagnosis

Coronary Artery Diseases although preventable are one of the leading cause of mortality worldwide. Due to the onerous nature of diagnosis, tackling CADs has proved challenging. This study addresses the automation of resource-intensive and time-consuming process of manually detecting stenotic lesions in coronary arteries in X-ray coronary angiography images. To overcome this challenge, we employ a specialized Convnext-V2 backbone based Mask RCNN model pre-trained for instance segmentation tasks. Our empirical findings affirm that the proposed model exhibits commendable performance in identifying stenotic lesions. Notably, our approach achieves a substantial F1 score of 0.5353 in this demanding task, underscoring its effectiveness in streamlining this intensive process.

cs.CV↗

arXiv2023

Task-guided Domain Gap Reduction for Monocular Depth Prediction in Endoscopy

Colorectal cancer remains one of the deadliest cancers in the world. In recent years computer-aided methods have aimed to enhance cancer screening and improve the quality and availability of colonoscopies by automatizing sub-tasks. One such task is predicting depth from monocular video frames, which can assist endoscopic navigation. As ground truth depth from standard in-vivo colonoscopy remains unobtainable due to hardware constraints, two approaches have aimed to circumvent the need for real training data: supervised methods trained on labeled synthetic data and self-supervised models trained on unlabeled real data. However, self-supervised methods depend on unreliable loss functions that struggle with edges, self-occlusion, and lighting inconsistency. Methods trained on synthetic data can provide accurate depth for synthetic geometries but do not use any geometric supervisory signal from real data and overfit to synthetic anatomies and properties. This work proposes a novel approach to leverage labeled synthetic and unlabeled real data. While previous domain adaptation methods indiscriminately enforce the distributions of both input data modalities to coincide, we focus on the end task, depth prediction, and translate only essential information between the input domains. Our approach results in more resilient and accurate depth maps of real colonoscopy sequences.

cs.CV↗

arXiv2023

Improving Medical Image Classification in Noisy Labels Using Only Self-supervised Pretraining

Noisy labels hurt deep learning-based supervised image classification performance as the models may overfit the noise and learn corrupted feature extractors. For natural image classification training with noisy labeled data, model initialization with contrastive self-supervised pretrained weights has shown to reduce feature corruption and improve classification performance. However, no works have explored: i) how other self-supervised approaches, such as pretext task-based pretraining, impact the learning with noisy label, and ii) any self-supervised pretraining methods alone for medical images in noisy label settings. Medical images often feature smaller datasets and subtle inter class variations, requiring human expertise to ensure correct classification. Thus, it is not clear if the methods improving learning with noisy labels in natural image datasets such as CIFAR would also help with medical images. In this work, we explore contrastive and pretext task-based self-supervised pretraining to initialize the weights of a deep learning classification model for two medical datasets with self-induced noisy labels -- NCT-CRC-HE-100K tissue histological images and COVID-QU-Ex chest X-ray images. Our results show that models initialized with pretrained weights obtained from self-supervised learning can effectively learn better features and improve robustness against noisy labels.

eess.IV↗

arXiv2023

CholecTriplet2022: Show me a tool and tell me the triplet -- an endoscopic vision challenge for surgical action triplet detection

Formalizing surgical activities as triplets of the used instruments, actions performed, and target anatomies is becoming a gold standard approach for surgical activity modeling. The benefit is that this formalization helps to obtain a more detailed understanding of tool-tissue interaction which can be used to develop better Artificial Intelligence assistance for image-guided surgery. Earlier efforts and the CholecTriplet challenge introduced in 2021 have put together techniques aimed at recognizing these triplets from surgical footage. Estimating also the spatial locations of the triplets would offer a more precise intraoperative context-aware decision support for computer-assisted intervention. This paper presents the CholecTriplet2022 challenge, which extends surgical action triplet modeling from recognition to detection. It includes weakly-supervised bounding box localization of every visible surgical instrument (or tool), as the key actors, and the modeling of each tool-activity in the form of triplet. The paper describes a baseline method and 10 new deep learning algorithms presented at the challenge to solve the task. It also provides thorough methodological comparisons of the methods, an in-depth analysis of the obtained results across multiple metrics, visual and procedural challenges; their significance, and useful insights for future research directions and applications in surgery.

eess.IV↗