Vision Mamba for Classification of Breast Ultrasound Images

Mamba-based models, VMamba and Vim, are a recent family of vision encoders that offer promising performance improvements in many computer vision tasks. This paper compares Mamba-based models with traditional Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) using the breast ultrasound BUSI and B datasets. Our evaluation, which includes multiple runs of experiments and statistical significance analysis, demonstrates that Mamba-based architectures frequently outperform CNN and ViT models with statistically significant results. These Mamba-based models effectively capture long-range dependencies while maintaining inductive biases, making them suitable for applications with limited data.

AdaFisher: Adaptive Second Order Optimization via Fisher Information

First-order optimization methods are currently the mainstream in training deep neural networks (DNNs). Optimizers like Adam incorporate limited curvature information by employing the diagonal matrix preconditioning of the stochastic gradient during the training. Despite their widespread, second-order optimization algorithms exhibit superior convergence properties compared to their first-order counterparts e.g. Adam and SGD. However, their practicality in training DNNs are still limited due to increased per-iteration computations and suboptimal accuracy compared to the first order methods. We present AdaFisher--an adaptive second-order optimizer that leverages a block-diagonal approximation to the Fisher information matrix for adaptive gradient preconditioning. AdaFisher aims to bridge the gap between enhanced convergence capabilities and computational efficiency in second-order optimization framework for training DNNs. Despite the slow pace of second-order optimizers, we showcase that AdaFisher can be reliably adopted for image classification, language modelling and stand out for its stability and robustness in hyperparameter tuning. We demonstrate that AdaFisher outperforms the SOTA optimizers in terms of both accuracy and convergence speed. Code available from \href{https://github.com/AtlasAnalyticsLab/AdaFisher}{https://github.com/AtlasAnalyticsLab/AdaFisher}

Vim4Path: Self-Supervised Vision Mamba for Histopathology Images

Representation learning from Gigapixel Whole Slide Images (WSI) poses a significant challenge in computational pathology due to the complicated nature of tissue structures and the scarcity of labeled data. Multi-instance learning methods have addressed this challenge, leveraging image patches to classify slides utilizing pretrained models using Self-Supervised Learning (SSL) approaches. The performance of both SSL and MIL methods relies on the architecture of the feature encoder. This paper proposes leveraging the Vision Mamba (Vim) architecture, inspired by state space models, within the DINO framework for representation learning in computational pathology. We evaluate the performance of Vim against Vision Transformers (ViT) on the Camelyon16 dataset for both patch-level and slide-level classification. Our findings highlight Vim's enhanced performance compared to ViT, particularly at smaller scales, where Vim achieves an 8.21 increase in ROC AUC for models of similar size. An explainability analysis further highlights Vim's capabilities, which reveals that Vim uniquely emulates the pathologist workflow-unlike ViT. This alignment with human expert analysis highlights Vim's potential in practical diagnostic settings and contributes significantly to developing effective representation-learning algorithms in computational pathology. We release the codes and pretrained weights at \url{https://github.com/AtlasAnalyticsLab/Vim4Path}.

End-to-End Supervised Multilabel Contrastive Learning

Multilabel representation learning is recognized as a challenging problem that can be associated with either label dependencies between object categories or data-related issues such as the inherent imbalance of positive/negative samples. Recent advances address these challenges from model- and data-centric viewpoints. In model-centric, the label correlation is obtained by an external model designs (e.g., graph CNN) to incorporate an inductive bias for training. However, they fail to design an end-to-end training framework, leading to high computational complexity. On the contrary, in data-centric, the realistic nature of the dataset is considered for improving the classification while ignoring the label dependencies. In this paper, we propose a new end-to-end training framework -- dubbed KMCL (Kernel-based Mutlilabel Contrastive Learning) -- to address the shortcomings of both model- and data-centric designs. The KMCL first transforms the embedded features into a mixture of exponential kernels in Gaussian RKHS. It is then followed by encoding an objective loss that is comprised of (a) reconstruction loss to reconstruct kernel representation, (b) asymmetric classification loss to address the inherent imbalance problem, and (c) contrastive loss to capture label correlation. The KMCL models the uncertainty of the feature encoder while maintaining a low computational footprint. Extensive experiments are conducted on image classification tasks to showcase the consistent improvements of KMCL over the SOTA methods. PyTorch implementation is provided in \url{https://github.com/mahdihosseini/KMCL}.

Computational Pathology: A Survey Review and The Way Forward

Computational Pathology (CoPath) is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CoPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology facilitating transformational changes in the diagnosis and treatment of cancer diseases. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CoPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CoPath. In this article we provide a comprehensive review of more than 700 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CoPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CoPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CoPath.

Pseudo-Inverted Bottleneck Convolution for DARTS Search Space

Differentiable Architecture Search (DARTS) has attracted considerable attention as a gradient-based Neural Architecture Search (NAS) method. Since the introduction of DARTS, there has been little work done on adapting the action space based on state-of-art architecture design principles for CNNs. In this work, we aim to address this gap by incrementally augmenting the DARTS search space with micro-design changes inspired by ConvNeXt and studying the trade-off between accuracy, evaluation layer count, and computational cost. To this end, we introduce the Pseudo-Inverted Bottleneck conv block intending to reduce the computational footprint of the inverted bottleneck block proposed in ConvNeXt. Our proposed architecture is much less sensitive to evaluation layer count and outperforms a DARTS network with similar size significantly, at layer counts as small as 2. Furthermore, with less layers, not only does it achieve higher accuracy with lower GMACs and parameter count, GradCAM comparisons show that our network is able to better detect distinctive features of target objects compared to DARTS.

Exploiting Explainable Metrics for Augmented SGD

Explaining the generalization characteristics of deep learning is an emerging topic in advanced machine learning. There are several unanswered questions about how learning under stochastic optimization really works and why certain strategies are better than others. In this paper, we address the following question: \textit{can we probe intermediate layers of a deep neural network to identify and quantify the learning quality of each layer?} With this question in mind, we propose new explainability metrics that measure the redundant information in a network's layers using a low-rank factorization framework and quantify a complexity measure that is highly correlated with the generalization performance of a given optimizer, network, and dataset. We subsequently exploit these metrics to augment the Stochastic Gradient Descent (SGD) optimizer by adaptively adjusting the learning rate in each layer to improve in generalization performance. Our augmented SGD -- dubbed RMSGD -- introduces minimal computational overhead compared to SOTA methods and outperforms them by exhibiting strong generalization characteristics across application, architecture, and dataset.

HistoKT: Cross Knowledge Transfer in Computational Pathology

The lack of well-annotated datasets in computational pathology (CPath) obstructs the application of deep learning techniques for classifying medical images. %Since pathologist time is expensive, dataset curation is intrinsically difficult. Many CPath workflows involve transferring learned knowledge between various image domains through transfer learning. Currently, most transfer learning research follows a model-centric approach, tuning network parameters to improve transfer results over few datasets. In this paper, we take a data-centric approach to the transfer learning problem and examine the existence of generalizable knowledge between histopathological datasets. First, we create a standardization workflow for aggregating existing histopathological data. We then measure inter-domain knowledge by training ResNet18 models across multiple histopathological datasets, and cross-transferring between them to determine the quantity and quality of innate shared knowledge. Additionally, we use weight distillation to share knowledge between models without additional training. We find that hard to learn, multi-class datasets benefit most from pretraining, and a two stage learning framework incorporating a large source domain such as ImageNet allows for better utilization of smaller datasets. Furthermore, we find that weight distillation enables models trained on purely histopathological features to outperform models using external natural image data.

Towards Robust and Automatic Hyper-Parameter Tunning

The task of hyper-parameter optimization (HPO) is burdened with heavy computational costs due to the intractability of optimizing both a model's weights and its hyper-parameters simultaneously. In this work, we introduce a new class of HPO method and explore how the low-rank factorization of the convolutional weights of intermediate layers of a convolutional neural network can be used to define an analytical response surface for optimizing hyper-parameters, using only training data. We quantify how this surface behaves as a surrogate to model performance and can be solved using a trust-region search algorithm, which we call autoHyper. The algorithm outperforms state-of-the-art such as Bayesian Optimization and generalizes across model, optimizer, and dataset selection. Our code can be found at \url{https://github.com/MathieuTuli/autoHyper}.

P4AI: Approaching AI Ethics through Principlism

The field of computer vision is rapidly evolving, particularly in the context of new methods of neural architecture design. These models contribute to (1) the Climate Crisis - increased CO2 emissions and (2) the Privacy Crisis - data leakage concerns. To address the often overlooked impact the Computer Vision (CV) community has on these crises, we outline a novel ethical framework, \textit{P4AI}: Principlism for AI, an augmented principlistic view of ethical dilemmas within AI. We then suggest using P4AI to make concrete recommendations to the community to mitigate the climate and privacy crises.