Phenotyping is the process of measuring an organism's observable traits. Manual phenotyping of crops is a labor-intensive, time-consuming, costly, and error prone process. Accurate, automated, high-throughput phenotyping can relieve a huge burden in the crop breeding pipeline. In this paper, we propose a scalable, high-throughput approach to automatically count and segment panicles (heads), a key phenotype, from aerial sorghum crop imagery. Our counting approach uses the image density map obtained from dot or region annotation as the target with a novel deep convolutional neural network architecture. We also propose a novel instance segmentation algorithm using the estimated density map, to identify the individual panicles in the presence of occlusion. With real Sorghum aerial images, we obtain a mean absolute error (MAE) of 1.06 for counting which is better than using well-known crowd counting approaches such as CCNN, MCNN and CSRNet models. The instance segmentation model also produces respectable results which will be ultimately useful in reducing the manual annotation workload for future data.
While these papers used the CCNN type architecture, the popular U-net architecture has been used in @cite_19 together with a scale consistency regularizer that forces collaborative predictions from the ensemble models. The U-net model has been widely used in medical imaging. , Ronnenberger , @cite_51 use the U-net for cell tracking in bio-medical imaging. Examples of works that allow for very deep networks include @cite_6 and @cite_27 , both of which use a VGG @cite_17 type architecture. Shi @cite_6 utilize a multi-scale architecture, where a part of their network uses complex ensemble averaging to combine image density maps from models built for different scales. Li @cite_27 introduce the dilated convolution to aggregate multi-scale contextual information in the CSRNet model (see Figure ). @cite_45 extended CSRNet by adding parallel branches for the last predictive layer. This allowed for uncertainty estimation as well as a way to improve the performance through ensemble averaging. Finally, it is worth mentioning the approach taken in @cite_12 that first estimates the head size and position in order to choose the hyper parameters for the CCNN.
@cite_6 @cite_19 @cite_27 @cite_45 @cite_51 @cite_12 @cite_17
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Deep learning (DL) based semantic segmentation methods have been providing state-of-the-art performance in the last few years. More specifically, these techniques have been successfully applied to medical image classification, segmentation, and detection tasks. One deep learning technique, U-Net, has become one of the most popular for these applications. In this paper, we propose a Recurrent Convolutional Neural Network (RCNN) based on U-Net as well as a Recurrent Residual Convolutional Neural Network (RRCNN) based on U-Net models, which are named RU-Net and R2U-Net respectively. The proposed models utilize the power of U-Net, Residual Network, as well as RCNN. There are several advantages of these proposed architectures for segmentation tasks. First, a residual unit helps when training deep architecture. Second, feature accumulation with recurrent residual convolutional layers ensures better feature representation for segmentation tasks. Third, it allows us to design better U-Net architecture with same number of network parameters with better performance for medical image segmentation. The proposed models are tested on three benchmark datasets such as blood vessel segmentation in retina images, skin cancer segmentation, and lung lesion segmentation. The experimental results show superior performance on segmentation tasks compared to equivalent models including U-Net and residual U-Net (ResU-Net). Convolutional neural networks (CNNs) have revolutionized medical image analysis over the past few years. The U-Net architecture is one of the most well-known CNN architectures for semantic segmentation and has achieved remarkable successes in many different medical image segmentation applications. The U-Net architecture consists of standard convolution layers, pooling layers, and upsampling layers. These convolution layers learn representative features of input images and construct segmentations based on the features. However, the features learned by standard convolution layers are not distinctive when the differences among different categories are subtle in terms of intensity, location, shape, and size. In this paper, we propose a novel CNN architecture, called Dense-Res-Inception Net (DRINet), which addresses this challenging problem. The proposed DRINet consists of three blocks, namely a convolutional block with dense connections, a deconvolutional block with residual inception modules, and an unpooling block. Our proposed architecture outperforms the U-Net in three different challenging applications, namely multi-class segmentation of cerebrospinal fluid on brain CT images, multi-organ segmentation on abdominal CT images, and multi-class brain tumor segmentation on MR images. How well does a classic deep net architecture like AlexNet or VGG19 classify on a standard dataset such as CIFAR-10 when its "width" --- namely, number of channels in convolutional layers, and number of nodes in fully-connected internal layers --- is allowed to increase to infinity? Such questions have come to the forefront in the quest to theoretically understand deep learning and its mysteries about optimization and generalization. They also connect deep learning to notions such as Gaussian processes and kernels. A recent paper [, 2018] introduced the Neural Tangent Kernel (NTK) which captures the behavior of fully-connected deep nets in the infinite width limit trained by gradient descent; this object was implicit in some other recent papers. A subsequent paper [, 2019] gave heuristic Monte Carlo methods to estimate the NTK and its extension, Convolutional Neural Tangent Kernel (CNTK) and used this to try to understand the limiting behavior on datasets like CIFAR-10. The current paper gives the first efficient exact algorithm (based upon dynamic programming) for computing CNTK as well as an efficient GPU implementation of this algorithm. This results in a significant new benchmark for performance of a pure kernel-based method on CIFAR-10, being 10 higher than the methods reported in [, 2019], and only 5 lower than the performance of the corresponding finite deep net architecture (once batch normalization etc. are turned off). We give the first non-asymptotic proof showing that a fully-trained sufficiently wide net is indeed equivalent to the kernel regression predictor using NTK. Our experiments also demonstrate that earlier Monte Carlo approximation can degrade the performance significantly, thus highlighting the power of our exact kernel computation, which we have applied even to the full CIFAR-10 dataset and 20-layer nets. Recovering images from undersampled linear measurements typically leads to an ill-posed linear inverse problem, that asks for proper statistical priors. Building effective priors is however challenged by the low train and test overhead dictated by real-time tasks; and the need for retrieving visually "plausible" and physically "feasible" images with minimal hallucination. To cope with these challenges, we design a cascaded network architecture that unrolls the proximal gradient iterations by permeating benefits from generative residual networks (ResNet) to modeling the proximal operator. A mixture of pixel-wise and perceptual costs is then deployed to train proximals. The overall architecture resembles back-and-forth projection onto the intersection of feasible and plausible images. Extensive computational experiments are examined for a global task of reconstructing MR images of pediatric patients, and a more local task of superresolving CelebA faces, that are insightful to design efficient architectures. Our observations indicate that for MRI reconstruction, a recurrent ResNet with a single residual block effectively learns the proximal. This simple architecture appears to significantly outperform the alternative deep ResNet architecture by 2dB SNR, and the conventional compressed-sensing MRI by 4dB SNR with 100x faster inference. For image superresolution, our preliminary results indicate that modeling the denoising proximal demands deep ResNets. Abstract Deep networks have set the state-of-the-art in most image analysis tasks by replacing handcrafted features with learned convolution filters within end-to-end trainable architectures. Still, the specifications of a convolutional network are subject to much manual design – the shape and size of the receptive field for convolutional operations is a very sensitive part that has to be tuned for different image analysis applications. 3D fully-convolutional multi-scale architectures with skip-connection that excel at semantic segmentation and landmark localisation have huge memory requirements and rely on large annotated datasets - an important limitation for wider adaptation in medical image analysis. We propose a novel and effective method based on trainable 3D convolution kernels that learns both filter coefficients and spatial filter offsets in a continuous space based on the principle of differentiable image interpolation first introduced for spatial transformer network. A deep network that incorporates this one binary extremely large and inflecting sparse kernel (OBELISK) filter requires fewer trainable parameters and less memory while achieving high quality results compared to fully-convolutional U-Net architectures on two challenging 3D CT multi-organ segmentation tasks. Extensive validation experiments indicate that the performance of sparse deformable convolutions is due to their ability to capture large spatial context with few expressive filter parameters and that network depth is not always necessary to learn complex shape and appearance features. A combination with conventional CNNs further improves the delineation of small organs with large shape variations and the fast inference time using flexible image sampling may offer new potential use cases for deep networks in computer-assisted, image-guided interventions. U-Net has been providing state-of-the-art performance in many medical image segmentation problems. Many modifications have been proposed for U-Net, such as attention U-Net, recurrent residual convolutional U-Net (R2-UNet), and U-Net with residual blocks or blocks with dense connections. However, all these modifications have an encoder-decoder structure with skip connections, and the number of paths for information flow is limited. We propose LadderNet in this paper, which can be viewed as a chain of multiple U-Nets. Instead of only one pair of encoder branch and decoder branch in U-Net, a LadderNet has multiple pairs of encoder-decoder branches, and has skip connections between every pair of adjacent decoder and decoder branches in each level. Inspired by the success of ResNet and R2-UNet, we use modified residual blocks where two convolutional layers in one block share the same weights. A LadderNet has more paths for information flow because of skip connections and residual blocks, and can be viewed as an ensemble of Fully Convolutional Networks (FCN). The equivalence to an ensemble of FCNs improves segmentation accuracy, while the shared weights within each residual block reduce parameter number. Semantic segmentation is essential for retinal disease detection. We tested LadderNet on two benchmark datasets for blood vessel segmentation in retinal images, and achieved superior performance over methods in the literature. The implementation is provided https: github.com juntang-zhuang LadderNet Feedforward multilayer networks trained by supervised learning have recently demonstrated state of the art performance on image labeling problems such as boundary prediction and scene parsing. As even very low error rates can limit practical usage of such systems, methods that perform closer to human accuracy remain desirable. In this work, we propose a new type of network with the following properties that address what we hypothesize to be limiting aspects of existing methods: (1) a wide' structure with thousands of features, (2) a large field of view, (3) recursive iterations that exploit statistical dependencies in label space, and (4) a parallelizable architecture that can be trained in a fraction of the time compared to benchmark multilayer convolutional networks. For the specific image labeling problem of boundary prediction, we also introduce a novel example weighting algorithm that improves segmentation accuracy. Experiments in the challenging domain of connectomic reconstruction of neural circuity from 3d electron microscopy data show that these "Deep And Wide Multiscale Recursive" (DAWMR) networks lead to new levels of image labeling performance. The highest performing architecture has twelve layers, interwoven supervised and unsupervised stages, and uses an input field of view of 157,464 voxels ( @math ) to make a prediction at each image location. We present an associated open source software package that enables the simple and flexible creation of DAWMR networks. Developing neural network image classification models often requires significant architecture engineering. In this paper, we study a method to learn the model architectures directly on the dataset of interest. As this approach is expensive when the dataset is large, we propose to search for an architectural building block on a small dataset and then transfer the block to a larger dataset. The key contribution of this work is the design of a new search space (which we call the "NASNet search space") which enables transferability. In our experiments, we search for the best convolutional layer (or "cell") on the CIFAR-10 dataset and then apply this cell to the ImageNet dataset by stacking together more copies of this cell, each with their own parameters to design a convolutional architecture, which we name a "NASNet architecture". We also introduce a new regularization technique called ScheduledDropPath that significantly improves generalization in the NASNet models. On CIFAR-10 itself, a NASNet found by our method achieves 2.4 error rate, which is state-of-the-art. Although the cell is not searched for directly on ImageNet, a NASNet constructed from the best cell achieves, among the published works, state-of-the-art accuracy of 82.7 top-1 and 96.2 top-5 on ImageNet. Our model is 1.2 better in top-1 accuracy than the best human-invented architectures while having 9 billion fewer FLOPS - a reduction of 28 in computational demand from the previous state-of-the-art model. When evaluated at different levels of computational cost, accuracies of NASNets exceed those of the state-of-the-art human-designed models. For instance, a small version of NASNet also achieves 74 top-1 accuracy, which is 3.1 better than equivalently-sized, state-of-the-art models for mobile platforms. Finally, the image features learned from image classification are generically useful and can be transferred to other computer vision problems. On the task of object detection, the learned features by NASNet used with the Faster-RCNN framework surpass state-of-the-art by 4.0 achieving 43.1 mAP on the COCO dataset. We explore multi-scale convolutional neural nets (CNNs) for image classification. Contemporary approaches extract features from a single output layer. By extracting features from multiple layers, one can simultaneously reason about high, mid, and low-level features during classification. The resulting multi-scale architecture can itself be seen as a feed-forward model that is structured as a directed acyclic graph (DAG-CNNs). We use DAG-CNNs to learn a set of multi-scale features that can be effectively shared between coarse and fine-grained classification tasks. While fine-tuning such models helps performance, we show that even "off-the-self" multi-scale features perform quite well. We present extensive analysis and demonstrate state-of-the-art classification performance on three standard scene benchmarks (SUN397, MIT67, and Scene15). In terms of the heavily benchmarked MIT67 and Scene15 datasets, our results reduce the lowest previously-reported error by 23.9 and 9.5 , respectively. Existing deep convolutional neural networks (CNNs) require a fixed-size (e.g., 224 @math 224) input image. This requirement is “artificial” and may reduce the recognition accuracy for the images or sub-images of an arbitrary size scale. In this work, we equip the networks with another pooling strategy, “spatial pyramid pooling”, to eliminate the above requirement. The new network structure, called SPP-net, can generate a fixed-length representation regardless of image size scale. Pyramid pooling is also robust to object deformations. With these advantages, SPP-net should in general improve all CNN-based image classification methods. On the ImageNet 2012 dataset, we demonstrate that SPP-net boosts the accuracy of a variety of CNN architectures despite their different designs. On the Pascal VOC 2007 and Caltech101 datasets, SPP-net achieves state-of-the-art classification results using a single full-image representation and no fine-tuning. The power of SPP-net is also significant in object detection. Using SPP-net, we compute the feature maps from the entire image only once, and then pool features in arbitrary regions (sub-images) to generate fixed-length representations for training the detectors. This method avoids repeatedly computing the convolutional features. In processing test images, our method is 24-102 @math faster than the R-CNN method, while achieving better or comparable accuracy on Pascal VOC 2007. In ImageNet Large Scale Visual Recognition Challenge (ILSVRC) 2014, our methods rank #2 in object detection and #3 in image classification among all 38 teams. This manuscript also introduces the improvement made for this competition. We explore architectures for general pixel-level prediction problems, from low-level edge detection to mid-level surface normal estimation to high-level semantic segmentation. Convolutional predictors, such as the fully-convolutional network (FCN), have achieved remarkable success by exploiting the spatial redundancy of neighboring pixels through convolutional processing. Though computationally efficient, we point out that such approaches are not statistically efficient during learning precisely because spatial redundancy limits the information learned from neighboring pixels. We demonstrate that (1) stratified sampling allows us to add diversity during batch updates and (2) sampled multi-scale features allow us to explore more nonlinear predictors (multiple fully-connected layers followed by ReLU) that improve overall accuracy. Finally, our objective is to show how a architecture can get performance better than (or comparable to) the architectures designed for a particular task. Interestingly, our single architecture produces state-of-the-art results for semantic segmentation on PASCAL-Context, surface normal estimation on NYUDv2 dataset, and edge detection on BSDS without contextual post-processing. Convolutional neural networks (CNNs) have achieved great successes in many computer vision problems. Unlike existing works that designed CNN architectures to improve performance on a single task of a single domain and not generalizable, we present IBN-Net, a novel convolutional architecture, which remarkably enhances a CNN’s modeling ability on one domain (e.g. Cityscapes) as well as its generalization capacity on another domain (e.g. GTA5) without finetuning. IBN-Net carefully integrates Instance Normalization (IN) and Batch Normalization (BN) as building blocks, and can be wrapped into many advanced deep networks to improve their performances. This work has three key contributions. (1) By delving into IN and BN, we disclose that IN learns features that are invariant to appearance changes, such as colors, styles, and virtuality reality, while BN is essential for preserving content related information. (2) IBN-Net can be applied to many advanced deep architectures, such as DenseNet, ResNet, ResNeXt, and SENet, and consistently improve their performance without increasing computational cost. (3) When applying the trained networks to new domains, e.g. from GTA5 to Cityscapes, IBN-Net achieves comparable improvements as domain adaptation methods, even without using data from the target domain. With IBN-Net, we won the 1st place on the WAD 2018 Challenge Drivable Area track, with an mIoU of 86.18 . Recent works have shown that exploiting multi-scale representations deeply learned via convolutional neural networks (CNN) is of tremendous importance for accurate contour detection. This paper presents a novel approach for predicting contours which advances the state of the art in two fundamental aspects, i.e. multi-scale feature generation and fusion. Different from previous works directly considering multi-scale feature maps obtained from the inner layers of a primary CNN architecture, we introduce a hierarchical deep model which produces more rich and complementary representations. Furthermore, to refine and robustly fuse the representations learned at different scales, the novel Attention-Gated Conditional Random Fields (AG-CRFs) are proposed. The experiments ran on two publicly available datasets (BSDS500 and NYUDv2) demonstrate the effectiveness of the latent AG-CRF model and of the overall hierarchical framework. Deep convolutional neural networks (DCNNs) have shown remarkable performance in image classification tasks in recent years. Generally, deep neural network architectures are stacks consisting of a large number of convolutional layers, and they perform downsampling along the spatial dimension via pooling to reduce memory usage. Concurrently, the feature map dimension (i.e., the number of channels) is sharply increased at downsampling locations, which is essential to ensure effective performance because it increases the diversity of high-level attributes. This also applies to residual networks and is very closely related to their performance. In this research, instead of sharply increasing the feature map dimension at units that perform downsampling, we gradually increase the feature map dimension at all units to involve as many locations as possible. This design, which is discussed in depth together with our new insights, has proven to be an effective means of improving generalization ability. Furthermore, we propose a novel residual unit capable of further improving the classification accuracy with our new network architecture. Experiments on benchmark CIFAR-10, CIFAR-100, and ImageNet datasets have shown that our network architecture has superior generalization ability compared to the original residual networks. Code is available at this https URL Deep convolutional neural networks (DCNNs) have shown remarkable performance in image classification tasks in recent years. Generally, deep neural network architectures are stacks consisting of a large number of convolutional layers, and they perform downsampling along the spatial dimension via pooling to reduce memory usage. Concurrently, the feature map dimension (i.e., the number of channels) is sharply increased at downsampling locations, which is essential to ensure effective performance because it increases the diversity of high-level attributes. This also applies to residual networks and is very closely related to their performance. In this research, instead of sharply increasing the feature map dimension at units that perform downsampling, we gradually increase the feature map dimension at all units to involve as many locations as possible. This design, which is discussed in depth together with our new insights, has proven to be an effective means of improving generalization ability. Furthermore, we propose a novel residual unit capable of further improving the classification accuracy with our new network architecture. Experiments on benchmark CIFAR-10, CIFAR-100, and ImageNet datasets have shown that our network architecture has superior generalization ability compared to the original residual networks. Code is available at https: github.com jhkim89 PyramidNet. Two architectures that generalize convolutional neural networks (CNNs) for the processing of signals supported on graphs are introduced. We start with the selection graph neural network (GNN), which replaces linear time invariant filters with linear shift invariant graph filters to generate convolutional features and reinterprets pooling as a possibly nonlinear subsampling stage where nearby nodes pool their information in a set of preselected sample nodes. A key component of the architecture is to remember the position of sampled nodes to permit computation of convolutional features at deeper layers. The second architecture, dubbed aggregation GNN, diffuses the signal through the graph and stores the sequence of diffused components observed by a designated node. This procedure effectively aggregates all components into a stream of information having temporal structure to which the convolution and pooling stages of regular CNNs can be applied. A multinode version of aggregation GNNs is further introduced for operation in large-scale graphs. An important property of selection and aggregation GNNs is that they reduce to conventional CNNs when particularized to time signals reinterpreted as graph signals in a circulant graph. Comparative numerical analyses are performed in a source localization application over synthetic and real-world networks. Performance is also evaluated for an authorship attribution problem and text category classification. Multinode aggregation GNNs are consistently the best-performing GNN architecture. We propose a new method for creating computationally efficient convolutional neural networks (CNNs) by using low-rank representations of convolutional filters. Rather than approximating filters in previously-trained networks with more efficient versions, we learn a set of small basis filters from scratch; during training, the network learns to combine these basis filters into more complex filters that are discriminative for image classification. To train such networks, a novel weight initialization scheme is used. This allows effective initialization of connection weights in convolutional layers composed of groups of differently-shaped filters. We validate our approach by applying it to several existing CNN architectures and training these networks from scratch using the CIFAR, ILSVRC and MIT Places datasets. Our results show similar or higher accuracy than conventional CNNs with much less compute. Applying our method to an improved version of VGG-11 network using global max-pooling, we achieve comparable validation accuracy using 41 less compute and only 24 of the original VGG-11 model parameters; another variant of our method gives a 1 percentage point increase in accuracy over our improved VGG-11 model, giving a top-5 center-crop validation accuracy of 89.7 while reducing computation by 16 relative to the original VGG-11 model. Applying our method to the GoogLeNet architecture for ILSVRC, we achieved comparable accuracy with 26 less compute and 41 fewer model parameters. Applying our method to a near state-of-the-art network for CIFAR, we achieved comparable accuracy with 46 less compute and 55 fewer parameters. Generating natural language descriptions for in-the-wild videos is a challenging task. Most state-of-the-art methods for solving this problem borrow existing deep convolutional neural network (CNN) architectures (AlexNet, GoogLeNet) to extract a visual representation of the input video. However, these deep CNN architectures are designed for single-label centered-positioned object classification. While they generate strong semantic features, they have no inherent structure allowing them to detect multiple objects of different sizes and locations in the frame. Our paper tries to solve this problem by integrating the base CNN into several fully convolutional neural networks (FCNs) to form a multi-scale network that handles multiple receptive field sizes in the original image. FCNs, previously applied to image segmentation, can generate class heat-maps efficiently compared to sliding window mechanisms, and can easily handle multiple scales. To further handle the ambiguity over multiple objects and locations, we incorporate the Multiple Instance Learning mechanism (MIL) to consider objects in different positions and at different scales simultaneously. We integrate our multi-scale multi-instance architecture with a sequence-to-sequence recurrent neural network to generate sentence descriptions based on the visual representation. Ours is the first end-to-end trainable architecture that is capable of multi-scale region processing. Evaluation on a Youtube video dataset shows the advantage of our approach compared to the original single-scale whole frame CNN model. Our flexible and efficient architecture can potentially be extended to support other video processing tasks. We investigate architectures of discriminatively trained deep Convolutional Networks (ConvNets) for action recognition in video. The challenge is to capture the complementary information on appearance from still frames and motion between frames. We also aim to generalise the best performing hand-crafted features within a data-driven learning framework. Our contribution is three-fold. First, we propose a two-stream ConvNet architecture which incorporates spatial and temporal networks. Second, we demonstrate that a ConvNet trained on multi-frame dense optical flow is able to achieve very good performance in spite of limited training data. Finally, we show that multi-task learning, applied to two different action classification datasets, can be used to increase the amount of training data and improve the performance on both. Our architecture is trained and evaluated on the standard video actions benchmarks of UCF-101 and HMDB-51, where it is competitive with the state of the art. It also exceeds by a large margin previous attempts to use deep nets for video classification. Early diagnosis of interstitial lung diseases is crucial for their treatment, but even experienced physicians find it difficult, as their clinical manifestations are similar. In order to assist with the diagnosis, computer-aided diagnosis (CAD) systems have been developed. These commonly rely on a fixed scale classifier that scans CT images, recognizes textural lung patterns and generates a map of pathologies. In a previous study, we proposed a method for classifying lung tissue patterns using a deep convolutional neural network (CNN), with an architecture designed for the specific problem. In this study, we present an improved method for training the proposed network by transferring knowledge from the similar domain of general texture classification. Six publicly available texture databases are used to pretrain networks with the proposed architecture, which are then fine-tuned on the lung tissue data. The resulting CNNs are combined in an ensemble and their fused knowledge is compressed back to a network with the original architecture. The proposed approach resulted in an absolute increase of about 2 in the performance of the proposed CNN. The results demonstrate the potential of transfer learning in the field of medical image analysis, indicate the textural nature of the problem and show that the method used for training a network can be as important as designing its architecture.