We propose and demonstrate a joint model of anatomical shapes, image features and clinical indicators for statistical shape modeling and medical image analysis. The key idea is to employ a copula model to separate the joint dependency structure from the marginal distributions of variables of interest. This separation provides flexibility on the assumptions made during the modeling process. The proposed method can handle binary, discrete, ordinal and continuous variables. We demonstrate a simple and efficient way to include binary, discrete and ordinal variables into the modeling. We build Bayesian conditional models based on observed partial clinical indicators, features or shape based on Gaussian processes capturing the dependency structure. We apply the proposed method on a stroke dataset to jointly model the shape of the lateral ventricles, the spatial distribution of the white matter hyperintensity associated with periventricular white matter disease, and clinical indicators. The proposed method yields interpretable joint models for data exploration and patient-specific statistical shape models for medical image analysis.
Detection of different types of image editing operations carried out on an image is an important problem in image forensics. It gives the information about the processing history of an image, and also can expose forgeries present in an image. There have been few methods proposed to detect different types of image editing operations in a single framework. However, all the operations have to be known a priori in the training phase. But, in real-forensics scenarios it may not be possible to know about the editing operations carried out on an image. To solve this problem, we propose a novel deep learning-based method which can differentiate between different types of image editing operations. The proposed method classifies image patches in a pair-wise fashion as either similarly or differently processed using a deep siamese neural network. Once the network learns feature that can discriminate between different image editing operations, it can differentiate between different image editing operations not present in the training stage. The experimental results show the efficacy of the proposed method in detecting/discriminating different image editing operations.
Background: Histopathology is an important modality for the diagnosis and management of many diseases in modern healthcare, and plays a critical role in cancer care. Pathology samples can be large and require multi-site sampling, leading to upwards of 20 slides for a single tumor, and the human-expert tasks of site selection and and quantitative assessment of mitotic figures are time consuming and subjective. Automating these tasks in the setting of a digital pathology service presents significant opportunities to improve workflow efficiency and augment human experts in practice. Approach: Multiple state-of-the-art deep learning techniques for histopathology image classification and mitotic figure detection were used in the development of OncoPetNet. Additionally, model-free approaches were used to increase speed and accuracy. The robust and scalable inference engine leverages Pytorch's performance optimizations as well as specifically developed speed up techniques in inference. Results: The proposed system, demonstrated significantly improved mitotic counting performance for 41 cancer cases across 14 cancer types compared to human expert baselines. In 21.9% of cases use of OncoPetNet led to change in tumor grading compared to human expert evaluation. In deployment, an effective 0.27 min/slide inference was achieved in a high throughput veterinary diagnostic pathology service across 2 centers processing 3,323 digital whole slide images daily. Conclusion: This work represents the first successful automated deployment of deep learning systems for real-time expert-level performance on important histopathology tasks at scale in a high volume clinical practice. The resulting impact outlines important considerations for model development, deployment, clinical decision making, and informs best practices for implementation of deep learning systems in digital histopathology practices.
This work proposes a new framework for deep learning that has been particularly tailored for hyperspectral image classification. We learn multiple levels of dictionaries in a robust fashion. The last layer is discriminative that learns a linear classifier. The training proceeds greedily, at a time a single level of dictionary is learnt and the coefficients used to train the next level. The coefficients from the final level are used for classification. Robustness is incorporated by minimizing the absolute deviations instead of the more popular Euclidean norm. The inbuilt robustness helps combat mixed noise (Gaussian and sparse) present in hyperspectral images. Results show that our proposed techniques outperforms all other deep learning methods Deep Belief Network (DBN), Stacked Autoencoder (SAE) and Convolutional Neural Network (CNN). The experiments have been carried out on benchmark hyperspectral imaging datasets.
The detrimental impacts of climate change include stronger and more destructive hurricanes happening all over the world. Identifying different damaged structures of an area including buildings and roads are vital since it helps the rescue team to plan their efforts to minimize the damage caused by a natural disaster. Semantic segmentation helps to identify different parts of an image. We implement a novel self-attention based semantic segmentation model on a high resolution UAV dataset and attain Mean IoU score of around 88% on the test set. The result inspires to use self-attention schemes in natural disaster damage assessment which will save human lives and reduce economic losses.
Conventional stereo suffers from a fundamental trade-off between imaging volume and signal-to-noise ratio (SNR) -- due to the conflicting impact of aperture size on both these variables. Inspired by the extended depth of field cameras, we propose a novel end-to-end learning-based technique to overcome this limitation, by introducing a phase mask at the aperture plane of the cameras in a stereo imaging system. The phase mask creates a depth-dependent point spread function, allowing us to recover sharp image texture and stereo correspondence over a significantly extended depth of field (EDOF) than conventional stereo. The phase mask pattern, the EDOF image reconstruction, and the stereo disparity estimation are all trained together using an end-to-end learned deep neural network. We perform theoretical analysis and characterization of the proposed approach and show a 6x increase in volume that can be imaged in simulation. We also build an experimental prototype and validate the approach using real-world results acquired using this prototype system.
In streaming data applications incoming samples are processed and discarded, therefore, intelligent decision-making is crucial for the performance of lifelong learning systems. In addition, the order in which samples arrive may heavily affect the performance of online (and offline) incremental learners. The recently introduced incremental cluster validity indices (iCVIs) provide valuable aid in addressing such class of problems. Their primary use-case has been cluster quality monitoring; nonetheless, they have been very recently integrated in a streaming clustering method to assist the clustering task itself. In this context, the work presented here introduces the first adaptive resonance theory (ART)-based model that uses iCVIs for unsupervised and semi-supervised online learning. Moreover, it shows for the first time how to use iCVIs to regulate ART vigilance via an iCVI-based match tracking mechanism. The model achieves improved accuracy and robustness to ordering effects by integrating an online iCVI framework as module B of a topological adaptive resonance theory predictive mapping (TopoARTMAP) -- thereby being named iCVI-TopoARTMAP -- and by employing iCVI-driven post-processing heuristics at the end of each learning step. The online iCVI framework provides assignments of input samples to clusters at each iteration in accordance to any of several iCVIs. The iCVI-TopoARTMAP maintains useful properties shared by ARTMAP models, such as stability, immunity to catastrophic forgetting, and the many-to-one mapping capability via the map field module. The performance (unsupervised and semi-supervised) and robustness to presentation order (unsupervised) of iCVI-TopoARTMAP were evaluated via experiments with a synthetic data set and deep embeddings of a real-world face image data set.
Monitoring the responses of plants to environmental changes is essential for plant biodiversity research. This, however, is currently still being done manually by botanists in the field. This work is very laborious, and the data obtained is, though following a standardized method to estimate plant coverage, usually subjective and has a coarse temporal resolution. To remedy these caveats, we investigate approaches using convolutional neural networks (CNNs) to automatically extract the relevant data from images, focusing on plant community composition and species coverages of 9 herbaceous plant species. To this end, we investigate several standard CNN architectures and different pretraining methods. We find that we outperform our previous approach at higher image resolutions using a custom CNN with a mean absolute error of 5.16%. In addition to these investigations, we also conduct an error analysis based on the temporal aspect of the plant cover images. This analysis gives insight into where problems for automatic approaches lie, like occlusion and likely misclassifications caused by temporal changes.
Computation of document image quality metrics often depends upon the availability of a ground truth image corresponding to the document. This limits the applicability of quality metrics in applications such as hyperparameter optimization of image processing algorithms that operate on-the-fly on unseen documents. This work proposes the use of surrogate models to learn the behavior of a given document quality metric on existing datasets where ground truth images are available. The trained surrogate model can later be used to predict the metric value on previously unseen document images without requiring access to ground truth images. The surrogate model is empirically evaluated on the Document Image Binarization Competition (DIBCO) and the Handwritten Document Image Binarization Competition (H-DIBCO) datasets.
The ability to quickly annotate medical imaging data plays a critical role in training deep learning frameworks for segmentation. Doing so for image volumes or video sequences is even more pressing as annotating these is particularly burdensome. To alleviate this problem, this work proposes a new method to efficiently segment medical imaging volumes or videos using point-wise annotations only. This allows annotations to be collected extremely quickly and remains applicable to numerous segmentation tasks. Our approach trains a deep learning model using an appropriate Positive/Unlabeled objective function using sparse point-wise annotations. While most methods of this kind assume that the proportion of positive samples in the data is known a-priori, we introduce a novel self-supervised method to estimate this prior efficiently by combining a Bayesian estimation framework and new stopping criteria. Our method iteratively estimates appropriate class priors and yields high segmentation quality for a variety of object types and imaging modalities. In addition, by leveraging a spatio-temporal tracking framework, we regularize our predictions by leveraging the complete data volume. We show experimentally that our approach outperforms state-of-the-art methods tailored to the same problem.