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General General

Distant Domain Transfer Learning for Medical Imaging.

In IEEE journal of biomedical and health informatics

Medical image processing is one of the most important topics in the field of the Internet of Medical Things (IoMT). Recently, deep learning methods have carried out state-of-the-art performances on medical imaging tasks. However, conventional deep learning has two major drawbacks: 1) insufficient training data and 2) the domain mismatch between the training data and the testing data. In this paper, we propose a novel transfer learning framework for medical image classification. Moreover, we apply our method to a recent issue (Coronavirus Diagnose). Several studies indicate that lung Computed Tomography (CT) images can be used for a fast and accurate COVID-19 diagnosis. However, well-labeled training data sets cannot be easily accessed due to the novelty of the disease and the privacy policies. The proposed method has two components: Reduced-size Unet Segmentation model and Distant Feature Fusion (DFF) classification model. This study is related to a not well-investigated but important transfer learning problem, termed Distant Domain Transfer Learning (DDTL). In this study, we develop a DDTL model for COVID-19 diagnose using unlabeled Office-31, Caltech-256, and chest X-ray image data sets as the source data, and a small set of labeled COVID-19 lung CT as the target data. The main contributions of this study are: 1) the proposed method benefits from unlabeled data in distant domains which can be easily accessed, 2) it can effectively handle the distribution shift between the training data and the testing data, 3) it has achieved 96% classification accuracy, which is 13% higher classification accuracy than "non-transfer" algorithms, and 8% higher than existing transfer and distant transfer algorithms.

Niu Shuteng, Liu Meryl, Liu Yongxin, Wang Jian, Song Houbing

2021-Jan-15

General General

A Novel Feature Selection Method for High-Dimensional Mixed Decision Tables.

In IEEE transactions on neural networks and learning systems

Attribute reduction, also called feature selection, is one of the most important issues of rough set theory, which is regarded as a vital preprocessing step in pattern recognition, machine learning, and data mining. Nowadays, high-dimensional mixed and incomplete data sets are very common in real-world applications. Certainly, the selection of a promising feature subset from such data sets is a very interesting, but challenging problem. Almost all of the existing methods generated a cover on the space of objects to determine important features. However, some tolerance classes in the cover are useless for the computational process. Thus, this article introduces a new concept of stripped neighborhood covers to reduce unnecessary tolerance classes from the original cover. Based on the proposed stripped neighborhood cover, we define a new reduct in mixed and incomplete decision tables, and then design an efficient heuristic algorithm to find this reduct. For each loop in the main loop of the proposed algorithm, we use an error measure to select an optimal feature and put it into the selected feature subset. Besides, to deal more efficiently with high-dimensional data sets, we also determine redundant features after each loop and remove them from the candidate feature subset. For the purpose of verifying the performance of the proposed algorithm, we carry out experiments on data sets downloaded from public data sources to compare with existing state-of-the-art algorithms. Experimental results showed that our algorithm outperforms compared algorithms, especially in classification accuracy.

Thuy Nguyen Ngoc, Wongthanavasu Sartra

2021-Jan-15

General General

PID Controller-Guided Attention Neural Network Learning for Fast and Effective Real Photographs Denoising.

In IEEE transactions on neural networks and learning systems

Real photograph denoising is extremely challenging in low-level computer vision since the noise is sophisticated and cannot be fully modeled by explicit distributions. Although deep-learning techniques have been actively explored for this issue and achieved convincing results, most of the networks may cause vanishing or exploding gradients, and usually entail more time and memory to obtain a remarkable performance. This article overcomes these challenges and presents a novel network, namely, PID controller guide attention neural network (PAN-Net), taking advantage of both the proportional-integral-derivative (PID) controller and attention neural network for real photograph denoising. First, a PID-attention network (PID-AN) is built to learn and exploit discriminative image features. Meanwhile, we devise a dynamic learning scheme by linking the neural network and control action, which significantly improves the robustness and adaptability of PID-AN. Second, we explore both the residual structure and share-source skip connections to stack the PID-ANs. Such a framework provides a flexible way to feature residual learning, enabling us to facilitate the network training and boost the denoising performance. Extensive experiments show that our PAN-Net achieves superior denoising results against the state-of-the-art in terms of image quality and efficiency.

Ma Ruijun, Zhang Bob, Zhou Yicong, Li Zhengming, Lei Fangyuan

2021-Jan-15

General General

Panoptic Feature Fusion Net: A Novel Instance Segmentation Paradigm for Biomedical and Biological Images.

In IEEE transactions on image processing : a publication of the IEEE Signal Processing Society

Instance segmentation is an important task for biomedical and biological image analysis. Due to the complicated background components, the high variability of object appearances, numerous overlapping objects, and ambiguous object boundaries, this task still remains challenging. Recently, deep learning based methods have been widely employed to solve these problems and can be categorized into proposal-free and proposal-based methods. However, both proposal-free and proposal-based methods suffer from information loss, as they focus on either global-level semantic or local-level instance features. To tackle this issue, we present a Panoptic Feature Fusion Net (PFFNet) that unifies the semantic and instance features in this work. Specifically, our proposed PFFNet contains a residual attention feature fusion mechanism to incorporate the instance prediction with the semantic features, in order to facilitate the semantic contextual information learning in the instance branch. Then, a mask quality sub-branch is designed to align the confidence score of each object with the quality of the mask prediction. Furthermore, a consistency regularization mechanism is designed between the semantic segmentation tasks in the semantic and instance branches, for the robust learning of both tasks. Extensive experiments demonstrate the effectiveness of our proposed PFFNet, which outperforms several state-of-the-art methods on various biomedical and biological datasets.

Liu Dongnan, Zhang Donghao, Song Yang, Huang Heng, Cai Weidong

2021-Jan-15

General General

Deep Learning and Computer Vision Strategies for Automated Gene Editing with a Single-Cell Electroporation Platform.

In SLAS technology

Single-cell delivery platforms like microinjection and nanoprobe electroporation enable unparalleled control over cell manipulation tasks but are generally limited in throughput. Here, we present an automated single-cell electroporation system capable of automatically detecting cells with artificial intelligence (AI) software and delivering exogenous cargoes of different sizes with uniform dosage. We implemented a fully convolutional network (FCN) architecture to precisely locate the nuclei and cytosol of six cell types with various shapes and sizes, using phase contrast microscopy. Nuclear staining or reporter fluorescence was used along with phase contrast images of cells within the same field of view to facilitate the manual annotation process. Furthermore, we leveraged the near-human inference capabilities of the FCN network in detecting stained nuclei to automatically generate ground-truth labels of thousands of cells within seconds, and observed no statistically significant difference in performance compared to training with manual annotations. The average detection sensitivity and precision of the FCN network were 95±1.7% and 90±1.8%, respectively, outperforming a traditional image-processing algorithm (72±7.2% and 72±5.5%) used for comparison. To test the platform, we delivered fluorescent-labeled proteins into adhered cells and measured a delivery efficiency of 90%. As a demonstration, we used the automated single-cell electroporation platform to deliver Cas9-guide RNA (gRNA) complexes into an induced pluripotent stem cell (iPSC) line to knock out a green fluorescent protein-encoding gene in a population of ~200 cells. The results demonstrate that automated single-cell delivery is a useful cell manipulation tool for applications that demand throughput, control, and precision.

Patino Cesar A, Mukherjee Prithvijit, Lemaitre Vincent, Pathak Nibir, Espinosa Horacio D

2021-Jan-15

CRISPR-Cas9, computer vision, deep learning, electroporation, single-cell

General General

Machine Learning Algorithms Applied to Identify Microbial Species by Their Motility.

In Life (Basel, Switzerland)

(1) Background: Future missions to potentially habitable places in the Solar System require biochemistry-independent methods for detecting potential alien life forms. The technology was not advanced enough for onboard machine analysis of microscopic observations to be performed in past missions, but recent increases in computational power make the use of automated in-situ analyses feasible. (2) Methods: Here, we present a semi-automated experimental setup, capable of distinguishing the movement of abiotic particles due to Brownian motion from the motility behavior of the bacteria Pseudoalteromonas haloplanktis, Planococcus halocryophilus, Bacillus subtilis, and Escherichia coli. Supervised machine learning algorithms were also used to specifically identify these species based on their characteristic motility behavior. (3) Results: While we were able to distinguish microbial motility from the abiotic movements due to Brownian motion with an accuracy exceeding 99%, the accuracy of the automated identification rates for the selected species does not exceed 82%. (4) Conclusions: Motility is an excellent biosignature, which can be used as a tool for upcoming life-detection missions. This study serves as the basis for the further development of a microscopic life recognition system for upcoming missions to Mars or the ocean worlds of the outer Solar System.

Riekeles Max, Schirmack Janosch, Schulze-Makuch Dirk

2021-Jan-12

automation, biosignature, life detection, machine learning, motility, species identification