arXiv subjects

Amit Sethi

Publications and source records attributed to Amit Sethi.

At least 55 records · Page 3Linked to original sources

arXiv2025

Scalable Whole Slide Image Representation Using K-Mean Clustering and Fisher Vector Aggregation

Whole slide images (WSIs) are high-resolution, gigapixel sized images that pose significant computational challenges for traditional machine learning models due to their size and heterogeneity.In this paper, we present a scalable and efficient methodology for WSI classification by leveraging patch-based feature extraction, clustering, and Fisher vector encoding. Initially, WSIs are divided into fixed size patches, and deep feature embeddings are extracted from each patch using a pre-trained convolutional neural network (CNN). These patch-level embeddings are subsequently clustered using K-means clustering, where each cluster aggregates semantically similar regions of the WSI. To effectively summarize each cluster, Fisher vector representations are computed by modeling the distribution of patch embeddings in each cluster as a parametric Gaussian mixture model (GMM). The Fisher vectors from each cluster are concatenated into a high-dimensional feature vector, creating a compact and informative representation of the entire WSI. This feature vector is then used by a classifier to predict the WSI's diagnostic label. Our method captures local and global tissue structures and yields robust performance for large-scale WSI classification, demonstrating superior accuracy and scalability compared to other approaches.

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arXiv2025

Evaluation Metric for Quality Control and Generative Models in Histopathology Images

Our study introduces ResNet-L2 (RL2), a novel metric for evaluating generative models and image quality in histopathology, addressing limitations of traditional metrics, such as Frechet inception distance (FID), when the data is scarce. RL2 leverages ResNet features with a normalizing flow to calculate RMSE distance in the latent space, providing reliable assessments across diverse histopathology datasets. We evaluated the performance of RL2 on degradation types, such as blur, Gaussian noise, salt-and-pepper noise, and rectangular patches, as well as diffusion processes. RL2's monotonic response to increasing degradation makes it well-suited for models that assess image quality, proving a valuable advancement for evaluating image generation techniques in histopathology. It can also be used to discard low-quality patches while sampling from a whole slide image. It is also significantly lighter and faster compared to traditional metrics and requires fewer images to give stable metric value.

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arXiv2024

Mitigating Instance-Dependent Label Noise: Integrating Self-Supervised Pretraining with Pseudo-Label Refinement

Deep learning models rely heavily on large volumes of labeled data to achieve high performance. However, real-world datasets often contain noisy labels due to human error, ambiguity, or resource constraints during the annotation process. Instance-dependent label noise (IDN), where the probability of a label being corrupted depends on the input features, poses a significant challenge because it is more prevalent and harder to address than instance-independent noise. In this paper, we propose a novel hybrid framework that combines self-supervised learning using SimCLR with iterative pseudo-label refinement to mitigate the effects of IDN. The self-supervised pre-training phase enables the model to learn robust feature representations without relying on potentially noisy labels, establishing a noise-agnostic foundation. Subsequently, we employ an iterative training process with pseudo-label refinement, where confidently predicted samples are identified through a multistage approach and their labels are updated to improve label quality progressively. We evaluate our method on the CIFAR-10 and CIFAR-100 datasets augmented with synthetic instance-dependent noise at varying noise levels. Experimental results demonstrate that our approach significantly outperforms several state-of-the-art methods, particularly under high noise conditions, achieving notable improvements in classification accuracy and robustness. Our findings suggest that integrating self-supervised learning with iterative pseudo-label refinement offers an effective strategy for training deep neural networks on noisy datasets afflicted by instance-dependent label noise.

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arXiv2024

Network Inversion of Convolutional Neural Nets

Neural networks have emerged as powerful tools across various applications, yet their decision-making process often remains opaque, leading to them being perceived as "black boxes." This opacity raises concerns about their interpretability and reliability, especially in safety-critical scenarios. Network inversion techniques offer a solution by allowing us to peek inside these black boxes, revealing the features and patterns learned by the networks behind their decision-making processes and thereby provide valuable insights into how neural networks arrive at their conclusions, making them more interpretable and trustworthy. This paper presents a simple yet effective approach to network inversion using a meticulously conditioned generator that learns the data distribution in the input space of the trained neural network, enabling the reconstruction of inputs that would most likely lead to the desired outputs. To capture the diversity in the input space for a given output, instead of simply revealing the conditioning labels to the generator, we encode the conditioning label information into vectors and intermediate matrices and further minimize the cosine similarity between features of the generated images.

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arXiv2024

Network Inversion and Its Applications

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arXiv2024

FLD+: Data-efficient Evaluation Metric for Generative Models

We introduce a new metric to assess the quality of generated images that is more reliable, data-efficient, compute-efficient, and adaptable to new domains than the previous metrics, such as Fréchet Inception Distance (FID). The proposed metric is based on normalizing flows, which allows for the computation of density (exact log-likelihood) of images from any domain. Thus, unlike FID, the proposed Flow-based Likelihood Distance Plus (FLD+) metric exhibits strongly monotonic behavior with respect to different types of image degradations, including noise, occlusion, diffusion steps, and generative model size. Additionally, because normalizing flow can be trained stably and efficiently, FLD+ achieves stable results with two orders of magnitude fewer images than FID (which requires more images to reliably compute Fréchet distance between features of large samples of real and generated images). We made FLD+ computationally even more efficient by applying normalizing flows to features extracted in a lower-dimensional latent space instead of using a pre-trained network. We also show that FLD+ can easily be retrained on new domains, such as medical images, unlike the networks behind previous metrics -- such as InceptionNetV3 pre-trained on ImageNet.

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arXiv2024

Efficient Whole Slide Image Classification through Fisher Vector Representation

The advancement of digital pathology, particularly through computational analysis of whole slide images (WSI), is poised to significantly enhance diagnostic precision and efficiency. However, the large size and complexity of WSIs make it difficult to analyze and classify them using computers. This study introduces a novel method for WSI classification by automating the identification and examination of the most informative patches, thus eliminating the need to process the entire slide. Our method involves two-stages: firstly, it extracts only a few patches from the WSIs based on their pathological significance; and secondly, it employs Fisher vectors (FVs) for representing features extracted from these patches, which is known for its robustness in capturing fine-grained details. This approach not only accentuates key pathological features within the WSI representation but also significantly reduces computational overhead, thus making the process more efficient and scalable. We have rigorously evaluated the proposed method across multiple datasets to benchmark its performance against comprehensive WSI analysis and contemporary weakly-supervised learning methodologies. The empirical results indicate that our focused analysis of select patches, combined with Fisher vector representation, not only aligns with, but at times surpasses, the classification accuracy of standard practices. Moreover, this strategy notably diminishes computational load and resource expenditure, thereby establishing an efficient and precise framework for WSI analysis in the realm of digital pathology.

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arXiv2024

Classification and Morphological Analysis of DLBCL Subtypes in H\&E-Stained Slides

We address the challenge of automated classification of diffuse large B-cell lymphoma (DLBCL) into its two primary subtypes: activated B-cell-like (ABC) and germinal center B-cell-like (GCB). Accurate classification between these subtypes is essential for determining the appropriate therapeutic strategy, given their distinct molecular profiles and treatment responses. Our proposed deep learning model demonstrates robust performance, achieving an average area under the curve (AUC) of (87.4 pm 5.7)\% during cross-validation. It shows a high positive predictive value (PPV), highlighting its potential for clinical application, such as triaging for molecular testing. To gain biological insights, we performed an analysis of morphological features of ABC and GCB subtypes. We segmented cell nuclei using a pre-trained deep neural network and compared the statistics of geometric and color features for ABC and GCB. We found that the distributions of these features were not very different for the two subtypes, which suggests that the visual differences between them are more subtle. These results underscore the potential of our method to assist in more precise subtype classification and can contribute to improved treatment management and outcomes for patients of DLBCL.

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arXiv2024

Clustered Patch Embeddings for Permutation-Invariant Classification of Whole Slide Images

Whole Slide Imaging (WSI) is a cornerstone of digital pathology, offering detailed insights critical for diagnosis and research. Yet, the gigapixel size of WSIs imposes significant computational challenges, limiting their practical utility. Our novel approach addresses these challenges by leveraging various encoders for intelligent data reduction and employing a different classification model to ensure robust, permutation-invariant representations of WSIs. A key innovation of our method is the ability to distill the complex information of an entire WSI into a single vector, effectively capturing the essential features needed for accurate analysis. This approach significantly enhances the computational efficiency of WSI analysis, enabling more accurate pathological assessments without the need for extensive computational resources. This breakthrough equips us with the capability to effectively address the challenges posed by large image resolutions in whole-slide imaging, paving the way for more scalable and effective utilization of WSIs in medical diagnostics and research, marking a significant advancement in the field.

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arXiv2024

PathoGen-X: A Cross-Modal Genomic Feature Trans-Align Network for Enhanced Survival Prediction from Histopathology Images

Accurate survival prediction is essential for personalized cancer treatment. However, genomic data - often a more powerful predictor than pathology data - is costly and inaccessible. We present the cross-modal genomic feature translation and alignment network for enhanced survival prediction from histopathology images (PathoGen-X). It is a deep learning framework that leverages both genomic and imaging data during training, relying solely on imaging data at testing. PathoGen-X employs transformer-based networks to align and translate image features into the genomic feature space, enhancing weaker imaging signals with stronger genomic signals. Unlike other methods, PathoGen-X translates and aligns features without projecting them to a shared latent space and requires fewer paired samples. Evaluated on TCGA-BRCA, TCGA-LUAD, and TCGA-GBM datasets, PathoGen-X demonstrates strong survival prediction performance, emphasizing the potential of enriched imaging models for accessible cancer prognosis.

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arXiv2024

WaveMixSR-V2: Enhancing Super-resolution with Higher Efficiency

Recent advancements in single image super-resolution have been predominantly driven by token mixers and transformer architectures. WaveMixSR utilized the WaveMix architecture, employing a two-dimensional discrete wavelet transform for spatial token mixing, achieving superior performance in super-resolution tasks with remarkable resource efficiency. In this work, we present an enhanced version of the WaveMixSR architecture by (1) replacing the traditional transpose convolution layer with a pixel shuffle operation and (2) implementing a multistage design for higher resolution tasks ($4\times$). Our experiments demonstrate that our enhanced model -- WaveMixSR-V2 -- outperforms other architectures in multiple super-resolution tasks, achieving state-of-the-art for the BSD100 dataset, while also consuming fewer resources, exhibits higher parameter efficiency, lower latency and higher throughput. Our code is available at https://github.com/pranavphoenix/WaveMixSR.

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arXiv2024

Network Inversion for Training-Like Data Reconstruction

Machine Learning models are often trained on proprietary and private data that cannot be shared, though the trained models themselves are distributed openly assuming that sharing model weights is privacy preserving, as training data is not expected to be inferred from the model weights. In this paper, we present Training-Like Data Reconstruction (TLDR), a network inversion-based approach to reconstruct training-like data from trained models. To begin with, we introduce a comprehensive network inversion technique that learns the input space corresponding to different classes in the classifier using a single conditioned generator. While inversion may typically return random and arbitrary input images for a given output label, we modify the inversion process to incentivize the generator to reconstruct training-like data by exploiting key properties of the classifier with respect to the training data along with some prior knowledge about the images. To validate our approach, we conduct empirical evaluations on multiple standard vision classification datasets, thereby highlighting the potential privacy risks involved in sharing machine learning models.

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arXiv2024

Cross-Domain Evaluation of Few-Shot Classification Models: Natural Images vs. Histopathological Images

In this study, we investigate the performance of few-shot classification models across different domains, specifically natural images and histopathological images. We first train several few-shot classification models on natural images and evaluate their performance on histopathological images. Subsequently, we train the same models on histopathological images and compare their performance. We incorporated four histopathology datasets and one natural images dataset and assessed performance across 5-way 1-shot, 5-way 5-shot, and 5-way 10-shot scenarios using a selection of state-of-the-art classification techniques. Our experimental results reveal insights into the transferability and generalization capabilities of few-shot classification models between diverse image domains. We analyze the strengths and limitations of these models in adapting to new domains and provide recommendations for optimizing their performance in cross-domain scenarios. This research contributes to advancing our understanding of few-shot learning in the context of image classification across diverse domains.

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arXiv2024

Normalizing Flow-Based Metric for Image Generation

We propose two new evaluation metrics to assess realness of generated images based on normalizing flows: a simpler and efficient flow-based likelihood distance (FLD) and a more exact dual-flow based likelihood distance (D-FLD). Because normalizing flows can be used to compute the exact likelihood, the proposed metrics assess how closely generated images align with the distribution of real images from a given domain. This property gives the proposed metrics a few advantages over the widely used Fréchet inception distance (FID) and other recent metrics. Firstly, the proposed metrics need only a few hundred images to stabilize (converge in mean), as opposed to tens of thousands needed for FID, and at least a few thousand for the other metrics. This allows confident evaluation of even small sets of generated images, such as validation batches inside training loops. Secondly, the network used to compute the proposed metric has over an order of magnitude fewer parameters compared to Inception-V3 used to compute FID, making it computationally more efficient. For assessing the realness of generated images in new domains (e.g., x-ray images), ideally these networks should be retrained on real images to model their distinct distributions. Thus, our smaller network will be even more advantageous for new domains. Extensive experiments show that the proposed metrics have the desired monotonic relationships with the extent of image degradation of various kinds.

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arXiv2024

FedStein: Enhancing Multi-Domain Federated Learning Through James-Stein Estimator

Federated Learning (FL) facilitates data privacy by enabling collaborative in-situ training across decentralized clients. Despite its inherent advantages, FL faces significant challenges of performance and convergence when dealing with data that is not independently and identically distributed (non-i.i.d.). While previous research has primarily addressed the issue of skewed label distribution across clients, this study focuses on the less explored challenge of multi-domain FL, where client data originates from distinct domains with varying feature distributions. We introduce a novel method designed to address these challenges FedStein: Enhancing Multi-Domain Federated Learning Through the James-Stein Estimator. FedStein uniquely shares only the James-Stein (JS) estimates of batch normalization (BN) statistics across clients, while maintaining local BN parameters. The non-BN layer parameters are exchanged via standard FL techniques. Extensive experiments conducted across three datasets and multiple models demonstrate that FedStein surpasses existing methods such as FedAvg and FedBN, with accuracy improvements exceeding 14% in certain domains leading to enhanced domain generalization. The code is available at https://github.com/sunnyinAI/FedStein

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arXiv2024

FLeNS: Federated Learning with Enhanced Nesterov-Newton Sketch

Federated learning faces a critical challenge in balancing communication efficiency with rapid convergence, especially for second-order methods. While Newton-type algorithms achieve linear convergence in communication rounds, transmitting full Hessian matrices is often impractical due to quadratic complexity. We introduce Federated Learning with Enhanced Nesterov-Newton Sketch (FLeNS), a novel method that harnesses both the acceleration capabilities of Nesterov's method and the dimensionality reduction benefits of Hessian sketching. FLeNS approximates the centralized Newton's method without relying on the exact Hessian, significantly reducing communication overhead. By combining Nesterov's acceleration with adaptive Hessian sketching, FLeNS preserves crucial second-order information while preserving the rapid convergence characteristics. Our theoretical analysis, grounded in statistical learning, demonstrates that FLeNS achieves super-linear convergence rates in communication rounds - a notable advancement in federated optimization. We provide rigorous convergence guarantees and characterize tradeoffs between acceleration, sketch size, and convergence speed. Extensive empirical evaluation validates our theoretical findings, showcasing FLeNS's state-of-the-art performance with reduced communication requirements, particularly in privacy-sensitive and edge-computing scenarios. The code is available at https://github.com/sunnyinAI/FLeNS

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arXiv2024

Efficient Quality Control of Whole Slide Pathology Images with Human-in-the-loop Training

Histopathology whole slide images (WSIs) are being widely used to develop deep learning-based diagnostic solutions, especially for precision oncology. Most of these diagnostic softwares are vulnerable to biases and impurities in the training and test data which can lead to inaccurate diagnoses. For instance, WSIs contain multiple types of tissue regions, at least some of which might not be relevant to the diagnosis. We introduce HistoROI, a robust yet lightweight deep learning-based classifier to segregate WSI into six broad tissue regions -- epithelium, stroma, lymphocytes, adipose, artifacts, and miscellaneous. HistoROI is trained using a novel human-in-the-loop and active learning paradigm that ensures variations in training data for labeling-efficient generalization. HistoROI consistently performs well across multiple organs, despite being trained on only a single dataset, demonstrating strong generalization. Further, we have examined the utility of HistoROI in improving the performance of downstream deep learning-based tasks using the CAMELYON breast cancer lymph node and TCGA lung cancer datasets. For the former dataset, the area under the receiver operating characteristic curve (AUC) for metastasis versus normal tissue of a neural network trained using weakly supervised learning increased from 0.88 to 0.92 by filtering the data using HistoROI. Similarly, the AUC increased from 0.88 to 0.93 for the classification between adenocarcinoma and squamous cell carcinoma on the lung cancer dataset. We also found that the performance of the HistoROI improves upon HistoQC for artifact detection on a test dataset of 93 annotated WSIs. The limitations of the proposed model are analyzed, and potential extensions are also discussed.

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arXiv2024

HER2 and FISH Status Prediction in Breast Biopsy H&E-Stained Images Using Deep Learning

The current standard for detecting human epidermal growth factor receptor 2 (HER2) status in breast cancer patients relies on HER2 amplification, identified through fluorescence in situ hybridization (FISH) or immunohistochemistry (IHC). However, hematoxylin and eosin (H\&E) tumor stains are more widely available, and accurately predicting HER2 status using H\&E could reduce costs and expedite treatment selection. Deep Learning algorithms for H&E have shown effectiveness in predicting various cancer features and clinical outcomes, including moderate success in HER2 status prediction. In this work, we employed a customized weak supervision classification technique combined with MoCo-v2 contrastive learning to predict HER2 status. We trained our pipeline on 182 publicly available H&E Whole Slide Images (WSIs) from The Cancer Genome Atlas (TCGA), for which annotations by the pathology team at Yale School of Medicine are publicly available. Our pipeline achieved an Area Under the Curve (AUC) of 0.85 across four different test folds. Additionally, we tested our model on 44 H&E slides from the TCGA-BRCA dataset, which had an HER2 score of 2+ and included corresponding HER2 status and FISH test results. These cases are considered equivocal for IHC, requiring an expensive FISH test on their IHC slides for disambiguation. Our pipeline demonstrated an AUC of 0.81 on these challenging H&E slides. Reducing the need for FISH test can have significant implications in cancer treatment equity for underserved populations.

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