Reviewerly/exHarmony huggingface dataset:
Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries

Standards-based clinical data normalization has become a key component of effective data integration and accurate phenotyping for secondary use of electronic healthcare records (EHR) data. HL7 Fast Healthcare Interoperability Resources (FHIR) is an emerging clinical data standard for exchanging electronic healthcare data and has been used in modeling and integrating both structured and unstructured EHR data for a variety of clinical research applications. The overall objective of this study is to develop and evaluate a FHIR-based EHR phenotyping framework for identification of patients with obesity and its multiple comorbidities from semi-structured discharge summaries leveraging a FHIR-based clinical data normalization pipeline (known as NLP2FHIR). We implemented a multi-class and multi-label classification system based on the i2b2 Obesity Challenge task to evaluate the FHIR-based EHR phenotyping framework. Two core parts of the framework are: (a) the conversion of discharge summaries into corresponding FHIR resources – Composition, Condition, MedicationStatement, Procedure and FamilyMemberHistory using the NLP2FHIR pipeline, and (b) the implementation of four machine learning algorithms (logistic regression, support vector machine, decision tree, and random forest) to train classifiers to predict disease state of obesity and 15 comorbidities using features extracted from standard FHIR resources and terminology expansions. We used the macro- and micro-averaged precision (P), recall (R), and F1 score (F1) measures to evaluate the classifier performance. We validated the framework using a second obesity dataset extracted from the MIMIC-III database. Using the NLP2FHIR pipeline, 1237 clinical discharge summaries from the 2008 i2b2 obesity challenge dataset were represented as the instances of the FHIR Composition resource consisting of 5677 records with 16 unique section types. After the NLP processing and FHIR modeling, a set of 244,438 FHIR clinical resource instances were generated. As the results of the four machine learning classifiers, the random forest algorithm performed the best with F1-micro(0.9466)/F1-macro(0.7887) and F1-micro(0.9536)/F1-macro(0.6524) for intuitive classification (reflecting medical professionals’ judgments) and textual classification (reflecting the judgments based on explicitly reported information of diseases), respectively. The MIMIC-III obesity dataset was successfully integrated for prediction with minimal configuration of the NLP2FHIR pipeline and machine learning models. The study demonstrated that the FHIR-based EHR phenotyping approach could effectively identify the state of obesity and multiple comorbidities using semi-structured discharge summaries. Our FHIR-based phenotyping approach is a first concrete step towards improving the data aspect of phenotyping portability across EHR systems and enhancing interpretability of the machine learning-based phenotyping algorithms.
Single Image Deraining via Recurrent Hierarchy Enhancement Network

Single image deraining is an important problem in many computer vision tasks since rain streaks can severely hamper and degrade the visibility of images. In this paper, we propose a novel network named Recurrent Hierarchy Enhancement Network (ReHEN) to remove rain streaks from rainy images stage by stage. Unlike previous deep convolutional network methods, we adopt a Hierarchy Enhancement Unit (HEU) to fully extract local hierarchical features and generate effective features. Then a Recurrent Enhancement Unit (REU) is added to keep the useful information from HEU and benefit the rain removal in the later stages. To focus on different scales, shapes, and densities of rain streaks adaptively, Squeeze-and-Excitation (SE) block is applied in both HEU and REU to assign different scale factors to high-level features. Experiments on five synthetic datasets and a real-world rainy image set show that the proposed method outperforms the state-of-the-art methods considerably. The source code is available at https://github.com/nnUyi/ReHEN.
Cross-Modal Image-Text Retrieval with Semantic Consistency

Cross-modal image-text retrieval has been a long-standing challenge in the multimedia community. Existing methods explore various complicated embedding spaces to assess the semantic similarity between a given image-text pair, but consider no/little about the consistency across them. To remedy this situation, we introduce the idea of semantic consistency for learning various embedding spaces jointly. Specifically, similar to the previous works, we start by constructing two different embedding spaces, namely the image-grounded embedding space and the text-grounded embedding space. However, instead of learning these two embedding spaces separately, we incorporate a semantic consistency constraint in the common ranking objective function such that both embedding spaces can be learned simultaneously and benefit from each other to gain performance improvement. We conduct extensive experiments on three benchmark datasets, \ie Flickr8k, Flickr30k and MS COCO. Results show that our model outperforms the state-of-the-art models on all three datasets, which can well demonstrate the effectiveness and superiority of the introduction of semantic consistency. Our source code is released at: \urlhttps://github.com/HuiChen24/SemanticConsistency.
LinesToFacePhoto

In this paper, we explore the task of generating photo-realistic face images from lines. Previous methods based on conditional generative adversarial networks (cGANs) have shown their power to generate visually plausible images when a conditional image and an output image share well-aligned structures. However, these models fail to synthesize face images with a whole set of well-defined structures, e.g. eyes, noses, mouths, etc., especially when the conditional line map lacks one or several parts. To address this problem, we propose a conditional self-attention generative adversarial network (CSAGAN). We introduce a conditional self-attention mechanism to cGANs to capture long-range dependencies between different regions in faces. We also build a multi-scale discriminator. The large-scale discriminator enforces the completeness of global structures and the small-scale discriminator encourages fine details, thereby enhancing the realism of generated face images. We evaluate the proposed model on the CelebA-HD dataset by two perceptual user studies and three quantitative metrics. The experiment results demonstrate that our method generates high-quality facial images while preserving facial structures. Our results outperform state-of-the-art methods both quantitatively and qualitatively.
Identity- and Pose-Robust Facial Expression Recognition through Adversarial Feature Learning

Existing facial expression recognition methods either focus on pose variations or identity bias, but not both simultaneously. This paper proposes an adversarial feature learning method to address both of these issues. Specifically, the proposed method consists of five components: an encoder, an expression classifier, a pose discriminator, a subject discriminator, and a generator. An encoder extracts feature representations, and an expression classifier tries to perform facial expression recognition using the extracted feature representations. The encoder and the expression classifier are trained collaboratively, so that the extracted feature representations are discriminative for expression recognition. A pose discriminator and a subject discriminator classify the pose and the subject from the extracted feature representations respectively. They are trained adversarially with the encoder. Thus, the extracted feature representations are robust to poses and subjects. A generator reconstructs facial images to further favor the feature representations. Experiments on five benchmark databases demonstrate the superiority of the proposed method to state-of-the-art work.
Generative Modeling for Small-Data Object Detection

This paper explores object detection in the small data regime, where only a limited number of annotated bounding boxes are available due to data rarity and annotation expense. This is a common challenge today with machine learning being applied to many new tasks where obtaining training data is more challenging, e.g. in medical images with rare diseases that doctors sometimes only see once in their life-time. In this work we explore this problem from a generative modeling perspective by learning to generate new images with associated bounding boxes, and using these for training an object detector. We show that simply training previously proposed generative models does not yield satisfactory performance due to them optimizing for image realism rather than object detection accuracy. To this end we develop a new model with a novel unrolling mechanism that jointly optimizes the generative model and a detector such that the generated images improve the performance of the detector. We show this method outperforms the state of the art on two challenging datasets, disease detection and small data pedestrian detection, improving the average precision on NIH Chest X-ray by a relative 20% and localization accuracy by a relative 50%.
SpecShield: Shielding Speculative Data from Microarchitectural Covert Channels

Hardware security has recently re-surfaced as a first-order concern to the confidentiality protections of computing systems. Meltdown and Spectre introduced a new class of microarchitectural exploits which leverage transient state as an attack vector, revealing fundamental security vulnerabilities of speculative execution in high-performance processors. These attacks profit from the fact that, during speculative execution, programs may execute instructions outside their legal control flows. This is used to gain access to restricted data, which is then exfiltrated through a covert channel. This paper proposes SpecShield, a family of microarchitectural mitigation techniques for shielding speculative data from covert channels used in transient execution attacks. Unlike prior work that has focused on closing individual covert channels used to leak sensitive information, SpecShield prevents the use of speculative data by downstream instructions until doing so is determined to be safe, thus isolating it from any covert channel. The most secure version of SpecShield eliminates transient execution attacks at a cost of 21% average performance degradation. A more aggressive version of SpecShield, which prevents the propagation of speculative data to known or probable covert channels provides only slightly relaxed security guarantees with an average of 10% performance impact.
Assessment of Artificial Neural Networks Learning Algorithms and Training Datasets for Solar Photovoltaic Power Production Prediction

The capability of accurately predicting the Solar Photovoltaic (PV) power productions is crucial to effectively control and manage the electrical grid. In this regard, the objective of this work is to propose an efficient Artificial Neural Network (ANN) model in which 10 different learning algorithms (i.e., different in the way in which the adjustment on the ANN internal parameters is formulated to effectively map the inputs to the outputs) and 23 different training datasets (i.e., different combinations of the real-time weather variables and the PV power production data) are investigated for accurate one day-ahead power production predictions with short computational time. In particular, the correlations between different combinations of the historical wind speed, ambient temperature, global solar radiation, PV power productions, and the time stamp of the year are examined for developing an efficient solar PV power production prediction model. The investigation is carried out on a 231 kWac grid-connected solar PV system located in Jordan. An ANN that receives in input the whole historical weather variables and PV power productions, and the time stamp of the year accompanied with Levenberg-Marquardt (LM) learning algorithm is found to provide the most accurate predictions with less computational efforts. Specifically, an enhancement reaches up to 15%, 1%, and 5% for the Root Mean Square Error (RMSE), Mean Absolute Error (MAE), and Coefficient of Determination (R2) performance metrics, respectively, compared to the Persistence prediction model of literature.
Strain field measurements over 3000 °C using 3D-Digital image correlation

With the development of aerospace and fusion engineering, understanding the mechanical behavior of materials under high-temperature conditions has become increasingly important. However, few studies are devoted to the ultra-high temperature range of 2000–3000 °C. In this study, with the aim of developing non-contact measuring techniques of mechanical deformation under ultra-high temperature, a high heat flux (~300 MW) comprehensive experimental platform is established, which includes a vacuum chamber, a three-dimensional digital image correlation (3D-DIC) system, infrared radiation thermometers and an electron beam heating system. Using the electron beam heating technique, the tungsten specimen can be heated to over 3000 °C. Owing to the use of a vacuum chamber, the thermally induced airflow disturbance at high temperature can be completely removed. Tantalum carbide (TaC) powder is chosen as the speckle material and speckle fabrication technology is developed to adapt ultra-high temperatures under vacuum conditions. In order to suppress the blackbody radiation at high temperature, three schemes based on blue light sources, self-radiating light sources and a dual wavelength optical filter technique are designed for three temperature ranges from room temperature to 3067 °C. Afterwards, full-field thermal deformation of the tungsten specimen above 3000 °C was determined based on the above strategies using the 3D-DIC technique. The feasibility and accuracy of the proposed methods are verified by comparing the measurement results with the thermal expansion strain data and model from available databases and literature. The standard deviations in different temperature intervals are 50 με for 25–1200 °C, 100–200 με for 1200–1800 °C and less than 500 με for 1800–3067 °C. The proposed methods and technologies are expected to lay a foundation for further developments in strain field measurements at ultra-high temperature.
End-to-End Detection-Segmentation System for Face Labeling

In this paper, we propose an end-to-end detection-segmentation system to implement detailed face labeling. Fully convolutional networks (FCN) has become the mainstream algorithm in the field of semantic segmentation due to the state-of-the-art performance. However, a general FCN usually produces smooth and homogeneous results. Moreover, when semantic category is extremely unbalanced in samples such as face labeling problem, features for some categories cannot be well explored by FCN. To alleviate these problems, a face image is firstly encoded to multi-level feature maps by a pyramid FCN, then features of different facial components are extracted separately according to the bounding box provided by a one-stage detection head. Three class-specific sub-networks are employed to process the extracted features to obtain the respective segmentation results. The skin-hair region can be decoded directly from the back end of the pyramid FCN. Finally, the overall segmentation result is obtained by combining different branches. Moreover, the proposed method trained on a single-face labeled dataset, can be directly used to implement detailed multi-face labeling tasks without any network modification and additional module or data. The overall structure can be trained in an end-to-end manner while maintaining a small network size (12 MB). Experiments show that the proposed method can generate more accurate (single or multi) face labeling results comparing with previous works and gets the state-of-the-art results in HELEN face dataset.
STICKER: An Energy-Efficient Multi-Sparsity Compatible Accelerator for Convolutional Neural Networks in 65-nm CMOS

STICKER is an energy-efficient convolutional neural network (NN) processor. It mainly improves energy efficiency by making full use of sparsity. The network sparsity can potentially lower storage and computation requirements. However, the sparsity distribution of both activations and weights ranges from 2% to 99% in different layers or models. Therefore, good support for the sparsity distribution is the key to improve the energy efficiency. Three new features are proposed in this article to support wide sparsity distribution efficiently. First, multi-sparsity control and data flow are implemented for finer sparsity granularity support. It can automatically switch the processor among nine sparsity modes for higher energy efficiency. Second, a multi-mode hierarchical data memory which can be reconfigured for networks with different sparsity modes is designed for higher storage efficiency. Third, a multi-sparsity-compatible set-associative convolution processing element (PE) array is designed to efficiently carry out convolution operations under different sparsity modes, especially when both activations and weights are sparse. STICKER was implemented in a 65-nm CMOS technology. With its wide-range sparsity-supported capacity, the peak energy efficiency reaches 62.1 TOPS/W when sparsity ratios of both activations and weights are 5%. In a completely pruned Alexnet model, STICKER achieves 2.82 TOPS/W energy efficiency 1.8 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\times $ </tex-math></inline-formula> higher than that of the state-of-the-art processors.
A Compare-Aggregate Model with Latent Clustering for Answer Selection

In this paper, we propose a novel method for a sentence-level answer-selection task that is a fundamental problem in natural language processing. First, we explore the effect of additional information by adopting a pretrained language model to compute the vector representation of the input text and by applying transfer learning from a large-scale corpus. Second, we enhance the compare-aggregate model by proposing a novel latent clustering method to compute additional information within the target corpus and by changing the objective function from listwise to pointwise. To evaluate the performance of the proposed approaches, experiments are performed with the WikiQA and TREC-QA datasets. The empirical results demonstrate the superiority of our proposed approach, which achieve state-of-the-art performance for both datasets.
Towards Memory Safe Enclave Programming with Rust-SGX

Intel Software Guard eXtension (SGX), a hardware supported trusted execution environment (TEE), is designed to protect security critical applications. However, it does not terminate traditional memory corruption vulnerabilities for the software running inside enclave, since enclave software is still developed with type unsafe languages such as C/C++. This paper presents RUST-SGX, an efficient and layered approach to exterminating memory corruption for software running inside SGX enclaves. The key idea is to enable the development of enclave programs with an efficient memory safe system language Rust with a RUST-SGX SDK by solving the key challenges of how to (1) make the SGX software memory safe and (2) meanwhile run as efficiently as with the SDK provided by Intel. We therefore propose to build RUST-SGX atop Intel SGX SDK, and tame unsafe components with formally proven memory safety. We have implemented RUST-SGX and tested with a series of benchmark programs. Our evaluation results show that RUST-SGX imposes little extra overhead (less than 5% with respect to the SGX specific features and services compared to software developed by Intel SGX SDK), and meanwhile have stronger memory safety.
Efficient Utilization of Missing Data in Cost-Sensitive Learning

Different from previous imputation methods which impute missing values in the incomplete samples by using the information in the complete samples, this paper proposes a Date-drive Incremental imputation Model, DIM for short, which uses all available information in the data set to impute missing values economically, effectively, orderly, and iteratively. To this end, we propose a scoring rule to rank the missing features by taking into account both the economical criterion and the effective imputation information. The economical criterion takes both the imputation cost and the discriminative ability of the feature into account, while the effective imputation information enables to use all observed information in the data set including the imputed missing values to impute the left missing values. During the imputation process, our DIM first detects the neednot-impute samples for reducing the imputation cost and noise, and then selects the missing features with the top rank to impute first. The imputation process orderly imputes the missing features until all missing values are imputed or the imputation cost is exhausted. Experimental results on UCI data sets demonstrated the advantages of our proposed DIM, compared to the comparison methods, in terms of prediction accuracy and classification accuracy.
A Weighted Majority Voting Ensemble Approach for Classification

Ensemble learning combines a series of base classifiers and the final result is assigned to the corresponding class by using a majority voting mechanism. However, the base classifiers in the ensemble cannot perform equally well. Therefore, the base classifiers should be assigned different weights in order to increase classification performance. In this study, a novel Weighted Majority Voting Ensemble (WMVE) approach is proposed, which evaluates individual performances of each classifier in the ensemble and adjusts their contributions to class decision. In the proposed weight adjustment model, only reward mechanism is provided, so punishment is not included. Classifiers that correctly classify observations which are not correctly classified by most of the classifiers gain more weights in the ensemble. In the experimental studies, increasing value of weight was calculated for each classifier in a heterogeneous collection of classification algorithms, including C4.5 decision tree, support vector machine, k-nearest neighbor, k-star, and naive Bayes. The proposed method (WMVE) was compared with the Simple Majority Voting Ensemble (SMVE) approach in terms of classification accuracy on 28 benchmark datasets. The effectiveness of the proposed method is confirmed by the experimental results.
SceneGraphNet: Neural Message Passing for 3D Indoor Scene Augmentation

In this paper we propose a neural message passing approach to augment an input 3D indoor scene with new objects matching their surroundings. Given an input, potentially incomplete, 3D scene and a query location, our method predicts a probability distribution over object types that fit well in that location. Our distribution is predicted though passing learned messages in a dense graph whose nodes represent objects in the input scene and edges represent spatial and structural relationships. By weighting messages through an attention mechanism, our method learns to focus on the most relevant surrounding scene context to predict new scene objects. We found that our method significantly outperforms state-of-the-art approaches in terms of correctly predicting objects missing in a scene based on our experiments in the SUNCG dataset. We also demonstrate other applications of our method, including context-based 3D object recognition and iterative scene generation.