pwc-archive/papers-with-abstracts huggingface dataset:
Object detection neural network improves Fourier ptychography reconstruction
Authors: Florian Ströhl, Suyog Jadhav, Balpreet S. Ahluwalia, Krishna Agarwal, and Dilip K. Prasad
Date: 2020-11-23 00:00:00
Tasks: Object, object-detection, Object Detection

High resolution microscopy is heavily dependent on superb optical elements and superresolution microscopy even more so. Correcting unavoidable optical aberrations during post-processing is an elegant method to reduce the optical system’s complexity. A prime method that promises superresolution, aberration correction, and quantitative phase imaging is Fourier ptychography. This microscopy technique combines many images of the sample, recorded at differing illumination angles akin to computed tomography and uses error minimisation between the recorded images with those generated by a forward model. The more precise knowledge of those illumination angles is available for the image formation forward model, the better the result. Therefore, illumination estimation from the raw data is an important step and supports correct phase recovery and aberration correction. Here, we derive how illumination estimation can be cast as an object detection problem that permits the use of a fast convolutional neural network (CNN) for this task. We find that faster-RCNN delivers highly robust results and outperforms classical approaches by far with an up to 3-fold reduction in estimation errors. Intriguingly, we find that conventionally beneficial smoothing and filtering of raw data is counterproductive in this type of application. We present a detailed analysis of the network’s performance and provide all our developed software openly.
Artefact removal in ground truth deficient fluctuations-based nanoscopy images using deep learning
Authors: Suyog Jadhav, Sebastian Acuña, Ida S. Opstad, Balpreet Singh Ahluwalia, Krishna Agarwal, and Dilip K. Prasad
Date: 2020-12-08 00:00:00
Tasks: Deep Learning, Denoising, Image Denoising, Super-Resolution

Image denoising or artefact removal using deep learning is possible in the availability of supervised training dataset acquired in real experiments or synthesized using known noise models. Neither of the conditions can be fulfilled for nanoscopy (super-resolution optical microscopy) images that are generated from microscopy videos through statistical analysis techniques. Due to several physical constraints, a supervised dataset cannot be measured. Further, the non-linear spatio-temporal mixing of data and valuable statistics of fluctuations from fluorescent molecules that compete with noise statistics. Therefore, noise or artefact models in nanoscopy images cannot be explicitly learned. Here, we propose a robust and versatile simulation-supervised training approach of deep learning auto-encoder architectures for the highly challenging nanoscopy images of sub-cellular structures inside biological samples. We show the proof of concept for one nanoscopy method and investigate the scope of generalizability across structures, and nanoscopy algorithms not included during simulation-supervised training. We also investigate a variety of loss functions and learning models and discuss the limitation of existing performance metrics for nanoscopy images. We generate valuable insights for this highly challenging and unsolved problem in nanoscopy, and set the foundation for the application of deep learning problems in nanoscopy for life sciences.
Deep Multi-Task Learning for SSVEP Detection and Visual Response Mapping
Authors: Hong Jing Khok, Victor Teck Chang Koh, Cuntai Guan
Date: 2020-10-10 00:00:00
Tasks: Electroencephalogram (EEG), Multi-Task Learning, SSVEP

Glaucoma is an eye disease that occurs without the onset of symptoms at initial, and late diagnosis results in irreversible degeneration of retinal ganglion cells. Standard automated perimetry is the gold standard for assessing glaucoma; however, the examination is subjective, where responses can fluctuate each time the test is performed, significantly confounding the test’s interpretation. In this study, we present our approach that aims to provide a rapid point-of-care diagnostics for glaucoma patients by eliminating the cognitive aspect in existing visual field assessment. Unlike existing methods that mostly report the foveal target detection’s accuracy, we employed a multi-task learning architecture that efficiently captures signals simultaneously from the fovea and the neighboring targets in the peripheral vision, generating a visual response map. Furthermore, we designed a multi-task learning module that learns multiple tasks in parallel efficiently. We evaluated our model classification on a 40-classes dataset, with yields 92% and 95% in accuracy and F1 score respectively. Our model is able to perform on a calibration-free user-independent scenario, which is desirable for clinical diagnostics. Our proposed approach could be a stepping stone for an objective assessment of glaucoma patients’ visual field.
Pan-Cancer Computational Histopathology (PC-CHiP) analysis using deep learning
Authors: Yu Fu, Alexander W Jung, Ramon Viñas Torne, Santiago Gonzalez, Harald Vöhringer, Artem Shmatko, Lucy Yates, Mercedes Jimenez-Linan, Luiza Moore, Moritz Gerstung
Date: 2020-07-27 00:00:00
Tasks: Deep Learning, Diagnostic, Prognosis, Transfer Learning

The diagnosis of cancer is typically based on histopathological assessment of tissue sections, and supplemented by genetic and other molecular tests1–6. Modern computer vision algorithms have high diagnostic accuracy and potential to augment histopathology workflows7–9. Here we use deep transfer learning to quantify histopathological patterns across 17,396 hematoxylin and eosin (H&E) stained histopathology slide images from 28 cancer types and correlate these with matched genomic, transcriptomic and survival data. This approach accurately classifies cancer types and provides spatially resolved tumor and normal distinction. Automatically learned computational histopathological features correlate with a large range of recurrent genetic aberrations pan-cancer. This includes whole genome duplications, which display universal features across cancer types, individual chromosomal aneuploidies, focal amplifications and deletions as well as driver gene mutations. There are wide-spread associations between bulk gene expression levels and histopathology, which reflect tumour composition and enables localising transcriptomically defined tumour infiltrating lymphocytes. Computational histopathology augments prognosis based on histopathological subtyping and grading and highlights prognostically relevant areas such as necrosis or lymphocytic aggregates. These findings demonstrate the large potential of computer vision to characterise the molecular basis of tumour histopathology and lay out a rationale for integrating molecular and histopathological data to augment diagnostic and prognostic workflows.
Semi-Supervised Disentangled Framework for Transferable Named Entity Recognition
Authors: Zhifeng Hao, Di Lv, Zijian Li, Ruichu Cai, Wen Wen, Boyan Xu
Date: 2020-12-22 00:00:00
Tasks: Cross-Lingual NER, Domain Adaptation, named-entity-recognition, Named Entity Recognition, Named Entity Recognition (NER), NER

Named entity recognition (NER) for identifying proper nouns in unstructured text is one of the most important and fundamental tasks in natural language processing. However, despite the widespread use of NER models, they still require a large-scale labeled data set, which incurs a heavy burden due to manual annotation. Domain adaptation is one of the most promising solutions to this problem, where rich labeled data from the relevant source domain are utilized to strengthen the generalizability of a model based on the target domain. However, the mainstream cross-domain NER models are still affected by the following two challenges (1) Extracting domain-invariant information such as syntactic information for cross-domain transfer. (2) Integrating domain-specific information such as semantic information into the model to improve the performance of NER. In this study, we present a semi-supervised framework for transferable NER, which disentangles the domain-invariant latent variables and domain-specific latent variables. In the proposed framework, the domain-specific information is integrated with the domain-specific latent variables by using a domain predictor. The domain-specific and domain-invariant latent variables are disentangled using three mutual information regularization terms, i.e., maximizing the mutual information between the domain-specific latent variables and the original embedding, maximizing the mutual information between the domain-invariant latent variables and the original embedding, and minimizing the mutual information between the domain-specific and domain-invariant latent variables. Extensive experiments demonstrated that our model can obtain state-of-the-art performance with cross-domain and cross-lingual NER benchmark data sets.
Efficient and Visualizable Convolutional Neural Networks for COVID-19 Classification Using Chest CT
Authors: Aksh Garg, Sana Salehi, Marianna La Rocca, Rachael Garner, Dominique Duncan
Date: 2020-12-22 00:00:00
Tasks: COVID-19 Diagnosis, Diagnostic, General Classification, Sensitivity, Specificity

With COVID-19 cases rising rapidly, deep learning has emerged as a promising diagnosis technique. However, identifying the most accurate models to characterize COVID-19 patients is challenging because comparing results obtained with different types of data and acquisition processes is non-trivial. In this paper we designed, evaluated, and compared the performance of 20 convolutional neutral networks in classifying patients as COVID-19 positive, healthy, or suffering from other pulmonary lung infections based on Chest CT scans, serving as the first to consider the EfficientNet family for COVID-19 diagnosis and employ intermediate activation maps for visualizing model performance. All models are trained and evaluated in Python using 4173 Chest CT images from the dataset entitled "A COVID multiclass dataset of CT scans," with 2168, 758, and 1247 images of patients that are COVID-19 positive, healthy, or suffering from other pulmonary infections, respectively. EfficientNet-B5 was identified as the best model with an F1 score of 0.9769+/-0.0046, accuracy of 0.9759+/-0.0048, sensitivity of 0.9788+/-0.0055, specificity of 0.9730+/-0.0057, and precision of 0.9751 +/- 0.0051. On an alternate 2-class dataset, EfficientNetB5 obtained an accuracy of 0.9845+/-0.0109, F1 score of 0.9599+/-0.0251, sensitivity of 0.9682+/-0.0099, specificity of 0.9883+/-0.0150, and precision of 0.9526 +/- 0.0523. Intermediate activation maps and Gradient-weighted Class Activation Mappings offered human-interpretable evidence of the model's perception of ground-class opacities and consolidations, hinting towards a promising use-case of artificial intelligence-assisted radiology tools. With a prediction speed of under 0.1 seconds on GPUs and 0.5 seconds on CPUs, our proposed model offers a rapid, scalable, and accurate diagnostic for COVID-19.
YolactEdge: Real-time Instance Segmentation on the Edge
Authors: Haotian Liu, Rafael A. Rivera Soto, Fanyi Xiao, Yong Jae Lee
Date: 2020-12-22 00:00:00
Tasks: Instance Segmentation, Real-time Instance Segmentation, Semantic Segmentation

We propose YolactEdge, the first competitive instance segmentation approach that runs on small edge devices at real-time speeds. Specifically, YolactEdge runs at up to 30.8 FPS on a Jetson AGX Xavier (and 172.7 FPS on an RTX 2080 Ti) with a ResNet-101 backbone on 550x550 resolution images. To achieve this, we make two improvements to the state-of-the-art image-based real-time method YOLACT: (1) applying TensorRT optimization while carefully trading off speed and accuracy, and (2) a novel feature warping module to exploit temporal redundancy in videos. Experiments on the YouTube VIS and MS COCO datasets demonstrate that YolactEdge produces a 3-5x speed up over existing real-time methods while producing competitive mask and box detection accuracy. We also conduct ablation studies to dissect our design choices and modules. Code and models are available at https://github.com/haotian-liu/yolact_edge.
Modeling Deep Learning Based Privacy Attacks on Physical Mail
Authors: Bingyao Huang, Ruyi Lian, Dimitris Samaras, Haibin Ling
Date: 2020-12-22 00:00:00
Tasks: Deep Learning, Denoising, Image Dehazing

Mail privacy protection aims to prevent unauthorized access to hidden content within an envelope since normal paper envelopes are not as safe as we think. In this paper, for the first time, we show that with a well designed deep learning model, the hidden content may be largely recovered without opening the envelope. We start by modeling deep learning-based privacy attacks on physical mail content as learning the mapping from the camera-captured envelope front face image to the hidden content, then we explicitly model the mapping as a combination of perspective transformation, image dehazing and denoising using a deep convolutional neural network, named Neural-STE (See-Through-Envelope). We show experimentally that hidden content details, such as texture and image structure, can be clearly recovered. Finally, our formulation and model allow us to design envelopes that can counter deep learning-based privacy attacks on physical mail.
Differentially Private Synthetic Medical Data Generation using Convolutional GANs
Authors: Amirsina Torfi, Edward A. Fox, Chandan K. Reddy
Date: 2020-12-22 00:00:00
Tasks: Deep Learning, image-classification, Image Classification, Synthetic Data Generation

Deep learning models have demonstrated superior performance in several application problems, such as image classification and speech processing. However, creating a deep learning model using health record data requires addressing certain privacy challenges that bring unique concerns to researchers working in this domain. One effective way to handle such private data issues is to generate realistic synthetic data that can provide practically acceptable data quality and correspondingly the model performance. To tackle this challenge, we develop a differentially private framework for synthetic data generation using R\'enyi differential privacy. Our approach builds on convolutional autoencoders and convolutional generative adversarial networks to preserve some of the critical characteristics of the generated synthetic data. In addition, our model can also capture the temporal information and feature correlations that might be present in the original data. We demonstrate that our model outperforms existing state-of-the-art models under the same privacy budget using several publicly available benchmark medical datasets in both supervised and unsupervised settings.
Explainable Abstract Trains Dataset
Authors: Manuel de Sousa Ribeiro, Ludwig Krippahl, Joao Leite
Date: 2020-12-15 00:00:00

The Explainable Abstract Trains Dataset is an image dataset containing simplified representations of trains. It aims to provide a platform for the application and research of algorithms for justification and explanation extraction. The dataset is accompanied by an ontology that conceptualizes and classifies the depicted trains based on their visual characteristics, allowing for a precise understanding of how each train was labeled. Each image in the dataset is annotated with multiple attributes describing the trains' features and with bounding boxes for the train elements.
Time-Travel Rephotography
Authors: Xuan Luo, Xuaner Zhang, Paul Yoo, Ricardo Martin-Brualla, Jason Lawrence, Steven M. Seitz
Date: 2020-12-22 00:00:00
Tasks: Colorization, Denoising, Image Restoration

Many historical people were only ever captured by old, faded, black and white photos, that are distorted due to the limitations of early cameras and the passage of time. This paper simulates traveling back in time with a modern camera to rephotograph famous subjects. Unlike conventional image restoration filters which apply independent operations like denoising, colorization, and superresolution, we leverage the StyleGAN2 framework to project old photos into the space of modern high-resolution photos, achieving all of these effects in a unified framework. A unique challenge with this approach is retaining the identity and pose of the subject in the original photo, while discarding the many artifacts frequently seen in low-quality antique photos. Our comparisons to current state-of-the-art restoration filters show significant improvements and compelling results for a variety of important historical people.
Underwater image filtering: methods, datasets and evaluation
Authors: Chau Yi Li, Riccardo Mazzon, Andrea Cavallaro
Date: 2020-12-22 00:00:00
Tasks: Image Restoration, Underwater Image Restoration

Underwater images are degraded by the selective attenuation of light that distorts colours and reduces contrast. The degradation extent depends on the water type, the distance between an object and the camera, and the depth under the water surface the object is at. Underwater image filtering aims to restore or to enhance the appearance of objects captured in an underwater image. Restoration methods compensate for the actual degradation, whereas enhancement methods improve either the perceived image quality or the performance of computer vision algorithms. The growing interest in underwater image filtering methods--including learning-based approaches used for both restoration and enhancement--and the associated challenges call for a comprehensive review of the state of the art. In this paper, we review the design principles of filtering methods and revisit the oceanology background that is fundamental to identify the degradation causes. We discuss image formation models and the results of restoration methods in various water types. Furthermore, we present task-dependent enhancement methods and categorise datasets for training neural networks and for method evaluation. Finally, we discuss evaluation strategies, including subjective tests and quality assessment measures. We complement this survey with a platform ( https://puiqe.eecs.qmul.ac.uk/ ), which hosts state-of-the-art underwater filtering methods and facilitates comparisons.
Autonomous Charging of Electric Vehicle Fleets to Enhance Renewable Generation Dispatchability
Authors: Reza Bayani, Saeed D. Manshadi, Guangyi Liu, Yawei Wang, Renchang Dai
Date: 2020-12-22 00:00:00
Tasks: Decision Making, Sequential Decision Making

A total 19% of generation capacity in California is offered by PV units and over some months, more than 10% of this energy is curtailed. In this research, a novel approach to reduce renewable generation curtailments and increasing system flexibility by means of electric vehicles' charging coordination is represented. The presented problem is a sequential decision making process, and is solved by fitted Q-iteration algorithm which unlike other reinforcement learning methods, needs fewer episodes of learning. Three case studies are presented to validate the effectiveness of the proposed approach. These cases include aggregator load following, ramp service and utilization of non-deterministic PV generation. The results suggest that through this framework, EVs successfully learn how to adjust their charging schedule in stochastic scenarios where their trip times, as well as solar power generation are unknown beforehand.
Improving Sample and Feature Selection with Principal Covariates Regression
Authors: Rose K. Cersonsky, Benjamin A. Helfrecht, Edgar A. Engel, Michele Ceriotti
Date: 2020-12-22 00:00:00
Tasks: feature selection, regression

Selecting the most relevant features and samples out of a large set of candidates is a task that occurs very often in the context of automated data analysis, where it can be used to improve the computational performance, and also often the transferability, of a model. Here we focus on two popular sub-selection schemes which have been applied to this end: CUR decomposition, that is based on a low-rank approximation of the feature matrix and Farthest Point Sampling, that relies on the iterative identification of the most diverse samples and discriminating features. We modify these unsupervised approaches, incorporating a supervised component following the same spirit as the Principal Covariates Regression (PCovR) method. We show that incorporating target information provides selections that perform better in supervised tasks, which we demonstrate with ridge regression, kernel ridge regression, and sparse kernel regression. We also show that incorporating aspects of simple supervised learning models can improve the accuracy of more complex models, such as feed-forward neural networks. We present adjustments to minimize the impact that any subselection may incur when performing unsupervised tasks. We demonstrate the significant improvements associated with the use of PCov-CUR and PCov-FPS selections for applications to chemistry and materials science, typically reducing by a factor of two the number of features and samples which are required to achieve a given level of regression accuracy.
Iteratively Reweighted Least Squares for Basis Pursuit with Global Linear Convergence Rate
Authors: Christian Kümmerle, Claudio Mayrink Verdun, Dominik Stöger
Date: 2020-12-22 00:00:00
Proceeding: NeurIPS 2021 12

The recovery of sparse data is at the core of many applications in machine learning and signal processing. While such problems can be tackled using $\ell_1$-regularization as in the LASSO estimator and in the Basis Pursuit approach, specialized algorithms are typically required to solve the corresponding high-dimensional non-smooth optimization for large instances. Iteratively Reweighted Least Squares (IRLS) is a widely used algorithm for this purpose due its excellent numerical performance. However, while existing theory is able to guarantee convergence of this algorithm to the minimizer, it does not provide a global convergence rate. In this paper, we prove that a variant of IRLS converges with a global linear rate to a sparse solution, i.e., with a linear error decrease occurring immediately from any initialization, if the measurements fulfill the usual null space property assumption. We support our theory by numerical experiments showing that our linear rate captures the correct dimension dependence. We anticipate that our theoretical findings will lead to new insights for many other use cases of the IRLS algorithm, such as in low-rank matrix recovery.
A Novel Genetic Search Scheme Based on Nature -- Inspired Evolutionary Algorithms for Self-Dual Codes
Authors: Adrian Korban, Serap Sahinkaya, Deniz Ustun
Date: 2020-12-22 00:00:00
Tasks: Evolutionary Algorithms

In this paper, a genetic algorithm, one of the evolutionary algorithms optimization methods, is used for the first time for the problem of finding extremal binary self-dual codes. We present a comparison of the computational times between a genetic algorithm and a linear search for different size search spaces and show that the genetic algorithm is capable of finding binary self-dual codes significantly faster than the linear search. Moreover, by employing a known matrix construction together with the genetic algorithm, we are able to obtain new binary self-dual codes of lengths 68 and 72 in a significantly short time. In particular, we obtain 11 new extremal binary self-dual codes of length 68 and 17 new binary self-dual codes of length 72.