scholarly journals BARcode DEmixing through Non-negative Spatial Regression (BarDensr)

2021 ◽  
Vol 17 (3) ◽  
pp. e1008256
Author(s):  
Shuonan Chen ◽  
Jackson Loper ◽  
Xiaoyin Chen ◽  
Alex Vaughan ◽  
Anthony M. Zador ◽  
...  
Keyword(s):  
State Of The Art ◽  
Spatial Regression ◽  
Image Data ◽  
Real Data ◽  
Optimization Methods ◽  
Spatial Density ◽  
Signal Recovery ◽  
Cloud Platform ◽  
Rna Transcripts ◽  
Different Types

Modern spatial transcriptomics methods can target thousands of different types of RNA transcripts in a single slice of tissue. Many biological applications demand a high spatial density of transcripts relative to the imaging resolution, leading to partial mixing of transcript rolonies in many voxels; unfortunately, current analysis methods do not perform robustly in this highly-mixed setting. Here we develop a new analysis approach, BARcode DEmixing through Non-negative Spatial Regression (BarDensr): we start with a generative model of the physical process that leads to the observed image data and then apply sparse convex optimization methods to estimate the underlying (demixed) rolony densities. We apply BarDensr to simulated and real data and find that it achieves state of the art signal recovery, particularly in densely-labeled regions or data with low spatial resolution. Finally, BarDensr is fast and parallelizable. We provide open-source code as well as an implementation for the ‘NeuroCAAS’ cloud platform.

scholarly journals BARcode DEmixing through Non-negative Spatial Regression (BarDensr)

2020 ◽  
Author(s):  
Shuonan Chen ◽  
Jackson Loper ◽  
Xiaoyin Chen ◽  
Tony Zador ◽  
Liam Paninski
Keyword(s):  
Convex Optimization ◽  
Spatial Resolution ◽  
Spatial Regression ◽  
Real Data ◽  
Computational Method ◽  
Spatial Density ◽  
Signal Recovery ◽  
Optimization Approach ◽  
Imaging Data ◽  
Imaging Resolution

AbstractModern spatial transcriptomics methods can target thousands of different types of RNA transcripts in a single slice of tissue. Many biological applications demand a high spatial density of transcripts relative to the imaging resolution, leading to partial mixing of transcript rolonies in many pixels; unfortunately, current analysis methods do not perform robustly in this highly-mixed setting. Here we develop a new analysis approach, BARcode DEmixing through Non-negative Spatial Regression (BarDensr): we start with a generative model of the physical process that leads to the observed image data and then apply sparse convex optimization methods to estimate the underlying (demixed) rolony densities. We apply Bar-Densr to simulated and real data and find that it achieves state of the art signal recovery, particularly in densely-labeled regions or data with low spatial resolution. Finally, BarDensr is fast and parallelizable. We provide open-source code as well as an implementation for the ‘NeuroCAAS’ cloud platform.Author SummarySpatial transcriptomics technologies allow us to simultaneously detect multiple molecular targets in the context of intact tissues. These experiments yield images that answer two questions: which kinds of molecules are present, and where are they located in the tissue? In many experiments (e.g., mapping RNA expression in fine neuronal processes), it is desirable to increase the signal density relative to the imaging resolution. This may lead to mixing of signals from multiple RNA molecules into single imaging pixels; thus we need to demix the signals from these images. Here we introduce BarDensr, a new computational method to perform this demixing. The method is based on a forward model of the imaging process, followed by a convex optimization approach to approximately ‘invert’ mixing induced during imaging. This new approach leads to significantly improved performance in demixing imaging data with dense expression and/or low spatial resolution.

scholarly journals A Reweighted Symmetric Smoothed Function Approximating L0-Norm Regularized Sparse Reconstruction Method

Symmetry ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 583 ◽  
Author(s):  
Jianhong Xiang ◽  
Huihui Yue ◽  
Xiangjun Yin ◽  
Guoqing Ruan
Keyword(s):  
Objective Function ◽  
Numerical Experiments ◽  
State Of The Art ◽  
Real Data ◽  
Sparse Signal ◽  
Sparse Signal Recovery ◽  
Signal Recovery ◽  
Reconstruction Method ◽  
Norm Minimization ◽  
Noisy Conditions

Sparse-signal recovery in noisy conditions is a problem that can be solved with current compressive-sensing (CS) technology. Although current algorithms based on L 1 regularization can solve this problem, the L 1 regularization mechanism cannot promote signal sparsity under noisy conditions, resulting in low recovery accuracy. Based on this, we propose a regularized reweighted composite trigonometric smoothed L 0 -norm minimization (RRCTSL0) algorithm in this paper. The main contributions of this paper are as follows: (1) a new smoothed symmetric composite trigonometric (CT) function is proposed to fit the L 0 -norm; (2) a new reweighted function is proposed; and (3) a new L 0 regularization objective function framework is constructed based on the idea of T i k h o n o v regularization. In the new objective function framework, Contributions (1) and (2) are combined as sparsity regularization terms, and errors as deviation terms. Furthermore, the conjugate-gradient (CG) method is used to optimize the objective function, so as to achieve accurate recovery of sparse signal and image under noisy conditions. The numerical experiments on both the simulated and real data verify that the proposed algorithm is superior to other state-of-the-art algorithms, and achieves advanced performance under noisy conditions.

scholarly journals ML-LOO: Detecting Adversarial Examples with Feature Attribution

2020 ◽  
Vol 34 (04) ◽  
pp. 6639-6647 ◽  
Author(s):  
Puyudi Yang ◽  
Jianbo Chen ◽  
Cho-Jui Hsieh ◽  
Jane-Ling Wang ◽  
Michael Jordan
Keyword(s):  
State Of The Art ◽  
Image Data ◽  
Real Data ◽  
Detection Methods ◽  
Data Sets ◽  
Confidence Levels ◽  
Significant Difference ◽  
Adversarial Examples ◽  
Scale Estimate ◽  
Complete Access

Deep neural networks obtain state-of-the-art performance on a series of tasks. However, they are easily fooled by adding a small adversarial perturbation to the input. The perturbation is often imperceptible to humans on image data. We observe a significant difference in feature attributions between adversarially crafted examples and original examples. Based on this observation, we introduce a new framework to detect adversarial examples through thresholding a scale estimate of feature attribution scores. Furthermore, we extend our method to include multi-layer feature attributions in order to tackle attacks that have mixed confidence levels. As demonstrated in extensive experiments, our method achieves superior performances in distinguishing adversarial examples from popular attack methods on a variety of real data sets compared to state-of-the-art detection methods. In particular, our method is able to detect adversarial examples of mixed confidence levels, and transfer between different attacking methods. We also show that our method achieves competitive performance even when the attacker has complete access to the detector.

scholarly journals G-Tric: generating three-way synthetic datasets with triclustering solutions

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
João Lobo ◽  
Rui Henriques ◽  
Sara C. Madeira
Keyword(s):  
State Of The Art ◽  
Synthetic Data ◽  
Ground Truth ◽  
Real Data ◽  
Three Dimensions ◽  
Additional Advantage ◽  
Urban Dynamics ◽  
Data Generator ◽  
Real World Datasets ◽  
Synthetic Datasets

Abstract Background Three-way data started to gain popularity due to their increasing capacity to describe inherently multivariate and temporal events, such as biological responses, social interactions along time, urban dynamics, or complex geophysical phenomena. Triclustering, subspace clustering of three-way data, enables the discovery of patterns corresponding to data subspaces (triclusters) with values correlated across the three dimensions (observations $$\times$$ × features $$\times$$ × contexts). With increasing number of algorithms being proposed, effectively comparing them with state-of-the-art algorithms is paramount. These comparisons are usually performed using real data, without a known ground-truth, thus limiting the assessments. In this context, we propose a synthetic data generator, G-Tric, allowing the creation of synthetic datasets with configurable properties and the possibility to plant triclusters. The generator is prepared to create datasets resembling real 3-way data from biomedical and social data domains, with the additional advantage of further providing the ground truth (triclustering solution) as output. Results G-Tric can replicate real-world datasets and create new ones that match researchers needs across several properties, including data type (numeric or symbolic), dimensions, and background distribution. Users can tune the patterns and structure that characterize the planted triclusters (subspaces) and how they interact (overlapping). Data quality can also be controlled, by defining the amount of missing, noise or errors. Furthermore, a benchmark of datasets resembling real data is made available, together with the corresponding triclustering solutions (planted triclusters) and generating parameters. Conclusions Triclustering evaluation using G-Tric provides the possibility to combine both intrinsic and extrinsic metrics to compare solutions that produce more reliable analyses. A set of predefined datasets, mimicking widely used three-way data and exploring crucial properties was generated and made available, highlighting G-Tric’s potential to advance triclustering state-of-the-art by easing the process of evaluating the quality of new triclustering approaches.

scholarly journals Deep Learning for Transient Image Reconstruction from ToF Data

Sensors ◽  
2021 ◽  
Vol 21 (6) ◽  
pp. 1962
Author(s):  
Enrico Buratto ◽  
Adriano Simonetto ◽  
Gianluca Agresti ◽  
Henrik Schäfer ◽  
Pietro Zanuttigh
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Light Response ◽  
Real Data ◽  
Depth Image ◽  
Learning Approach ◽  
Multiple Reflections ◽  
Noisy Input ◽  
Novel Approach ◽  
Incoming Light

In this work, we propose a novel approach for correcting multi-path interference (MPI) in Time-of-Flight (ToF) cameras by estimating the direct and global components of the incoming light. MPI is an error source linked to the multiple reflections of light inside a scene; each sensor pixel receives information coming from different light paths which generally leads to an overestimation of the depth. We introduce a novel deep learning approach, which estimates the structure of the time-dependent scene impulse response and from it recovers a depth image with a reduced amount of MPI. The model consists of two main blocks: a predictive model that learns a compact encoded representation of the backscattering vector from the noisy input data and a fixed backscattering model which translates the encoded representation into the high dimensional light response. Experimental results on real data show the effectiveness of the proposed approach, which reaches state-of-the-art performances.

scholarly journals Multiple objects tracking in the UAV system based on hierarchical deep high-resolution network

2021 ◽  
Author(s):  
Wei Huang ◽  
Xiaoshu Zhou ◽  
Mingchao Dong ◽  
Huaiyu Xu
Keyword(s):  
High Resolution ◽  
Object Tracking ◽  
High Performance ◽  
State Of The Art ◽  
Class Imbalance ◽  
Unified Framework ◽  
Multiple Objects ◽  
Tracking Process ◽  
Objects Tracking ◽  
Different Types

AbstractRobust and high-performance visual multi-object tracking is a big challenge in computer vision, especially in a drone scenario. In this paper, an online Multi-Object Tracking (MOT) approach in the UAV system is proposed to handle small target detections and class imbalance challenges, which integrates the merits of deep high-resolution representation network and data association method in a unified framework. Specifically, while applying tracking-by-detection architecture to our tracking framework, a Hierarchical Deep High-resolution network (HDHNet) is proposed, which encourages the model to handle different types and scales of targets, and extract more effective and comprehensive features during online learning. After that, the extracted features are fed into different prediction networks for interesting targets recognition. Besides, an adjustable fusion loss function is proposed by combining focal loss and GIoU loss to solve the problems of class imbalance and hard samples. During the tracking process, these detection results are applied to an improved DeepSORT MOT algorithm in each frame, which is available to make full use of the target appearance features to match one by one on a practical basis. The experimental results on the VisDrone2019 MOT benchmark show that the proposed UAV MOT system achieves the highest accuracy and the best robustness compared with state-of-the-art methods.

scholarly journals Fighting Together against the Pandemic: Learning Multiple Models on Tomography Images for COVID-19 Diagnosis

AI ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 261-273
Author(s):  
Mario Manzo ◽  
Simone Pellino
Keyword(s):  
Network Architecture ◽  
State Of The Art ◽  
Ensemble Classification ◽  
Effective Vaccine ◽  
Rt Pcr ◽  
Neural Network Architecture ◽  
Experimental Phase ◽  
Different Types ◽  
Polymerase Chain ◽  
Better Than

COVID-19 has been a great challenge for humanity since the year 2020. The whole world has made a huge effort to find an effective vaccine in order to save those not yet infected. The alternative solution is early diagnosis, carried out through real-time polymerase chain reaction (RT-PCR) tests or thorax Computer Tomography (CT) scan images. Deep learning algorithms, specifically convolutional neural networks, represent a methodology for image analysis. They optimize the classification design task, which is essential for an automatic approach with different types of images, including medical. In this paper, we adopt a pretrained deep convolutional neural network architecture in order to diagnose COVID-19 disease from CT images. Our idea is inspired by what the whole of humanity is achieving, as the set of multiple contributions is better than any single one for the fight against the pandemic. First, we adapt, and subsequently retrain for our assumption, some neural architectures that have been adopted in other application domains. Secondly, we combine the knowledge extracted from images by the neural architectures in an ensemble classification context. Our experimental phase is performed on a CT image dataset, and the results obtained show the effectiveness of the proposed approach with respect to the state-of-the-art competitors.

scholarly journals InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dominik Jens Elias Waibel ◽  
Sayedali Shetab Boushehri ◽  
Carsten Marr
Keyword(s):  
Image Processing ◽  
Deep Learning ◽  
Specific Problem ◽  
State Of The Art ◽  
Image Data ◽  
Semantic Segmentation ◽  
Parameter Tuning ◽  
Cellular Processes ◽  
Minimal Effort ◽  
Instance Segmentation

Abstract Background Deep learning contributes to uncovering molecular and cellular processes with highly performant algorithms. Convolutional neural networks have become the state-of-the-art tool to provide accurate and fast image data processing. However, published algorithms mostly solve only one specific problem and they typically require a considerable coding effort and machine learning background for their application. Results We have thus developed InstantDL, a deep learning pipeline for four common image processing tasks: semantic segmentation, instance segmentation, pixel-wise regression and classification. InstantDL enables researchers with a basic computational background to apply debugged and benchmarked state-of-the-art deep learning algorithms to their own data with minimal effort. To make the pipeline robust, we have automated and standardized workflows and extensively tested it in different scenarios. Moreover, it allows assessing the uncertainty of predictions. We have benchmarked InstantDL on seven publicly available datasets achieving competitive performance without any parameter tuning. For customization of the pipeline to specific tasks, all code is easily accessible and well documented. Conclusions With InstantDL, we hope to empower biomedical researchers to conduct reproducible image processing with a convenient and easy-to-use pipeline.

scholarly journals Image Classification for the Automatic Feature Extraction in Human Worn Fashion Data

Mathematics ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 624
Author(s):  
Stefan Rohrmanstorfer ◽  
Mikhail Komarov ◽  
Felix Mödritscher
Keyword(s):  
Neural Networks ◽  
Feature Extraction ◽  
Image Classification ◽  
Convolutional Neural Networks ◽  
Data Augmentation ◽  
State Of The Art ◽  
Image Data ◽  
Classification Model ◽  
Upper Body ◽  
Automatic Feature Extraction

With the always increasing amount of image data, it has become a necessity to automatically look for and process information in these images. As fashion is captured in images, the fashion sector provides the perfect foundation to be supported by the integration of a service or application that is built on an image classification model. In this article, the state of the art for image classification is analyzed and discussed. Based on the elaborated knowledge, four different approaches will be implemented to successfully extract features out of fashion data. For this purpose, a human-worn fashion dataset with 2567 images was created, but it was significantly enlarged by the performed image operations. The results show that convolutional neural networks are the undisputed standard for classifying images, and that TensorFlow is the best library to build them. Moreover, through the introduction of dropout layers, data augmentation and transfer learning, model overfitting was successfully prevented, and it was possible to incrementally improve the validation accuracy of the created dataset from an initial 69% to a final validation accuracy of 84%. More distinct apparel like trousers, shoes and hats were better classified than other upper body clothes.

Comparison of two different types of fractional-order COVID-19 distributed time-delay models with real data application

2021 ◽  
pp. 2150219
Author(s):  
Liangli Yang ◽  
Yongmei Su ◽  
Xinjian Zhuo
Keyword(s):  
Time Delay ◽  
Fractional Order ◽  
Distributed Delay ◽  
Real Data ◽  
Least Square ◽  
Order Model ◽  
The Real ◽  
Fractional Order Model ◽  
Different Types ◽  
Distributed Time Delay

The outbreak of COVID-19 has a great impact on the world. Considering that there are different infection delays among different populations, which can be expressed as distributed delay, and the distributed time-delay is rarely used in fractional-order model to simulate the real data, here we establish two different types of fractional order (Caputo and Caputo–Fabrizio) COVID-19 models with distributed time-delay. Parameters are estimated by the least-square method according to the report data of China and other 12 countries. The results of Caputo and Caputo–Fabrizio model with distributed time-delay and without delay, the integer-order model with distributed delay are compared. These show that the fractional-order model can be better in fitting the real data. Moreover, Caputo order is better in short-term time fitting, Caputo–Fabrizio order is better in long-term fitting and prediction. Finally, the influence of several parameters is simulated in Caputo order model, which further verifies the importance of taking strict quarantine measures and paying close attention to the incubation period population.

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