IFSENet : Harnessing Sparse Iterations for Interactive Few-shot Segmentation Excellence

Training a computer vision system to segment a novel class typically requires collecting and painstakingly annotating lots of images with objects from that class. Few-shot segmentation techniques reduce the required number of images to learn to segment a new class, but careful annotations of object boundaries are still required. On the other hand, interactive segmentation techniques only focus on incrementally improving the segmentation of one object at a time (typically, using clicks given by an expert) in a class-agnostic manner. We combine the two concepts to drastically reduce the effort required to train segmentation models for novel classes. Instead of trivially feeding interactive segmentation masks as ground truth to a few-shot segmentation model, we propose IFSENet, which can accept sparse supervision on a single or few support images in the form of clicks to generate masks on support (training, at least clicked upon once) as well as query (test, never clicked upon) images. To trade-off effort for accuracy flexibly, the number of images and clicks can be incrementally added to the support set to further improve the segmentation of support as well as query images. The proposed model approaches the accuracy of previous state-of-the-art few-shot segmentation models with considerably lower annotation effort (clicks instead of maps), when tested on Pascal and SBD datasets on query images. It also works well as an interactive segmentation method on support images.

Advancing Gene Selection in Oncology: A Fusion of Deep Learning and Sparsity for Precision Gene Selection

Gene selection plays a pivotal role in oncology research for improving outcome prediction accuracy and facilitating cost-effective genomic profiling for cancer patients. This paper introduces two gene selection strategies for deep learning-based survival prediction models. The first strategy uses a sparsity-inducing method while the second one uses importance based gene selection for identifying relevant genes. Our overall approach leverages the power of deep learning to model complex biological data structures, while sparsity-inducing methods ensure the selection process focuses on the most informative genes, minimizing noise and redundancy. Through comprehensive experimentation on diverse genomic and survival datasets, we demonstrate that our strategy not only identifies gene signatures with high predictive power for survival outcomes but can also streamlines the process for low-cost genomic profiling. The implications of this research are profound as it offers a scalable and effective tool for advancing personalized medicine and targeted cancer therapies. By pushing the boundaries of gene selection methodologies, our work contributes significantly to the ongoing efforts in cancer genomics, promising improved diagnostic and prognostic capabilities in clinical settings.

Network Inversion of Binarised Neural Nets

While the deployment of neural networks, yielding impressive results, becomes more prevalent in various applications, their interpretability and understanding remain a critical challenge. Network inversion, a technique that aims to reconstruct the input space from the model's learned internal representations, plays a pivotal role in unraveling the black-box nature of input to output mappings in neural networks. In safety-critical scenarios, where model outputs may influence pivotal decisions, the integrity of the corresponding input space is paramount, necessitating the elimination of any extraneous "garbage" to ensure the trustworthiness of the network. Binarised Neural Networks (BNNs), characterized by binary weights and activations, offer computational efficiency and reduced memory requirements, making them suitable for resource-constrained environments. This paper introduces a novel approach to invert a trained BNN by encoding it into a CNF formula that captures the network's structure, allowing for both inference and inversion.

Utilizing Radiomic Feature Analysis For Automated MRI Keypoint Detection: Enhancing Graph Applications

Graph neural networks (GNNs) present a promising alternative to CNNs and transformers in certain image processing applications due to their parameter-efficiency in modeling spatial relationships. Currently, a major area of research involves the converting non-graph input data for GNN-based models, notably in scenarios where the data originates from images. One approach involves converting images into nodes by identifying significant keypoints within them. Super-Retina, a semi-supervised technique, has been utilized for detecting keypoints in retinal images. However, its limitations lie in the dependency on a small initial set of ground truth keypoints, which is progressively expanded to detect more keypoints. Having encountered difficulties in detecting consistent initial keypoints in brain images using SIFT and LoFTR, we proposed a new approach: radiomic feature-based keypoint detection. Demonstrating the anatomical significance of the detected keypoints was achieved by showcasing their efficacy in improving registration processes guided by these keypoints. Subsequently, these keypoints were employed as the ground truth for the keypoint detection method (LK-SuperRetina). Furthermore, the study showcases the application of GNNs in image matching, highlighting their superior performance in terms of both the number of good matches and confidence scores. This research sets the stage for expanding GNN applications into various other applications, including but not limited to image classification, segmentation, and registration.

Classification of Various Types of Damages in Honeycomb Composite Sandwich Structures using Guided Wave Structural Health Monitoring

Classification of damages in honeycomb composite sandwich structure (HCSS) is important to decide remedial actions. However, previous studies have only detected damages using deviations of monitoring signal from healthy (baseline) using a guided wave (GW) based structural health monitoring system. Classification between various types of damages has not been reported for challenging cases. We show that using careful feature engineering and machine learning it is possible to classify between various types of damages such as core crush (CC), high density core (HDC), lost film adhesive (LFA) and teflon release film (TRF). We believe that we are the first to report numerical models for four types of damages in HCSS, which is followed up with experimental validation. We found that two out of four damages affect the GW signal in a particularly similar manner. We extracted and evaluated multiple features from time as well as frequency domains, and also experimented with features relative to as baseline as well as those that were baseline-free. Using Pearson's correlation coefficient based filtering, redundant features were eliminated. Finally, using an optimal feature set determined using feature elimination, high accuracy was achieved with a random forest classifier on held-out signals. For evaluating performance of the proposed method for different damage sizes, we used simulated data obtained from extensive parametric studies and got an accuracy of 77.89%. Interpretability studies to determine importance of various features showed that features computed using the baseline signal prove more effective as compared to baseline-free features.

Combining Datasets with Different Label Sets for Improved Nucleus Segmentation and Classification

Segmentation and classification of cell nuclei in histopathology images using deep neural networks (DNNs) can save pathologists' time for diagnosing various diseases, including cancers, by automating cell counting and morphometric assessments. It is now well-known that the accuracy of DNNs increases with the sizes of annotated datasets available for training. Although multiple datasets of histopathology images with nuclear annotations and class labels have been made publicly available, the set of class labels differ across these datasets. We propose a method to train DNNs for instance segmentation and classification on multiple datasets where the set of classes across the datasets are related but not the same. Specifically, our method is designed to utilize a coarse-to-fine class hierarchy, where the set of classes labeled and annotated in a dataset can be at any level of the hierarchy, as long as the classes are mutually exclusive. Within a dataset, the set of classes need not even be at the same level of the class hierarchy tree. Our results demonstrate that segmentation and classification metrics for the class set used by the test split of a dataset can improve by pre-training on another dataset that may even have a different set of classes due to the expansion of the training set enabled by our method. Furthermore, generalization to previously unseen datasets also improves by combining multiple other datasets with different sets of classes for training. The improvement is both qualitative and quantitative. The proposed method can be adapted for various loss functions, DNN architectures, and application domains.

Domain-Adaptive Learning: Unsupervised Adaptation for Histology Images with Improved Loss Function Combination

This paper presents a novel approach for unsupervised domain adaptation (UDA) targeting H&E stained histology images. Existing adversarial domain adaptation methods may not effectively align different domains of multimodal distributions associated with classification problems. The objective is to enhance domain alignment and reduce domain shifts between these domains by leveraging their unique characteristics. Our approach proposes a novel loss function along with carefully selected existing loss functions tailored to address the challenges specific to histology images. This loss combination not only makes the model accurate and robust but also faster in terms of training convergence. We specifically focus on leveraging histology-specific features, such as tissue structure and cell morphology, to enhance adaptation performance in the histology domain. The proposed method is extensively evaluated in accuracy, robustness, and generalization, surpassing state-of-the-art techniques for histology images. We conducted extensive experiments on the FHIST dataset and the results show that our proposed method - Domain Adaptive Learning (DAL) significantly surpasses the ViT-based and CNN-based SoTA methods by 1.41% and 6.56% respectively.

Transforming Breast Cancer Diagnosis: Towards Real-Time Ultrasound to Mammogram Conversion for Cost-Effective Diagnosis

Ultrasound (US) imaging is better suited for intraoperative settings because it is real-time and more portable than other imaging techniques, such as mammography. However, US images are characterized by lower spatial resolution noise-like artifacts. This research aims to address these limitations by providing surgeons with mammogram-like image quality in real-time from noisy US images. Unlike previous approaches for improving US image quality that aim to reduce artifacts by treating them as (speckle noise), we recognize their value as informative wave interference pattern (WIP). To achieve this, we utilize the Stride software to numerically solve the forward model, generating ultrasound images from mammograms images by solving wave-equations. Additionally, we leverage the power of domain adaptation to enhance the realism of the simulated ultrasound images. Then, we utilize generative adversarial networks (GANs) to tackle the inverse problem of generating mammogram-quality images from ultrasound images. The resultant images have considerably more discernible details than the original US images.

Reverse Knowledge Distillation: Training a Large Model using a Small One for Retinal Image Matching on Limited Data

Retinal image matching plays a crucial role in monitoring disease progression and treatment response. However, datasets with matched keypoints between temporally separated pairs of images are not available in abundance to train transformer-based model. We propose a novel approach based on reverse knowledge distillation to train large models with limited data while preventing overfitting. Firstly, we propose architectural modifications to a CNN-based semi-supervised method called SuperRetina that help us improve its results on a publicly available dataset. Then, we train a computationally heavier model based on a vision transformer encoder using the lighter CNN-based model, which is counter-intuitive in the field knowledge-distillation research where training lighter models based on heavier ones is the norm. Surprisingly, such reverse knowledge distillation improves generalization even further. Our experiments suggest that high-dimensional fitting in representation space may prevent overfitting unlike training directly to match the final output. We also provide a public dataset with annotations for retinal image keypoint detection and matching to help the research community develop algorithms for retinal image applications.

Heterogeneous graphs model spatial relationships between biological entities for breast cancer diagnosis

The heterogeneity of breast cancer presents considerable challenges for its early detection, prognosis, and treatment selection. Convolutional neural networks often neglect the spatial relationships within histopathological images, which can limit their accuracy. Graph neural networks (GNNs) offer a promising solution by coding the spatial relationships within images. Prior studies have investigated the modeling of histopathological images as cell and tissue graphs, but they have not fully tapped into the potential of extracting interrelationships between these biological entities. In this paper, we present a novel approach using a heterogeneous GNN that captures the spatial and hierarchical relations between cell and tissue graphs to enhance the extraction of useful information from histopathological images. We also compare the performance of a cross-attention-based network and a transformer architecture for modeling the intricate relationships within tissue and cell graphs. Our model demonstrates superior efficiency in terms of parameter count and achieves higher accuracy compared to the transformer-based state-of-the-art approach on three publicly available breast cancer datasets -- BRIGHT, BreakHis, and BACH.