pwc-archive/papers-with-abstracts huggingface dataset:
Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome
Authors: Tiffany J. Callahan, Adrianne L. Stefanski, Jin-Dong Kim, William A. Baumgartner Jr., Jordan M. Wyrwa, Lawrence E. Hunter
Date: 2022-07-28 00:00:00

Preeclampsia is a leading cause of maternal and fetal morbidity and mortality. Currently, the only definitive treatment of preeclampsia is delivery of the placenta, which is central to the pathogenesis of the disease. Transcriptional profiling of human placenta from pregnancies complicated by preeclampsia has been extensively performed to identify differentially expressed genes (DEGs). The decisions to investigate DEGs experimentally are biased by many factors, causing many DEGs to remain uninvestigated. A set of DEGs which are associated with a disease experimentally, but which have no known association to the disease in the literature are known as the ignorome. Preeclampsia has an extensive body of scientific literature, a large pool of DEG data, and only one definitive treatment. Tools facilitating knowledge-based analyses, which are capable of combining disparate data from many sources in order to suggest underlying mechanisms of action, may be a valuable resource to support discovery and improve our understanding of this disease. In this work we demonstrate how a biomedical knowledge graph (KG) can be used to identify novel preeclampsia molecular mechanisms. Existing open source biomedical resources and publicly available high-throughput transcriptional profiling data were used to identify and annotate the function of currently uninvestigated preeclampsia-associated DEGs. Experimentally investigated genes associated with preeclampsia were identified from PubMed abstracts using text-mining methodologies. The relative complement of the text-mined- and meta-analysis-derived lists were identified as the uninvestigated preeclampsia-associated DEGs (n=445), i.e., the preeclampsia ignorome. Using the KG to investigate relevant DEGs revealed 53 novel clinically relevant and biologically actionable mechanistic associations.
Detecting Spam Reviews on Vietnamese E-commerce Websites
Authors: Co Van Dinh, Son T. Luu, Anh Gia-Tuan Nguyen
Date: 2022-07-27 00:00:00
Tasks: Binary Classification, Multi-class Classification

The reviews of customers play an essential role in online shopping. People often refer to reviews or comments of previous customers to decide whether to buy a new product. Catching up with this behavior, some people create untruths and illegitimate reviews to hoax customers about the fake quality of products. These are called spam reviews, confusing consumers on online shopping platforms and negatively affecting online shopping behaviors. We propose the dataset called ViSpamReviews, which has a strict annotation procedure for detecting spam reviews on e-commerce platforms. Our dataset consists of two tasks: the binary classification task for detecting whether a review is spam or not and the multi-class classification task for identifying the type of spam. The PhoBERT obtained the highest results on both tasks, 86.89% and 72.17%, respectively, by macro average F1 score.
GLEAN: Generative Latent Bank for Image Super-Resolution and Beyond
Authors: Kelvin C. K. Chan, Xiangyu Xu, Xintao Wang, Jinwei Gu, Chen Change Loy
Date: 2022-07-29 00:00:00
Tasks: Colorization, Decoder, Image Colorization, Image Restoration, Image Super-Resolution, Super-Resolution

We show that pre-trained Generative Adversarial Networks (GANs) such as StyleGAN and BigGAN can be used as a latent bank to improve the performance of image super-resolution. While most existing perceptual-oriented approaches attempt to generate realistic outputs through learning with adversarial loss, our method, Generative LatEnt bANk (GLEAN), goes beyond existing practices by directly leveraging rich and diverse priors encapsulated in a pre-trained GAN. But unlike prevalent GAN inversion methods that require expensive image-specific optimization at runtime, our approach only needs a single forward pass for restoration. GLEAN can be easily incorporated in a simple encoder-bank-decoder architecture with multi-resolution skip connections. Employing priors from different generative models allows GLEAN to be applied to diverse categories (\eg~human faces, cats, buildings, and cars). We further present a lightweight version of GLEAN, named LightGLEAN, which retains only the critical components in GLEAN. Notably, LightGLEAN consists of only 21% of parameters and 35% of FLOPs while achieving comparable image quality. We extend our method to different tasks including image colorization and blind image restoration, and extensive experiments show that our proposed models perform favorably in comparison to existing methods. Codes and models are available at https://github.com/open-mmlab/mmediting.
StyleLight: HDR Panorama Generation for Lighting Estimation and Editing
Authors: Guangcong Wang, Yinuo Yang, Chen Change Loy, Ziwei Liu
Date: 2022-07-29 00:00:00
Tasks: Lighting Estimation

We present a new lighting estimation and editing framework to generate high-dynamic-range (HDR) indoor panorama lighting from a single limited field-of-view (LFOV) image captured by low-dynamic-range (LDR) cameras. Existing lighting estimation methods either directly regress lighting representation parameters or decompose this problem into LFOV-to-panorama and LDR-to-HDR lighting generation sub-tasks. However, due to the partial observation, the high-dynamic-range lighting, and the intrinsic ambiguity of a scene, lighting estimation remains a challenging task. To tackle this problem, we propose a coupled dual-StyleGAN panorama synthesis network (StyleLight) that integrates LDR and HDR panorama synthesis into a unified framework. The LDR and HDR panorama synthesis share a similar generator but have separate discriminators. During inference, given an LDR LFOV image, we propose a focal-masked GAN inversion method to find its latent code by the LDR panorama synthesis branch and then synthesize the HDR panorama by the HDR panorama synthesis branch. StyleLight takes LFOV-to-panorama and LDR-to-HDR lighting generation into a unified framework and thus greatly improves lighting estimation. Extensive experiments demonstrate that our framework achieves superior performance over state-of-the-art methods on indoor lighting estimation. Notably, StyleLight also enables intuitive lighting editing on indoor HDR panoramas, which is suitable for real-world applications. Code is available at https://style-light.github.io.
PageNet: Towards End-to-End Weakly Supervised Page-Level Handwritten Chinese Text Recognition
Authors: Dezhi Peng, Lianwen Jin, Yuliang Liu, Canjie Luo, Songxuan Lai
Date: 2022-07-29 00:00:00
Tasks: Handwritten Chinese Text Recognition, Line Detection, Weakly-supervised Learning

Handwritten Chinese text recognition (HCTR) has been an active research topic for decades. However, most previous studies solely focus on the recognition of cropped text line images, ignoring the error caused by text line detection in real-world applications. Although some approaches aimed at page-level text recognition have been proposed in recent years, they either are limited to simple layouts or require very detailed annotations including expensive line-level and even character-level bounding boxes. To this end, we propose PageNet for end-to-end weakly supervised page-level HCTR. PageNet detects and recognizes characters and predicts the reading order between them, which is more robust and flexible when dealing with complex layouts including multi-directional and curved text lines. Utilizing the proposed weakly supervised learning framework, PageNet requires only transcripts to be annotated for real data; however, it can still output detection and recognition results at both the character and line levels, avoiding the labor and cost of labeling bounding boxes of characters and text lines. Extensive experiments conducted on five datasets demonstrate the superiority of PageNet over existing weakly supervised and fully supervised page-level methods. These experimental results may spark further research beyond the realms of existing methods based on connectionist temporal classification or attention. The source code is available at https://github.com/shannanyinxiang/PageNet.
Artifact Identification in X-ray Diffraction Data using Machine Learning Methods
Authors: Howard Yanxon, James Weng, Hannah Parraga, Wenqian Xu, Uta Ruett, Nicholas Schwarz
Date: 2022-07-29 00:00:00
Tasks: BIG-bench Machine Learning

The in situ synchrotron high-energy X-ray powder diffraction (XRD) technique is highly utilized by researchers to analyze the crystallographic structures of materials in functional devices (e.g., battery materials) or in complex sample environments (e.g., diamond anvil cells or syntheses reactors). An atomic structure of a material can be identified by its diffraction pattern, along with detailed analysis such as Rietveld refinement which indicates how the measured structure deviates from the ideal structure (e.g., internal stresses or defects). For in situ experiments, a series of XRD images is usually collected on the same sample at different conditions (e.g., adiabatic conditions), yielding different states of matter, or simply collected continuously as a function of time to track the change of a sample over a chemical or physical process. In situ experiments are usually performed with area detectors, collecting 2D images composed of diffraction rings for ideal powders. Depending on the material's form, one may observe different characteristics other than the typical Debye Scherrer rings for a realistic sample and its environments, such as textures or preferred orientations and single crystal diffraction spots in the 2D XRD image. In this work, we present an investigation of machine learning methods for fast and reliable identification and separation of the single crystal diffraction spots in XRD images. The exclusion of artifacts during an XRD image integration process allows a precise analysis of the powder diffraction rings of interest. We observe that the gradient boosting method can consistently produce high accuracy results when it is trained with small subsets of highly diverse datasets. The method dramatically decreases the amount of time spent on identifying and separating single crystal spots in comparison to the conventional method.
Recognition of Handwritten Chinese Text by Segmentation: A Segment-annotation-free Approach
Authors: Dezhi Peng, Lianwen Jin, Weihong Ma, Canyu Xie, Hesuo Zhang, Shenggao Zhu, Jing Li
Date: 2022-07-29 00:00:00
Tasks: Handwritten Chinese Text Recognition, Segmentation, Weakly-supervised Learning

Online and offline handwritten Chinese text recognition (HTCR) has been studied for decades. Early methods adopted oversegmentation-based strategies but suffered from low speed, insufficient accuracy, and high cost of character segmentation annotations. Recently, segmentation-free methods based on connectionist temporal classification (CTC) and attention mechanism, have dominated the field of HCTR. However, people actually read text character by character, especially for ideograms such as Chinese. This raises the question: are segmentation-free strategies really the best solution to HCTR? To explore this issue, we propose a new segmentation-based method for recognizing handwritten Chinese text that is implemented using a simple yet efficient fully convolutional network. A novel weakly supervised learning method is proposed to enable the network to be trained using only transcript annotations; thus, the expensive character segmentation annotations required by previous segmentation-based methods can be avoided. Owing to the lack of context modeling in fully convolutional networks, we propose a contextual regularization method to integrate contextual information into the network during the training stage, which can further improve the recognition performance. Extensive experiments conducted on four widely used benchmarks, namely CASIA-HWDB, CASIA-OLHWDB, ICDAR2013, and SCUT-HCCDoc, show that our method significantly surpasses existing methods on both online and offline HCTR, and exhibits a considerably higher inference speed than CTC/attention-based approaches.
Using Multi-modal Data for Improving Generalizability and Explainability of Disease Classification in Radiology
Authors: Pranav Agnihotri, Sara Ketabi, Khashayar, Namdar, Farzad Khalvati
Date: 2022-07-29 00:00:00
Tasks: Explainable Models

Traditional datasets for the radiological diagnosis tend to only provide the radiology image alongside the radiology report. However, radiology reading as performed by radiologists is a complex process, and information such as the radiologist's eye-fixations over the course of the reading has the potential to be an invaluable data source to learn from. Nonetheless, the collection of such data is expensive and time-consuming. This leads to the question of whether such data is worth the investment to collect. This paper utilizes the recently published Eye-Gaze dataset to perform an exhaustive study on the impact on performance and explainability of deep learning (DL) classification in the face of varying levels of input features, namely: radiology images, radiology report text, and radiologist eye-gaze data. We find that the best classification performance of X-ray images is achieved with a combination of radiology report free-text and radiology image, with the eye-gaze data providing no performance boost. Nonetheless, eye-gaze data serving as secondary ground truth alongside the class label results in highly explainable models that generate better attention maps compared to models trained to do classification and attention map generation without eye-gaze data.
Open-radiomics: A Collection of Standardized Datasets and a Technical Protocol for Reproducible Radiomics Machine Learning Pipelines
Authors: Khashayar Namdar, Matthias W. Wagner, Birgit B. Ertl-Wagner, Farzad Khalvati
Date: 2022-07-29 00:00:00
Tasks: BIG-bench Machine Learning, Survival Analysis

Background: As an important branch of machine learning pipelines in medical imaging, radiomics faces two major challenges namely reproducibility and accessibility. In this work, we introduce open-radiomics, a set of radiomics datasets along with a comprehensive radiomics pipeline based on our proposed technical protocol to improve the reproducibility of the results. Methods: We curated large-scale radiomics datasets based on three open-source datasets; BraTS 2020 for high-grade glioma (HGG) versus low-grade glioma (LGG) classification and survival analysis, BraTS 2023 for O6-methylguanine-DNA methyltransferase classification, and non-small cell lung cancer survival analysis from the Cancer Imaging Archive. Using BraTS 2020 Magnetic Resonance Imaging (MRI) dataset, we applied our protocol to 369 brain tumor patients (76 LGG, 293 HGG). Leveraging PyRadiomics for LGG vs. HGG classification, we generated 288 datasets from 4 MRI sequences, 3 binWidths, 6 normalization methods, and 4 tumor subregions. Random Forest classifiers were trained and validated (60%,20%,20%) across 100 different data splits (28,800 test results), evaluating Area Under the Receiver Operating Characteristic Curve (AUROC). Results: Unlike binWidth and image normalization, tumor subregion and imaging sequence significantly affected performance of the models. T1 contrast-enhanced sequence and the union of Necrotic and the non-enhancing tumor core subregions resulted in the highest AUROCs (average test AUROC 0.951, 95% confidence interval of (0.949, 0.952)). Although several settings and data splits (28 out of 28800) yielded test AUROC of 1, they were irreproducible. Conclusion: Our experiments demonstrate the sources of variability in radiomics pipelines (e.g., tumor subregion) can have a significant impact on the results, which may lead to superficial perfect performances that are irreproducible.
Image Quality Assessment: Integrating Model-Centric and Data-Centric Approaches
Authors: Peibei Cao, Dingquan Li, Kede Ma
Date: 2022-07-29 00:00:00
Tasks: Image Quality Assessment

Learning-based image quality assessment (IQA) has made remarkable progress in the past decade, but nearly all consider the two key components -- model and data -- in isolation. Specifically, model-centric IQA focuses on developing ``better'' objective quality methods on fixed and extensively reused datasets, with a great danger of overfitting. Data-centric IQA involves conducting psychophysical experiments to construct ``better'' human-annotated datasets, which unfortunately ignores current IQA models during dataset creation. In this paper, we first design a series of experiments to probe computationally that such isolation of model and data impedes further progress of IQA. We then describe a computational framework that integrates model-centric and data-centric IQA. As a specific example, we design computational modules to quantify the sampling-worthiness of candidate images. Experimental results show that the proposed sampling-worthiness module successfully spots diverse failures of the examined blind IQA models, which are indeed worthy samples to be included in next-generation datasets.
Robust Quantitative Susceptibility Mapping via Approximate Message Passing with Parameter Estimation
Authors: Shuai Huang, James J. Lah, Jason W. Allen, Deqiang Qiu
Date: 2022-07-29 00:00:00
Tasks: parameter estimation, SSIM

Purpose: For quantitative susceptibility mapping (QSM), the lack of ground-truth in clinical settings makes it challenging to determine suitable parameters for the dipole inversion. We propose a probabilistic Bayesian approach for QSM with built-in parameter estimation, and incorporate the nonlinear formulation of the dipole inversion to achieve a robust recovery of the susceptibility maps. Theory: From a Bayesian perspective, the image wavelet coefficients are approximately sparse and modelled by the Laplace distribution. The measurement noise is modelled by a Gaussian-mixture distribution with two components, where the second component is used to model the noise outliers. Through probabilistic inference, the susceptibility map and distribution parameters can be jointly recovered using approximate message passing (AMP). Methods: We compare our proposed AMP with built-in parameter estimation (AMP-PE) to the state-of-the-art L1-QSM, FANSI and MEDI approaches on the simulated and in vivo datasets, and perform experiments to explore the optimal settings of AMP-PE. Reproducible code is available at https://github.com/EmoryCN2L/QSM_AMP_PE Results: On the simulated Sim2Snr1 dataset, AMP-PE achieved the lowest NRMSE, DFCM and the highest SSIM, while MEDI achieved the lowest HFEN. On the in vivo datasets, AMP-PE is robust and successfully recovers the susceptibility maps using the estimated parameters, whereas L1-QSM, FANSI and MEDI typically require additional visual fine-tuning to select or double-check working parameters. Conclusion: AMP-PE provides automatic and adaptive parameter estimation for QSM and avoids the subjectivity from the visual fine-tuning step, making it an excellent choice for the clinical setting.
Improving Small Lesion Segmentation in CT Scans using Intensity Distribution Supervision: Application to Small Bowel Carcinoid Tumor
Authors: Seung Yeon Shin, Thomas C. Shen, Stephen A. Wank, Ronald M. Summers
Date: 2022-07-29 00:00:00
Tasks: Lesion Segmentation, Organ Segmentation, Segmentation

Finding small lesions is very challenging due to lack of noticeable features, severe class imbalance, as well as the size itself. One approach to improve small lesion segmentation is to reduce the region of interest and inspect it at a higher sensitivity rather than performing it for the entire region. It is usually implemented as sequential or joint segmentation of organ and lesion, which requires additional supervision on organ segmentation. Instead, we propose to utilize an intensity distribution of a target lesion at no additional labeling cost to effectively separate regions where the lesions are possibly located from the background. It is incorporated into network training as an auxiliary task. We applied the proposed method to segmentation of small bowel carcinoid tumors in CT scans. We observed improvements for all metrics (33.5% $\rightarrow$ 38.2%, 41.3% $\rightarrow$ 47.8%, 30.0% $\rightarrow$ 35.9% for the global, per case, and per tumor Dice scores, respectively.) compared to the baseline method, which proves the validity of our idea. Our method can be one option for explicitly incorporating intensity distribution information of a target in network training.
Can Shuffling Video Benefit Temporal Bias Problem: A Novel Training Framework for Temporal Grounding
Authors: Jiachang Hao, Haifeng Sun, Pengfei Ren, Jingyu Wang, Qi Qi, Jianxin Liao
Date: 2022-07-29 00:00:00
Tasks: Language-Based Temporal Localization, Sentence

Temporal grounding aims to locate a target video moment that semantically corresponds to the given sentence query in an untrimmed video. However, recent works find that existing methods suffer a severe temporal bias problem. These methods do not reason the target moment locations based on the visual-textual semantic alignment but over-rely on the temporal biases of queries in training sets. To this end, this paper proposes a novel training framework for grounding models to use shuffled videos to address temporal bias problem without losing grounding accuracy. Our framework introduces two auxiliary tasks, cross-modal matching and temporal order discrimination, to promote the grounding model training. The cross-modal matching task leverages the content consistency between shuffled and original videos to force the grounding model to mine visual contents to semantically match queries. The temporal order discrimination task leverages the difference in temporal order to strengthen the understanding of long-term temporal contexts. Extensive experiments on Charades-STA and ActivityNet Captions demonstrate the effectiveness of our method for mitigating the reliance on temporal biases and strengthening the model's generalization ability against the different temporal distributions. Code is available at https://github.com/haojc/ShufflingVideosForTSG.
AlphaVC: High-Performance and Efficient Learned Video Compression
Authors: Yibo Shi, Yunying Ge, Jing Wang, Jue Mao
Date: 2022-07-29 00:00:00
Tasks: Decoder, motion prediction, Video Compression, Vocal Bursts Intensity Prediction

Recently, learned video compression has drawn lots of attention and show a rapid development trend with promising results. However, the previous works still suffer from some criticial issues and have a performance gap with traditional compression standards in terms of widely used PSNR metric. In this paper, we propose several techniques to effectively improve the performance. First, to address the problem of accumulative error, we introduce a conditional-I-frame as the first frame in the GoP, which stabilizes the reconstructed quality and saves the bit-rate. Second, to efficiently improve the accuracy of inter prediction without increasing the complexity of decoder, we propose a pixel-to-feature motion prediction method at encoder side that helps us to obtain high-quality motion information. Third, we propose a probability-based entropy skipping method, which not only brings performance gain, but also greatly reduces the runtime of entropy coding. With these powerful techniques, this paper proposes AlphaVC, a high-performance and efficient learned video compression scheme. To the best of our knowledge, AlphaVC is the first E2E AI codec that exceeds the latest compression standard VVC on all common test datasets for both PSNR (-28.2% BD-rate saving) and MSSSIM (-52.2% BD-rate saving), and has very fast encoding (0.001x VVC) and decoding (1.69x VVC) speeds.