Multiple Instance Learning (MIL) represents the predominant framework in Whole Slide Image (WSI) classification, covering aspects such as sub-typing, diagnosis, and beyond. Current MIL models predominantly rely on instance-level features derived from pretrained models such as ResNet. These models segment each WSI into independent patches and extract features from these local patches, leading to a significant loss of global spatial context and restricting the model's focus to merely local features. To address this issue, we propose a novel MIL framework, named SAM-MIL, that emphasizes spatial contextual awareness and explicitly incorporates spatial context by extracting comprehensive, image-level information. The Segment Anything Model (SAM) represents a pioneering visual segmentation foundational model that can capture segmentation features without the need for additional fine-tuning, rendering it an outstanding tool for extracting spatial context directly from raw WSIs. Our approach includes the design of group feature extraction based on spatial context and a SAM-Guided Group Masking strategy to mitigate class imbalance issues. We implement a dynamic mask ratio for different segmentation categories and supplement these with representative group features of categories. Moreover, SAM-MIL divides instances to generate additional pseudo-bags, thereby augmenting the training set, and introduces consistency of spatial context across pseudo-bags to further enhance the model's performance. Experimental results on the CAMELYON-16 and TCGA Lung Cancer datasets demonstrate that our proposed SAM-MIL model outperforms existing mainstream methods in WSIs classification. Our open-source implementation code is is available at https://github.com/FangHeng/SAM-MIL.
Distillation-based self-supervised learning typically leads to more compressed representations due to its radical clustering process and the implementation of a sharper target distribution. To overcome this limitation and preserve more information from input, we introduce UDI, conceptualized as Unsqueezed Distillation-based self-supervised learning (SSL). UDI enriches the learned representation by encouraging multimodal prediction distilled from a consolidated profile of local predictions that are derived via stratified sampling. Our evaluations show that UDI not only promotes semantically meaningful representations at instance level, delivering superior or competitive results to state-of-the-art SSL methods in image classification, but also effectively preserves the nuisance of input, which yields significant improvement in dense prediction tasks, including object detection and segmentation. Additionally, UDI performs competitively in low-shot image classification, improving the scalability of joint-embedding pipelines. Various visualizations and ablation studies are presented to further elucidate the mechanisms behind UDI. Our source code is available at https://github.com/ISL-CV/udi.
Vision Transformer (ViT) is becoming widely popular in automating accurate disease diagnosis in medical imaging owing to its robust self-attention mechanism. However, ViTs remain vulnerable to adversarial attacks that may thwart the diagnosis process by leading it to intentional misclassification of critical disease. In this paper, we propose a novel image classification pipeline, namely, S-E Pipeline, that performs multiple pre-processing steps that allow ViT to be trained on critical features so as to reduce the impact of input perturbations by adversaries. Our method uses a combination of segmentation and image enhancement techniques such as Contrast Limited Adaptive Histogram Equalization (CLAHE), Unsharp Masking (UM), and High-Frequency Emphasis filtering (HFE) as preprocessing steps to identify critical features that remain intact even after adversarial perturbations. The experimental study demonstrates that our novel pipeline helps in reducing the effect of adversarial attacks by 72.22% for the ViT-b32 model and 86.58% for the ViT-l32 model. Furthermore, we have shown an end-to-end deployment of our proposed method on the NVIDIA Jetson Orin Nano board to demonstrate its practical use case in modern hand-held devices that are usually resource-constrained.
Low-rank adaptation, also known as LoRA, has emerged as a prominent method for parameter-efficient fine-tuning of foundation models. Despite its computational efficiency, LoRA still yields inferior performance compared to full fine-tuning. In this paper, we first uncover a fundamental connection between the optimization processes of LoRA and full fine-tuning: using LoRA for optimization is mathematically equivalent to full fine-tuning using a low-rank gradient for parameter updates. And this low-rank gradient can be expressed in terms of the gradients of the two low-rank matrices in LoRA. Leveraging this insight, we introduce LoRA-Pro, a method that enhances LoRA's performance by strategically adjusting the gradients of these low-rank matrices. This adjustment allows the low-rank gradient to more accurately approximate the full fine-tuning gradient, thereby narrowing the performance gap between LoRA and full fine-tuning. Furthermore, we theoretically derive the optimal solutions for adjusting the gradients of the low-rank matrices, applying them during fine-tuning in LoRA-Pro. We conduct extensive experiments across natural language understanding, dialogue generation, mathematical reasoning, code generation, and image classification tasks, demonstrating that LoRA-Pro substantially improves LoRA's performance, effectively narrowing the gap with full fine-tuning. Code is publicly available at https://github.com/mrflogs/LoRA-Pro.
Deep neural networks have been extensively applied in the medical domain for various tasks, including image classification, segmentation, and landmark detection. However, their application is often hindered by data scarcity, both in terms of available annotations and images. This study introduces a novel application of denoising diffusion probabilistic models (DDPMs) to the landmark detection task, specifically addressing the challenge of limited annotated data in x-ray imaging. Our key innovation lies in leveraging DDPMs for self-supervised pre-training in landmark detection, a previously unexplored approach in this domain. This method enables accurate landmark detection with minimal annotated training data (as few as 50 images), surpassing both ImageNet supervised pre-training and traditional self-supervised techniques across three popular x-ray benchmark datasets. To our knowledge, this work represents the first application of diffusion models for self-supervised learning in landmark detection, which may offer a valuable pre-training approach in few-shot regimes, for mitigating data scarcity.
Recent advancements in graph-based approaches for multiplexed immunofluorescence (mIF) images have significantly propelled the field forward, offering deeper insights into patient-level phenotyping. However, current graph-based methodologies encounter two primary challenges: (1) Cellular Heterogeneity, where existing approaches fail to adequately address the inductive biases inherent in graphs, particularly the homophily characteristic observed in cellular connectivity and; (2) Scalability, where handling cellular graphs from high-dimensional images faces difficulties in managing a high number of cells. To overcome these limitations, we introduce Mew, a novel framework designed to efficiently process mIF images through the lens of multiplex network. Mew innovatively constructs a multiplex network comprising two distinct layers: a Voronoi network for geometric information and a Cell-type network for capturing cell-wise homogeneity. This framework equips a scalable and efficient Graph Neural Network (GNN), capable of processing the entire graph during training. Furthermore, Mew integrates an interpretable attention module that autonomously identifies relevant layers for image classification. Extensive experiments on a real-world patient dataset from various institutions highlight Mew's remarkable efficacy and efficiency, marking a significant advancement in mIF image analysis. The source code of Mew can be found here: \url{https://github.com/UNITES-Lab/Mew}
Stochastic optimization plays a crucial role in the advancement of deep learning technologies. Over the decades, significant effort has been dedicated to improving the training efficiency and robustness of deep neural networks, via various strategies including gradient normalization (GN) and gradient centralization (GC). Nevertheless, to the best of our knowledge, no one has considered to capture the optimal gradient descent trajectory, by adaptively controlling gradient descent direction. To address this concern, this paper is the first attempt to study a new optimization technique for deep neural networks, using the sum normalization of a gradient vector as coefficients, to dynamically regularize gradients and thus to effectively control optimization direction. The proposed technique is hence named as the adaptive gradient regularization (AGR). It can be viewed as an adaptive gradient clipping method. The theoretical analysis reveals that the AGR can effectively smooth the loss landscape, and hence can significantly improve the training efficiency and model generalization performance. We note that AGR can greatly improve the training efficiency of vanilla optimizers' including Adan and AdamW, by adding only three lines of code. The final experiments conducted on image generation, image classification, and language representation, demonstrate that the AGR method can not only improve the training efficiency but also enhance the model generalization performance.
Recent studies have underscored the capabilities of natural imaging foundation models to serve as powerful feature extractors, even in a zero-shot setting for medical imaging data. Most commonly, a shallow multi-layer perceptron (MLP) is appended to the feature extractor to facilitate end-to-end learning and downstream prediction tasks such as classification, thus representing the de facto standard. However, as graph neural networks (GNNs) have become a practicable choice for various tasks in medical research in the recent past, we direct attention to the question of how effective GNNs are compared to MLP prediction heads for the task of 3D medical image classification, proposing them as a potential alternative. In our experiments, we devise a subject-level graph for each volumetric dataset instance. Therein latent representations of all slices in the volume, encoded through a DINOv2 pretrained vision transformer (ViT), constitute the nodes and their respective node features. We use public datasets to compare the classification heads numerically and evaluate various graph construction and graph convolution methods in our experiments. Our findings show enhancements of the GNN in classification performance and substantial improvements in runtime compared to an MLP prediction head. Additional robustness evaluations further validate the promising performance of the GNN, promoting them as a suitable alternative to traditional MLP classification heads. Our code is publicly available at: https://github.com/compai-lab/2024-miccai-grail-kiechle
Deep learning models have achieved tremendous success in most of the industries in recent years. The evolution of these models has also led to an increase in the model size and energy requirement, making it difficult to deploy in production on low compute devices. An increase in the number of connected devices around the world warrants compressed models that can be easily deployed at the local devices with low compute capacity and power accessibility. A wide range of solutions have been proposed by different researchers to reduce the size and complexity of such models, prominent among them are, Weight Quantization, Parameter Pruning, Network Pruning, low-rank representation, weights sharing, neural architecture search, knowledge distillation etc. In this research work, we investigate the performance impacts on various trained deep learning models, compressed using quantization and pruning techniques. We implemented both, quantization and pruning, compression techniques on popular deep learning models used in the image classification, object detection, language models and generative models-based problem statements. We also explored performance of various large language models (LLMs) after quantization and low rank adaptation. We used the standard evaluation metrics (model's size, accuracy, and inference time) for all the related problem statements and concluded this paper by discussing the challenges and future work.
Nowadays, deep learning models are increasingly required to be both interpretable and highly accurate. We present an approach that integrates Kolmogorov-Arnold Network (KAN) classification heads and Fuzzy Pooling into convolutional neural networks (CNNs). By utilizing the interpretability of KAN and the uncertainty handling capabilities of fuzzy logic, the integration shows potential for improved performance in image classification tasks. Our comparative analysis demonstrates that the modified CNN architecture with KAN and Fuzzy Pooling achieves comparable or higher accuracy than traditional models. The findings highlight the effectiveness of combining fuzzy logic and KAN to develop more interpretable and efficient deep learning models. Future work will aim to expand this approach across larger datasets.
Through a simple multiple choice language prompt a VQA model can operate as a zero-shot image classifier, producing a classification label. Compared to typical image encoders, VQA models offer an advantage: VQA-produced image embeddings can be infused with the most relevant visual information through tailored language prompts. Nevertheless, for most tasks, zero-shot VQA performance is lacking, either because of unfamiliar category names, or dissimilar pre-training data and test data distributions. We propose a simple method to boost VQA performance for image classification using only a handful of labeled examples and a multiple-choice question. This few-shot method is training-free and maintains the dynamic and flexible advantages of the VQA model. Rather than relying on the final language output, our approach uses multiple-choice questions to extract prompt-specific latent representations, which are enriched with relevant visual information. These representations are combined to create a final overall image embedding, which is decoded via reference to latent class prototypes constructed from the few labeled examples. We demonstrate this method outperforms both pure visual encoders and zero-shot VQA baselines to achieve impressive performance on common few-shot tasks including MiniImageNet, Caltech-UCSD Birds, and CIFAR-100. Finally, we show our approach does particularly well in settings with numerous diverse visual attributes such as the fabric, article-style, texture, and view of different articles of clothing, where other few-shot approaches struggle, as we can tailor our image representations only on the semantic features of interest.
Due to the varying intensity of pavement cracks, the complexity of topological structure, and the noise of texture background, image classification for asphalt pavement cracking has proven to be a challenging problem. Fatigue cracking, also known as alligator cracking, is one of the common distresses of asphalt pavement. It is thus important to detect and monitor the condition of alligator cracking on roadway pavements. Most research in this area has typically focused on pixel-level detection of cracking using limited datasets. A novel deep convolutional neural network that can achieve two objectives is proposed. The first objective of the proposed neural network is to classify presence of fatigue cracking based on pavement surface images. The second objective is to classify the fatigue cracking severity level based on the Distress Identification Manual (DIM) standard. In this paper, a databank of 4484 high-resolution pavement surface images is established in which images are taken locally in the Town of Blacksburg, Virginia, USA. In the data pre-preparation, over 4000 images are labeled into 4 categories manually according to DIM standards. A four-layer convolutional neural network model is then built to achieve the goal of classification of images by pavement crack severity category. The trained model reached the highest accuracy among all existing methods. After only 30 epochs of training, the model achieved a crack existence classification accuracy of 96.23% and a severity level classification accuracy of 96.74%. After 20 epochs of training, the model achieved a pavement marking presence classification accuracy of 97.64%.
Colorectal polyps are generally benign alterations that, if not identified promptly and managed successfully, can progress to cancer and cause affectations on the colon mucosa, known as adenocarcinoma. Today advances in Deep Learning have demonstrated the ability to achieve significant performance in image classification and detection in medical diagnosis applications. Nevertheless, these models are prone to overfitting, and making decisions based only on point estimations may provide incorrect predictions. Thus, to obtain a more informed decision, we must consider point estimations along with their reliable uncertainty quantification. In this paper, we built different Bayesian neural network approaches based on the flexibility of posterior distribution to develop semantic segmentation of colorectal polyp images. We found that these models not only provide state-of-the-art performance on the segmentation of this medical dataset but also, yield accurate uncertainty estimates. We applied multiplicative normalized flows(MNF) and reparameterization trick on the UNET, FPN, and LINKNET architectures tested with multiple backbones in deterministic and Bayesian versions. We report that the FPN + EfficientnetB7 architecture with MNF is the most promising option given its IOU of 0.94 and Expected Calibration Error (ECE) of 0.004, combined with its superiority in identifying difficult-to-detect colorectal polyps, which is effective in clinical areas where early detection prevents the development of colon cancer.
The task of multi-label image classification involves recognizing multiple objects within a single image. Considering both valuable semantic information contained in the labels and essential visual features presented in the image, tight visual-linguistic interactions play a vital role in improving classification performance. Moreover, given the potential variance in object size and appearance within a single image, attention to features of different scales can help to discover possible objects in the image. Recently, Transformer-based methods have achieved great success in multi-label image classification by leveraging the advantage of modeling long-range dependencies, but they have several limitations. Firstly, existing methods treat visual feature extraction and cross-modal fusion as separate steps, resulting in insufficient visual-linguistic alignment in the joint semantic space. Additionally, they only extract visual features and perform cross-modal fusion at a single scale, neglecting objects with different characteristics. To address these issues, we propose a Hierarchical Scale-Aware Vision-Language Transformer (HSVLT) with two appealing designs: (1)~A hierarchical multi-scale architecture that involves a Cross-Scale Aggregation module, which leverages joint multi-modal features extracted from multiple scales to recognize objects of varying sizes and appearances in images. (2)~Interactive Visual-Linguistic Attention, a novel attention mechanism module that tightly integrates cross-modal interaction, enabling the joint updating of visual, linguistic and multi-modal features. We have evaluated our method on three benchmark datasets. The experimental results demonstrate that HSVLT surpasses state-of-the-art methods with lower computational cost.
Multispectral (MS) snapshot cameras equipped with a MS filter array (MSFA), capture multiple spectral bands in a single shot, resulting in a raw mosaic image where each pixel holds only one channel value. The fully-defined MS image is estimated from the raw one through \textit{demosaicing}, which inevitably introduces spatio-spectral artifacts. Moreover, training on fully-defined MS images can be computationally intensive, particularly with deep neural networks (DNNs), and may result in features lacking discrimination power due to suboptimal learning of spatio-spectral interactions. Furthermore, outdoor MS image acquisition occurs under varying lighting conditions, leading to illumination-dependent features. This paper presents an original approach to learn discriminant and illumination-robust features directly from raw images. It involves: \textit{raw spectral constancy} to mitigate the impact of illumination, \textit{MSFA-preserving} transformations suited for raw image augmentation to train DNNs on diverse raw textures, and \textit{raw-mixing} to capture discriminant spatio-spectral interactions in raw images. Experiments on MS image classification show that our approach outperforms both handcrafted and recent deep learning-based methods, while also requiring significantly less computational effort. The source code is available at https://github.com/AnisAmziane/RawTexture.
This paper aims to adapt the source model to the target environment, leveraging small user feedback (i.e., labeled target data) readily available in real-world applications. We find that existing semi-supervised domain adaptation (SemiSDA) methods often suffer from poorly improved adaptation performance when directly utilizing such feedback data, as shown in Figure 1. We analyze this phenomenon via a novel concept called Negatively Biased Feedback (NBF), which stems from the observation that user feedback is more likely for data points where the model produces incorrect predictions. To leverage this feedback while avoiding the issue, we propose a scalable adapting approach, Retrieval Latent Defending. This approach helps existing SemiSDA methods to adapt the model with a balanced supervised signal by utilizing latent defending samples throughout the adaptation process. We demonstrate the problem caused by NBF and the efficacy of our approach across various benchmarks, including image classification, semantic segmentation, and a real-world medical imaging application. Our extensive experiments reveal that integrating our approach with multiple state-of-the-art SemiSDA methods leads to significant performance improvements.
Advances in generative models increase the need for sample quality assessment. To do so, previous methods rely on a pre-trained feature extractor to embed the generated samples and real samples into a common space for comparison. However, different feature extractors might lead to inconsistent assessment outcomes. Moreover, these methods are not applicable for domains where a robust, universal feature extractor does not yet exist, such as medical images or 3D assets. In this paper, we propose to directly examine the latent space of the trained generative model to infer generated sample quality. This is feasible because the quality a generated sample directly relates to the amount of training data resembling it, and we can infer this information by examining the density of the latent space. Accordingly, we use a latent density score function to quantify sample quality. We show that the proposed score correlates highly with the sample quality for various generative models including VAEs, GANs and Latent Diffusion Models. Compared with previous quality assessment methods, our method has the following advantages: 1) pre-generation quality estimation with reduced computational cost, 2) generalizability to various domains and modalities, and 3) applicability to latent-based image editing and generation methods. Extensive experiments demonstrate that our proposed methods can benefit downstream tasks such as few-shot image classification and latent face image editing. Code is available at https://github.com/cvlab-stonybrook/LS-sample-quality.
In this study, we present the Graph Sub-Graph Network (GSN), a novel hybrid image classification model merging the strengths of Convolutional Neural Networks (CNNs) for feature extraction and Graph Neural Networks (GNNs) for structural modeling. GSN employs k-means clustering to group graph nodes into clusters, facilitating the creation of subgraphs. These subgraphs are then utilized to learn representative `atoms` for dictionary learning, enabling the identification of sparse, class-distinguishable features. This integrated approach is particularly relevant in domains like medical imaging, where discerning subtle feature differences is crucial for accurate classification. To evaluate the performance of our proposed GSN, we conducted experiments on benchmark datasets, including PascalVOC and HAM10000. Our results demonstrate the efficacy of our model in optimizing dictionary configurations across varied classes, which contributes to its effectiveness in medical classification tasks. This performance enhancement is primarily attributed to the integration of CNNs, GNNs, and graph learning techniques, which collectively improve the handling of datasets with limited labeled examples. Specifically, our experiments show that the model achieves a higher accuracy on benchmark datasets such as Pascal VOC and HAM10000 compared to conventional CNN approaches.
In deep learning, achieving high performance on image classification tasks requires diverse training sets. However, dataset diversity is incompletely understood. The current best practice is to try to maximize dataset size and class balance. Yet large, class-balanced datasets are not guaranteed to be diverse: images can still be arbitrarily similar. We hypothesized that, for a given model architecture, better model performance can be achieved by maximizing dataset diversity more directly. This could open a path for performance improvement without additional computational resources or architectural advances. To test this hypothesis, we introduce a comprehensive framework of diversity measures, developed in ecology, that generalizes familiar quantities like Shannon entropy by accounting for similarities and differences among images. (Dataset size and class balance emerge from this framework as special cases.) By analyzing thousands of subsets from seven medical datasets representing ultrasound, X-ray, CT, and pathology images, we found that the best correlates of performance were not size or class balance but $A$ -- ``big alpha'' -- a set of generalized entropy measures interpreted as the effective number of image-class pairs in the dataset, after accounting for similarities among images. One of these, $A_0$, explained 67\% of the variance in balanced accuracy across all subsets, vs. 54\% for class balance and just 39\% for size. The best pair was size and $A_1$ (79\%), which outperformed size and class balance (74\%). $A$ performed best for subsets from individual datasets as well as across datasets, supporting the generality of these results. We propose maximizing $A$ as a potential new way to improve the performance of deep learning in medical imaging.
Histopathological image classification constitutes a pivotal task in computer-aided diagnostics. The precise identification and categorization of histopathological images are of paramount significance for early disease detection and treatment. In the diagnostic process of pathologists, a multi-tiered approach is typically employed to assess abnormalities in cell regions at different magnifications. However, feature extraction is often performed at a single granularity, overlooking the multi-granular characteristics of cells. To address this issue, we propose the Fuzzy-guided Multi-granularity Deep Neural Network (FMDNN). Inspired by the multi-granular diagnostic approach of pathologists, we perform feature extraction on cell structures at coarse, medium, and fine granularity, enabling the model to fully harness the information in histopathological images. We incorporate the theory of fuzzy logic to address the challenge of redundant key information arising during multi-granular feature extraction. Cell features are described from different perspectives using multiple fuzzy membership functions, which are fused to create universal fuzzy features. A fuzzy-guided cross-attention module guides universal fuzzy features toward multi-granular features. We propagate these features through an encoder to all patch tokens, aiming to achieve enhanced classification accuracy and robustness. In experiments on multiple public datasets, our model exhibits a significant improvement in accuracy over commonly used classification methods for histopathological image classification and shows commendable interpretability.