We present uSplit, a dedicated approach for trained image decomposition in the context of fluorescence microscopy images. We find that best results using regular deep architectures are achieved when large image patches are used during training, making memory consumption the limiting factor to further improving performance. We therefore introduce lateral contextualization (LC), a memory efficient way to train powerful networks and show that LC leads to consistent and significant improvements on the task at hand. We integrate LC with U-Nets, Hierarchical AEs, and Hierarchical VAEs, for which we formulate a modified ELBO loss. Additionally, LC enables training deeper hierarchical models than otherwise possible and, interestingly, helps to reduce tiling artefacts that are inherently impossible to avoid when using tiled VAE predictions. We apply uSplit to five decomposition tasks, one on a synthetic dataset, four others derived from real microscopy data. LC achieves SOTA results (average improvements to the best baseline of 2.36 dB PSNR), while simultaneously requiring considerably less GPU memory.
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Benefiting from powerful convolutional neural networks (CNNs), learning-based image inpainting methods have made significant breakthroughs over the years. However, some nature of CNNs (e.g. local prior, spatially shared parameters) limit the performance in the face of broken images with diverse and complex forms. Recently, a class of attention-based network architectures, called transformer, has shown significant performance on natural language processing fields and high-level vision tasks. Compared with CNNs, attention operators are better at long-range modeling and have dynamic weights, but their computational complexity is quadratic in spatial resolution, and thus less suitable for applications involving higher resolution images, such as image inpainting. In this paper, we design a novel attention linearly related to the resolution according to Taylor expansion. And based on this attention, a network called $T$-former is designed for image inpainting. Experiments on several benchmark datasets demonstrate that our proposed method achieves state-of-the-art accuracy while maintaining a relatively low number of parameters and computational complexity. The code can be found at \href{//github.com/dengyecode/T-former_image_inpainting}{github.com/dengyecode/T-former\_image\_inpainting}
A salient characteristic of large pre-trained language models (PTLMs) is a remarkable improvement in their generalization capability and emergence of new capabilities with increasing model capacity and pre-training dataset size. Consequently, we are witnessing the development of enormous models pushing the state-of-the-art. It is, however, imperative to realize that this inevitably leads to prohibitively long training times, extortionate computing costs, and a detrimental environmental impact. Significant efforts are underway to make PTLM training more efficient through innovations in model architectures, training pipelines, and loss function design, with scant attention being paid to optimizing the utility of training data. The key question that we ask is whether it is possible to train PTLMs by employing only highly informative subsets of the training data while maintaining downstream performance? Building upon the recent progress in informative data subset selection, we show how we can employ submodular optimization to select highly representative subsets of the training corpora. Our results demonstrate that the proposed framework can be applied to efficiently train multiple PTLMs (BERT, BioBERT, GPT-2) using only a fraction of data while retaining up to $\sim99\%$ of the performance of the fully-trained models.
A change point detection (CPD) framework assisted by a predictive machine learning model called ''Predict and Compare'' is introduced and characterised in relation to other state-of-the-art online CPD routines which it outperforms in terms of false positive rate and out-of-control average run length. The method's focus is on improving standard methods from sequential analysis such as the CUSUM rule in terms of these quality measures. This is achieved by replacing typically used trend estimation functionals such as the running mean with more sophisticated predictive models (Predict step), and comparing their prognosis with actual data (Compare step). The two models used in the Predict step are the ARIMA model and the LSTM recursive neural network. However, the framework is formulated in general terms, so as to allow the use of other prediction or comparison methods than those tested here. The power of the method is demonstrated in a tribological case study in which change points separating the run-in, steady-state, and divergent wear phases are detected in the regime of very few false positives.
This paper introduces a novel Bayesian approach to detect changes in the variance of a Gaussian sequence model, focusing on quantifying the uncertainty in the change point locations and providing a scalable algorithm for inference. Such a measure of uncertainty is necessary when change point methods are deployed in sensitive applications, for example, when one is interested in determining whether an organ is viable for transplant. The key of our proposal is framing the problem as a product of multiple single changes in the scale parameter. We fit the model through an iterative procedure similar to what is done for additive models. The novelty is that each iteration returns a probability distribution on time instances, which captures the uncertainty in the change point location. Leveraging a recent result in the literature, we can show that our proposal is a variational approximation of the exact model posterior distribution. We study the algorithm's convergence and the change point localization rate. Extensive experiments in simulation studies illustrate the performance of our method and the possibility of generalizing it to more complex data-generating mechanisms. We apply the new model to an experiment involving a novel technique to assess the viability of a liver and oceanographic data.
Quantization is a widely adopted technique for deep neural networks to reduce the memory and computational resources required. However, when quantized, most models would need a suitable calibration process to keep their performance intact, which requires data from the target domain, such as a fraction of the dataset used in model training and model validation (i.e. calibration dataset). In this study, we investigate the use of synthetic data as a substitute for the calibration with real data for the quantization method. We propose a data generation method based on Generative Adversarial Networks that are trained prior to the model quantization step. We compare the performance of models quantized using data generated by StyleGAN2-ADA and our pre-trained DiStyleGAN, with quantization using real data and an alternative data generation method based on fractal images. Overall, the results of our experiments demonstrate the potential of leveraging synthetic data for calibration during the quantization process. In our experiments, the percentage of accuracy degradation of the selected models was less than 0.6%, with our best performance achieved on MobileNetV2 (0.05%). The code is available at: //github.com/ThanosM97/gsoc2022-openvino
The task of detecting 3D objects in point cloud has a pivotal role in many real-world applications. However, 3D object detection performance is behind that of 2D object detection due to the lack of powerful 3D feature extraction methods. In order to address this issue, we propose to build a 3D backbone network to learn rich 3D feature maps by using sparse 3D CNN operations for 3D object detection in point cloud. The 3D backbone network can inherently learn 3D features from almost raw data without compressing point cloud into multiple 2D images and generate rich feature maps for object detection. The sparse 3D CNN takes full advantages of the sparsity in the 3D point cloud to accelerate computation and save memory, which makes the 3D backbone network achievable. Empirical experiments are conducted on the KITTI benchmark and results show that the proposed method can achieve state-of-the-art performance for 3D object detection.
Retrieving object instances among cluttered scenes efficiently requires compact yet comprehensive regional image representations. Intuitively, object semantics can help build the index that focuses on the most relevant regions. However, due to the lack of bounding-box datasets for objects of interest among retrieval benchmarks, most recent work on regional representations has focused on either uniform or class-agnostic region selection. In this paper, we first fill the void by providing a new dataset of landmark bounding boxes, based on the Google Landmarks dataset, that includes $94k$ images with manually curated boxes from $15k$ unique landmarks. Then, we demonstrate how a trained landmark detector, using our new dataset, can be leveraged to index image regions and improve retrieval accuracy while being much more efficient than existing regional methods. In addition, we further introduce a novel regional aggregated selective match kernel (R-ASMK) to effectively combine information from detected regions into an improved holistic image representation. R-ASMK boosts image retrieval accuracy substantially at no additional memory cost, while even outperforming systems that index image regions independently. Our complete image retrieval system improves upon the previous state-of-the-art by significant margins on the Revisited Oxford and Paris datasets. Code and data will be released.
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.
In this paper, we focus on three problems in deep learning based medical image segmentation. Firstly, U-net, as a popular model for medical image segmentation, is difficult to train when convolutional layers increase even though a deeper network usually has a better generalization ability because of more learnable parameters. Secondly, the exponential ReLU (ELU), as an alternative of ReLU, is not much different from ReLU when the network of interest gets deep. Thirdly, the Dice loss, as one of the pervasive loss functions for medical image segmentation, is not effective when the prediction is close to ground truth and will cause oscillation during training. To address the aforementioned three problems, we propose and validate a deeper network that can fit medical image datasets that are usually small in the sample size. Meanwhile, we propose a new loss function to accelerate the learning process and a combination of different activation functions to improve the network performance. Our experimental results suggest that our network is comparable or superior to state-of-the-art methods.
Recent advance in fluorescence microscopy enables acquisition of 3D image volumes with better quality and deeper penetration into tissue. Segmentation is a required step to characterize and analyze biological structures in the images. 3D segmentation using deep learning has achieved promising results in microscopy images. One issue is that deep learning techniques require a large set of groundtruth data which is impractical to annotate manually for microscopy volumes. This paper describes a 3D nuclei segmentation method using 3D convolutional neural networks. A set of synthetic volumes and the corresponding groundtruth volumes are generated automatically using a generative adversarial network. Segmentation results demonstrate that our proposed method is capable of segmenting nuclei successfully in 3D for various data sets.
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