Resting-state functional Magnetic Resonance Imaging (fMRI) is a powerful imaging technique for studying functional development of the brain in utero. However, unpredictable and excessive movement of fetuses has limited clinical application since it causes substantial signal fluctuations which can systematically alter observed patterns of functional connectivity. Previous studies have focused on the accurate estimation of the motion parameters in case of large fetal head movement and used a 3D single step interpolation approach at each timepoint to recover motion-free fMRI images. This does not guarantee that the reconstructed image corresponds to the minimum error representation of fMRI time series given the acquired data. Here, we propose a novel technique based on four dimensional iterative reconstruction of the scattered slices acquired during fetal fMRI. The accuracy of the proposed method was quantitatively evaluated on a group of real clinical fMRI fetuses. The results indicate improvements of reconstruction quality compared to the conventional 3D interpolation approach.
In this paper, we investigate the application of deep convolutional GANs on car image generation. We improve upon the commonly used DCGAN architecture by implementing Wasserstein loss to decrease mode collapse and introducing dropout at the end of the discrimiantor to introduce stochasticity. Furthermore, we introduce convolutional layers at the end of the generator to improve expressiveness and smooth noise. All of these improvements upon the DCGAN architecture comprise our proposal of the novel BoolGAN architecture, which is able to decrease the FID from 195.922 (baseline) to 165.966.
Computed Tomography Angiography is a key modality providing insights into the cerebrovascular vessel tree that are crucial for the diagnosis and treatment of ischemic strokes, in particular in cases of large vessel occlusions (LVO). Thus, the clinical workflow greatly benefits from an automated detection of patients suffering from LVOs. This work uses convolutional neural networks for case-level classification trained with elastic deformation of the vessel tree segmentation masks to artificially augment training data. Using only masks as the input to our model uniquely allows us to apply such deformations much more aggressively than one could with conventional image volumes while retaining sample realism. The neural network classifies the presence of an LVO and the affected hemisphere. In a 5-fold cross validated ablation study, we demonstrate that the use of the suggested augmentation enables us to train robust models even from few data sets. Training the EfficientNetB1 architecture on 100 data sets, the proposed augmentation scheme was able to raise the ROC AUC to 0.85 from a baseline value of 0.56 using no augmentation. The best performance was achieved using a 3D-DenseNet yielding an AUC of 0.87. The augmentation had positive impact in classification of the affected hemisphere as well, where the 3D-DenseNet reached an AUC of 0.93 on both sides.
Automated image processing approaches are indispensable for many biomedical experiments and help to cope with the increasing amount of microscopy image data in a fast and reproducible way. Especially state-of-the-art deep learning-based approaches most often require large amounts of annotated training data to produce accurate and generalist outputs, but they are often compromised by the general lack of those annotated data sets. In this work, we propose how conditional generative adversarial networks can be utilized to generate realistic image data for 3D fluorescence microscopy from annotation masks of 3D cellular structures. In combination with mask simulation approaches, we demonstrate the generation of fully-annotated 3D microscopy data sets that we make publicly available for training or benchmarking. An additional positional conditioning of the cellular structures enables the reconstruction of position-dependent intensity characteristics and allows to generate image data of different quality levels. A patch-wise working principle and a subsequent full-size reassemble strategy is used to generate image data of arbitrary size and different organisms. We present this as a proof-of-concept for the automated generation of fully-annotated training data sets requiring only a minimum of manual interaction to alleviate the need of manual annotations.
Deep learning methods have played a more and more important role in hyperspectral image classification. However, the general deep learning methods mainly take advantage of the information of sample itself or the pairwise information between samples while ignore the intrinsic data structure within the whole data. To tackle this problem, this work develops a novel deep manifold embedding method(DMEM) for hyperspectral image classification. First, each class in the image is modelled as a specific nonlinear manifold and the geodesic distance is used to measure the correlation between the samples. Then, based on the hierarchical clustering, the manifold structure of the data can be captured and each nonlinear data manifold can be divided into several sub-classes. Finally, considering the distribution of each sub-class and the correlation between different subclasses, the DMEM is constructed to preserve the estimated geodesic distances on the data manifold between the learned low dimensional features of different samples. Experiments over three real-world hyperspectral image datasets have demonstrated the effectiveness of the proposed method.
The ability to recognise and make analogies is often used as a measure or test of human intelligence. The ability to solve Bongard problems is an example of such a test. It has also been postulated that the ability to rapidly construct novel abstractions is critical to being able to solve analogical problems. Given an image, the ability to construct a program that would generate that image is one form of abstraction, as exemplified in the Dreamcoder project. In this paper, we present a preliminary examination of whether programs constructed by Dreamcoder can be used for analogical reasoning to solve certain Bongard problems. We use Dreamcoder to discover programs that generate the images in a Bongard problem and represent each of these as a sequence of state transitions. We decorate the states using positional information in an automated manner and then encode the resulting sequence into logical facts in Prolog. We use inductive logic programming (ILP), to learn an (interpretable) theory for the abstract concept involved in an instance of a Bongard problem. Experiments on synthetically created Bongard problems for concepts such as 'above/below' and 'clockwise/counterclockwise' demonstrate that our end-to-end system can solve such problems. We study the importance and completeness of each component of our approach, highlighting its current limitations and pointing to directions for improvement in our formulation as well as in elements of any Dreamcoder-like program synthesis system used for such an approach.
We study the training of Vision Transformers for semi-supervised image classification. Transformers have recently demonstrated impressive performance on a multitude of supervised learning tasks. Surprisingly, we find Vision Transformers perform poorly on a semi-supervised ImageNet setting. In contrast, Convolutional Neural Networks (CNNs) achieve superior results in small labeled data regime. Further investigation reveals that the reason is CNNs have strong spatial inductive bias. Inspired by this observation, we introduce a joint semi-supervised learning framework, Semiformer, which contains a Transformer branch, a Convolutional branch and a carefully designed fusion module for knowledge sharing between the branches. The Convolutional branch is trained on the limited supervised data and generates pseudo labels to supervise the training of the transformer branch on unlabeled data. Extensive experiments on ImageNet demonstrate that Semiformer achieves 75.5\% top-1 accuracy, outperforming the state-of-the-art. In addition, we show Semiformer is a general framework which is compatible with most modern Transformer and Convolutional neural architectures.
Image semantic segmentation technology is one of the key technologies for intelligent systems to understand natural scenes. As one of the important research directions in the field of visual intelligence, this technology has broad application scenarios in the fields of mobile robots, drones, smart driving, and smart security. However, in the actual application of mobile robots, problems such as inaccurate segmentation semantic label prediction and loss of edge information of segmented objects and background may occur. This paper proposes an improved structure of a semantic segmentation network based on a deep learning network that combines self-attention neural network and neural network architecture search methods. First, a neural network search method NAS (Neural Architecture Search) is used to find a semantic segmentation network with multiple resolution branches. In the search process, combine the self-attention network structure module to adjust the searched neural network structure, and then combine the semantic segmentation network searched by different branches to form a fast semantic segmentation network structure, and input the picture into the network structure to get the final forecast result. The experimental results on the Cityscapes dataset show that the accuracy of the algorithm is 69.8%, and the segmentation speed is 48/s. It achieves a good balance between real-time and accuracy, can optimize edge segmentation, and has a better performance in complex scenes. Good robustness is suitable for practical application.
Though image-level weakly supervised semantic segmentation (WSSS) has achieved great progress with Class Activation Map (CAM) as the cornerstone, the large supervision gap between classification and segmentation still hampers the model to generate more complete and precise pseudo masks for segmentation. In this study, we explore two implicit but intuitive constraints, i.e., cross-view feature semantic consistency and intra(inter)-class compactness(dispersion), to narrow the supervision gap. To this end, we propose two novel pixel-to-prototype contrast regularization terms that are conducted cross different views and within per single view of an image, respectively. Besides, we adopt two sample mining strategies, named semi-hard prototype mining and hard pixel sampling, to better leverage hard examples while reducing incorrect contrasts caused due to the absence of precise pixel-wise labels. Our method can be seamlessly incorporated into existing WSSS models without any changes to the base network and does not incur any extra inference burden. Experiments on standard benchmark show that our method consistently improves two strong baselines by large margins, demonstrating the effectiveness of our method. Specifically, built on top of SEAM, we improve the initial seed mIoU on PASCAL VOC 2012 from 55.4% to 61.5%. Moreover, armed with our method, we increase the segmentation mIoU of EPS from 70.8% to 73.6%, achieving new state-of-the-art.
The field of Machine Learning, a subset of Artificial Intelligence, has led to remarkable advancements in many areas, including medicine. Machine Learning algorithms require large datasets to train computer models successfully. Although there are medical image datasets available, more image datasets are needed from a variety of medical entities, especially cancer pathology. Even more scarce are ML-ready image datasets. To address this need, we created an image dataset (LC25000) with 25,000 color images in 5 classes. Each class contains 5,000 images of the following histologic entities: colon adenocarcinoma, benign colonic tissue, lung adenocarcinoma, lung squamous cell carcinoma, and benign lung tissue. All images are de-identified, HIPAA compliant, validated, and freely available for download to AI researchers.