Reviewerly/exHarmony huggingface dataset:
A Question-and-Answer System to Extract Data From Free-Text Oncological Pathology Reports (CancerBERT Network): Development Study

Information in pathology reports is critical for cancer care. Natural language processing (NLP) systems used to extract information from pathology reports are often narrow in scope or require extensive tuning. Consequently, there is growing interest in automated deep learning approaches. A powerful new NLP algorithm, bidirectional encoder representations from transformers (BERT), was published in late 2018. BERT set new performance standards on tasks as diverse as question answering, named entity recognition, speech recognition, and more.The aim of this study is to develop a BERT-based system to automatically extract detailed tumor site and histology information from free-text oncological pathology reports.We pursued three specific aims: extract accurate tumor site and histology descriptions from free-text pathology reports, accommodate the diverse terminology used to indicate the same pathology, and provide accurate standardized tumor site and histology codes for use by downstream applications. We first trained a base language model to comprehend the technical language in pathology reports. This involved unsupervised learning on a training corpus of 275,605 electronic pathology reports from 164,531 unique patients that included 121 million words. Next, we trained a question-and-answer (Q&A) model that connects a Q&A layer to the base pathology language model to answer pathology questions. Our Q&A system was designed to search for the answers to two predefined questions in each pathology report: What organ contains the tumor? and What is the kind of tumor or carcinoma? This involved supervised training on 8197 pathology reports, each with ground truth answers to these 2 questions determined by certified tumor registrars. The data set included 214 tumor sites and 193 histologies. The tumor site and histology phrases extracted by the Q&A model were used to predict International Classification of Diseases for Oncology, Third Edition (ICD-O-3), site and histology codes. This involved fine-tuning two additional BERT models: one to predict site codes and another to predict histology codes. Our final system includes a network of 3 BERT-based models. We call this CancerBERT network (caBERTnet). We evaluated caBERTnet using a sequestered test data set of 2050 pathology reports with ground truth answers determined by certified tumor registrars.caBERTnet's accuracies for predicting group-level site and histology codes were 93.53% (1895/2026) and 97.6% (1993/2042), respectively. The top 5 accuracies for predicting fine-grained ICD-O-3 site and histology codes with 5 or more samples each in the training data set were 92.95% (1794/1930) and 96.01% (1853/1930), respectively.We have developed an NLP system that outperforms existing algorithms at predicting ICD-O-3 codes across an extensive range of tumor sites and histologies. Our new system could help reduce treatment delays, increase enrollment in clinical trials of new therapies, and improve patient outcomes.
Prediction of Epidemic Disease Dynamics on the Infection Risk Using Machine Learning Algorithms

Accurate forecast for the public is more important to many organisations especially health organisations on infectious disease dynamics that prevails in prevention or decrease in disease transmission. With multiple data availability in healthcare and medical sectors, precise analysis of such data helps in disease detection and better health care of all individuals. With the existing computational power and big data, there are more chances in predicting an epidemic outbreak. The basic idea of this paper is to analyse and predict the spread of epidemic diseases mainly on the focus on infection risk. A machine learning model using Multivariate Logistic Regression on Modified SEIR has to be built to predict the epidemic disease dynamics on the infection risk.
A Robust Real-Time Detecting and Tracking Framework for Multiple Kinds of Unmarked Object

A rodent real-time tracking framework is proposed to automatically detect and track multi-objects in real time and output the coordinates of each object, which combines deep learning (YOLO v3: You Only Look Once, v3), the Kalman Filter, improved Hungarian algorithm, and the nine-point position correction algorithm. A model of a Rat-YOLO is trained in our experiment. The Kalman Filter model is established in an acceleration model to predict the position of the rat in the next frame. The predicted data is used to fill the losing position of rats if the Rat-YOLO doesn't work in the current frame, and to associate the ID between the last frame and current frame. The Hungarian assigned algorithm is used to show the relationship between the objects of the last frame and the objects of the current frame and match the ID of the objects. The nine-point position correction algorithm is presented to adjust the correctness of the Rat-YOLO result and the predicted results. As the training of deep learning needs more datasets than our experiment, and it is time-consuming to process manual marking, automatic software for generating labeled datasets is proposed under a fixed scene and the labeled datasets are manually verified in term of their correctness. Besides this, in an off-line experiment, a mask is presented to remove the highlight. In this experiment, we select the 500 frames of the data as the training datasets and label these images with the automatic label generating software. A video (of 2892 frames) is tested by the trained Rat model and the accuracy of detecting all the three rats is around 72.545%, however, the Rat-YOLO combining the Kalman Filter and nine-point position correction arithmetic improved the accuracy to 95.194%.
Robust Tracking Control of Interval Type-2 Positive Takagi–Sugeno Fuzzy Systems With External Disturbance

Nonlinear positive systems are ubiquitous in practical applications. The constraint of positive conditions makes the design of this system still quite challenging even for the existing advanced control theory. In addition, when uncertainty and external disturbance also act on the positive nonlinear system at the same time, it will aggravate the complexity of the problem. In response to this problem, for the first time, this article presents a feasible robust tracking control strategy for the positive nonlinear systems with external disturbance and subject to uncertainty. In the proposed control strategy, the positive Takagi–Sugeno (T–S) fuzzy model is used to effectively represent the nonlinearity of the positive system, and the interval type-2 (IT2) fuzzy sets are used to deal with the uncertainty. The focus of tracking control is to design a reasonable IT2 fuzzy controller, which can make the states of the plant follow those of the given stable positive reference system as accurately as possible under the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$H_\infty$</tex-math></inline-formula> performance. Different from the tracking control research of general systems in the existing literature, in the tracking control analysis of positive systems, the generation of nonconvex conditions is inevitable. This article smoothly removes the obstacle of this problem. In addition, this article successfully attempts to relax the conservativeness of the basic analysis conditions by improving IT2 membership-function-dependent method, thereby improving the tracking effect under <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$H_\infty$</tex-math></inline-formula> performance. Finally, a detailed simulation example is given to verify the effectiveness of the proposed strategy.
Few-Shot Table-to-Text Generation with Prototype Memory

Neural table-to-text generation models have achieved remarkable progress on an array of tasks.However, due to the data-hungry nature of neural models, their performances strongly rely on large-scale training examples, limiting their applicability in real-world applications.To address this, we propose a new framework: Prototype-to-Generate (P2G), for table-to-text generation under the few-shot scenario.The proposed framework utilizes the retrieved prototypes, which are jointly selected by an IR system and a novel prototype selector to help the model bridging the structural gap between tables and texts.Experimental results on three benchmark datasets with three state-of-the-art models demonstrate that the proposed framework significantly improves the model performance across various evaluation metrics.
Identification of Orthotropic Elastic Properties of Wood by a Synthetic Image Approach Based on Digital Image Correlation

This work aims to determine the orthotropic linear elastic constitutive parameters of Pinus pinaster Ait. wood from a single uniaxial compressive experimental test, under quasi-static loading conditions, based on two different specimen configurations: (a) on-axis rectangular specimens oriented on the radial-tangential plane, (b) off-axis specimens with a grain angle of about 60° (radial-tangential plane). Using digital image correlation (DIC), full-field displacement and strain maps are obtained and used to identify the four orthotropic elastic parameters using the finite element model updating (FEMU) technique. Based on the FE data, a synthetic image reconstruction approach is proposed by coupling the inverse identification method with synthetically deformed images, which are then processed by DIC and compared with the experimental results. The proposed methodology is first validated by employing a DIC-levelled FEA reference in the identification procedure. The impact of the DIC setting parameters on the identification results is systematically investigated. This influence appears to be stronger when the parameter is less sensitive to the experimental setup used. When using on-axis specimen configuration, three orthotropic parameters of Pinus pinaster (ER, ET and νRT) are correctly identified, while the shear modulus (GRT) is robustly identified when using off-axis specimen configuration.
Cartography Active Learning

We propose Cartography Active Learning (CAL), a novel Active Learning (AL) algorithm that exploits the behavior of the model on individual instances during training as a proxy to find the most informative instances for labeling.CAL is inspired by data maps, which were recently proposed to derive insights into dataset quality (Swayamdipta et al., 2020).We compare our method on popular text classification tasks to commonly used AL strategies, which instead rely on post-training behavior.We demonstrate that CAL is competitive to other common AL methods, showing that training dynamics derived from small seed data can be successfully used for AL.We provide insights into our new AL method by analyzing batch-level statistics utilizing the data maps.Our results further show that CAL results in a more data-efficient learning strategy, achieving comparable or better results with considerably less training data.
Blind Camcording-Resistant Video Watermarking in the DTCWT and SVD Domain

Video watermarking techniques can be used to prevent unauthorized users from illegally distributing videos across (social) media networks. However, current watermarking solutions are unable to embed a perceptually invisible watermark which is robust to the distortions introduced by camcording. These watermark-disrupting distortions include lossy compression, the addition of noise, frame-rate conversion and geometric distortions. In this paper, we present a novel video watermarking technique that is blind and robust to camcording attacks. The proposed approach uses the integration of the dual-tree complex wavelet transform (DTCWT) and singular value decomposition (SVD) to achieve robustness against geometric attacks. The experimental results validate our technique’s superior imperceptibility and robustness to several attacks when compared to existing peer mechanisms. In conclusion, the proposed technique can be used to protect against illegal distribution of video content.
A comprehensive method to design and assess mixed reality simulations

Abstract The scientific literature highlights how Mixed Reality (MR) simulations allow obtaining several benefits in healthcare education. Simulation-based training, boosted by MR, offers an exciting and immersive learning experience that helps health professionals to acquire knowledge and skills, without exposing patients to unnecessary risks. High engagement, informational overload, and unfamiliarity with virtual elements could expose students to cognitive overload and acute stress. The implementation of effective simulation design strategies able to preserve the psychological safety of learners and the investigation of the impacts and effects of simulations are two open challenges to be faced. In this context, the present study proposes a method to design a medical simulation and evaluate its effectiveness, with the final aim to achieve the learning outcomes and do not compromise the students' psychological safety. The method has been applied in the design and development of an MR application to simulate the rachicentesis procedure for diagnostic purposes in adults. The MR application has been tested by involving twenty students of the 6 th year of Medicine and Surgery of Università Politecnica delle Marche. Multiple measurement techniques such as self-report, physiological indices, and observer ratings of performance, cognitive and emotional states of learners have been implemented to improve the rigour of the study. Also, a user-experience analysis has been accomplished to discriminate between two different devices: Vox Gear Plus® and Microsoft Hololens®. To compare the results with a reference, students performed the simulation also without using the MR application. The use of MR resulted in increased stress measured by physiological parameters without a high increase in perceived workload. It satisfies the objective to enhance the realism of the simulation without generating cognitive overload, which favours productive learning. The user experience (UX) has found greater benefits in involvement, immersion, and realism; however, it has emphasized the technological limitations of devices such as obstruction, loss of depth (Vox Gear Plus), and narrow FOV (Microsoft Hololens).
Hyperstyle

In software engineering, it is not enough to simply write code that only works as intended, even if it is free from vulnerabilities and bugs. Every programming language has a style guide and a set of best practices defined by its community, which help practitioners to build solutions that have a clear structure and therefore are easy to read and maintain. To introduce assessment of code quality into the educational process, we developed a tool called Hyperstyle. To make it reflect the needs of the programming community and at the same time be easily extendable, we built it upon several existing professional linters and code checkers. Hyperstyle supports four programming languages (Python, Java, Kotlin, and Javascript) and can be used as a standalone tool or integrated into a MOOC platform. We have integrated the tool into two educational platforms, Stepik and JetBrains Academy, and it has been used to process about one million submissions every week since May 2021.
A Novel Forensic Readiness Framework Applicable to the Drone Forensics Field

The Drone Forensics (DRFs) field is a branch of digital forensics, which involves the identification, capture, preservation, reconstruction, analysis, and documentation of drone incidents. Several models have been proposed in the literature for the DRF field, which generally discusses DRF from a reactive forensic perspective; however, the proactive forensic perspective is missing. Therefore, this paper proposes a novel forensic readiness framework called Drone Forensics Readiness Framework (DRFRF) using the design science method. It consists of two stages: (i) proactive forensic stage and (ii) reactive forensic stage. It considers centralized logging of all events of all the applicants within the drone device in preparation for an examination. It will speed up gathering data when an investigation is needed, permitting the forensic investigators to handle the examination and analysis directly. Additionally, digital forensics analysts can increase the possible use of digital evidence while decreasing the charge of performing forensic readiness. Thus, both the time and cost required to perform forensic readiness could be saved. The completeness, logicalness, and usefulness of DRFRF were compared to those of other models already existing in the DRF domain. The results showed the novelty and efficiency of DRFRF and its applicability to the situations before and after drone incidents.
Energy-Efficient Multiprocessor-Based Computation and Communication Resource Allocation in Two-Tier Federated Learning Networks

In conventional federated learning (FL), multiple edge devices holding local data jointly train a machine learning model by communicating learning updates with a centralized aggregator without exchanging their data samples. Owing to the communication and computation bottleneck at the centralized aggregator and inaccurate learning model caused by the non-independent and identically distributed (IID) data, we here consider a two-tier FL network, in which Internet of Things (IoT) nodes are the core clients that hold data, the model aggregators at the middle tier are the low altitude aerial platforms (UAVs), and the model aggregator at the top-most layer is the high-altitude aerial platform (UAV with relatively high altitude). Under the assumption that each IoT node has parallel computing ability, we study the energy-efficient computation and communication resource allocation in such a network within some time budget. Upon formulating the problem as an optimization problem, we solve the computation and communication resource allocation problems as the separate subproblems within a time frame, and then propose an iterative algorithm to solve the entire problem jointly. More specifically, we solve both the energy-efficient computation and communication resource allocation subproblems using the dual decomposition technique, and then apply a bisection search-based recursive technique to solve the entire energy efficiency problem jointly. Moreover, we propose offline and online client scheduling schemes that not only select the optimal edge nodes for association but also assign workload to each client based on the data quality and workload constraint. With real data, extensive simulations are conducted to verify the effectiveness of the proposed resource allocation scheme. The results further reveal that the learning performance not only is dependent on the computation and communication energy consumption of the FL process but also the model divergence weight owing to the non-IID data at client IoT nodes.
A lightweight weakly supervised learning segmentation algorithm for imbalanced image based on rotation density peaks

Image segmentation has been an important technique in the field of image processing. Fine-level manual annotations are very limited and difficult for a large collection of imbalanced images, where each image contains quite different small objects. However, we find that these imbalanced images have similar decision graphs obtained by a lightweight and simple clustering algorithm Density Peaks (DPeaks). Hence, in this paper, we propose a weakly supervised image segmentation algorithm. It trains a decision curve from decision graphs of a few sample imbalanced images by SVM and Support Vector Regression (SVR), which is effective for identifying the sparse region of an imbalanced image. Besides, RangeTree is applied to accelerate RDP for large images due to the high complexity of DPeaks Clustering. Experiments prove that the proposed algorithm works well on imbalanced image data sets, not only it can recognize main things, but also has the ability to identify some relatively small objects.
Categorized contrast enhanced mammography dataset for diagnostic and artificial intelligence research

Abstract Contrast-enhanced spectral mammography (CESM) is a relatively recent imaging modality with increased diagnostic accuracy compared to digital mammography (DM). New deep learning (DL) models were developed that have accuracies equal to that of an average radiologist. However, most studies trained the DL models on DM images as no datasets exist for CESM images. We aim to resolve this limitation by releasing a Categorized Digital Database for Low energy and Subtracted Contrast Enhanced Spectral Mammography images (CDD-CESM) to evaluate decision support systems. The dataset includes 2006 images, with an average resolution of 2355 × 1315, consisting of 310 mass images, 48 architectural distortion images, 222 asymmetry images, 238 calcifications images, 334 mass enhancement images, 184 non-mass enhancement images, 159 postoperative images, 8 post neoadjuvant chemotherapy images, and 751 normal images, with 248 images having more than one finding. This is the first dataset to incorporate data selection, segmentation annotation, medical reports, and pathological diagnosis for all cases. Moreover, we propose and evaluate a DL-based technique to automatically segment abnormal findings in images.
De-Speckling Breast Cancer Ultrasound Images Using a Rotationally Invariant Block Matching Based Non-Local Means (RIBM-NLM) Method

The ultrasonic technique is an indispensable imaging modality for diagnosis of breast cancer in young women due to its ability in efficiently capturing the tissue properties, and decreasing nega-tive recognition rate thereby avoiding non-essential biopsies. Despite the advantages, ultrasound images are affected by speckle noise, generating fine-false structures that decrease the contrast of the images and diminish the actual boundaries of tissues on ultrasound image. Moreover, speckle noise negatively impacts the subsequent stages in image processing pipeline, such as edge detec-tion, segmentation, feature extraction, and classification. Previous studies have formulated vari-ous speckle reduction methods in ultrasound images; however, these methods suffer from being unable to retain finer edge details and require more processing time. In this study, we propose a breast ultrasound de-speckling method based on rotational invariant block matching non-local means (RIBM-NLM) filtering. The effectiveness of our method has been demonstrated by com-paring our results with three established de-speckling techniques, the switching bilateral filter (SBF), the non-local means filter (NLMF), and the optimized non-local means filter (ONLMF) on 250 images from public dataset and 6 images from private dataset. Evaluation metrics, including Self-Similarity Index Measure (SSIM), Peak Signal to Noise Ratio (PSNR), and Mean Square Error (MSE) were utilized to measure performance. With the proposed method, we were able to record average SSIM of 0.8915, PSNR of 65.97, MSE of 0.014, RMSE of 0.119, and computational speed of 82 seconds at noise variance of 20dB using the public dataset, all with p-value of less than 0.001 compared against NLMF, ONLMF, and SBF. Similarly, the proposed method achieved av-erage SSIM of 0.83, PSNR of 66.26, MSE of 0.015, RMSE of 0.124, and computational speed of 83 seconds at noise variance of 20dB using the private dataset, all with p-value of less than 0.001 compared against NLMF, ONLMF, and SBF.
Federated Learning: The Pioneering Distributed Machine Learning and Privacy-Preserving Data Technology

Federated learning (pioneered by Google) is a new class of machine learning models trained on distributed data sets, and equally important, a key privacy-preserving data technology. The contribution of this article is to place it in perspective to other data science technologies.