arXiv subjects

Wei Shao

Publications and source records attributed to Wei Shao.

At least 127 records · Page 7Linked to original sources

arXiv2022

A Sentence is Worth 128 Pseudo Tokens: A Semantic-Aware Contrastive Learning Framework for Sentence Embeddings

Contrastive learning has shown great potential in unsupervised sentence embedding tasks, e.g., SimCSE. However, We find that these existing solutions are heavily affected by superficial features like the length of sentences or syntactic structures. In this paper, we propose a semantics-aware contrastive learning framework for sentence embeddings, termed Pseudo-Token BERT (PT-BERT), which is able to exploit the pseudo-token space (i.e., latent semantic space) representation of a sentence while eliminating the impact of superficial features such as sentence length and syntax. Specifically, we introduce an additional pseudo token embedding layer independent of the BERT encoder to map each sentence into a sequence of pseudo tokens in a fixed length. Leveraging these pseudo sequences, we are able to construct same-length positive and negative pairs based on the attention mechanism to perform contrastive learning. In addition, we utilize both the gradient-updating and momentum-updating encoders to encode instances while dynamically maintaining an additional queue to store the representation of sentence embeddings, enhancing the encoder's learning performance for negative examples. Experiments show that our model outperforms the state-of-the-art baselines on six standard semantic textual similarity (STS) tasks. Furthermore, experiments on alignments and uniformity losses, as well as hard examples with different sentence lengths and syntax, consistently verify the effectiveness of our method.

cs.CL↗

arXiv2021

Bridging the gap between prostate radiology and pathology through machine learning

Prostate cancer is the second deadliest cancer for American men. While Magnetic Resonance Imaging (MRI) is increasingly used to guide targeted biopsies for prostate cancer diagnosis, its utility remains limited due to high rates of false positives and false negatives as well as low inter-reader agreements. Machine learning methods to detect and localize cancer on prostate MRI can help standardize radiologist interpretations. However, existing machine learning methods vary not only in model architecture, but also in the ground truth labeling strategies used for model training. In this study, we compare different labeling strategies, namely, pathology-confirmed radiologist labels, pathologist labels on whole-mount histopathology images, and lesion-level and pixel-level digital pathologist labels (previously validated deep learning algorithm on histopathology images to predict pixel-level Gleason patterns) on whole-mount histopathology images. We analyse the effects these labels have on the performance of the trained machine learning models. Our experiments show that (1) radiologist labels and models trained with them can miss cancers, or underestimate cancer extent, (2) digital pathologist labels and models trained with them have high concordance with pathologist labels, and (3) models trained with digital pathologist labels achieve the best performance in prostate cancer detection in two different cohorts with different disease distributions, irrespective of the model architecture used. Digital pathologist labels can reduce challenges associated with human annotations, including labor, time, inter- and intra-reader variability, and can help bridge the gap between prostate radiology and pathology by enabling the training of reliable machine learning models to detect and localize prostate cancer on MRI.

eess.IV↗

arXiv2021

Investigating the Reliability of Self-report Data in the Wild: The Quest for Ground Truth

Inferring human mental state (e.g., emotion, depression, engagement) with sensing technology is one of the most valuable challenges in the affective computing area, which has a profound impact in all industries interacting with humans. The self-report survey is the most common way to quantify how people think, but prone to subjectivity and various responses bias. It is usually used as the ground truth for human mental state prediction. In recent years, many data-driven machine learning models are built based on self-report annotations as the target value. In this research, we investigate the reliability of self-report surveys in the wild by studying the confidence level of responses and survey completion time. We conduct a case study (i.e., student engagement inference) by recruiting 23 students in a high school setting over a period of 4 weeks. Our participants volunteered 488 self-reported responses and data from their wearable sensors. We also find the physiologically measured student engagement and perceived student engagement are not always consistent. The findings from this research have great potential to benefit future studies in predicting engagement, depression, stress, and other emotion-related states in the field of affective computing and sensing technologies.

cs.HC↗

arXiv2021

Generative Adversarial Networks for Spatio-temporal Data: A Survey

Generative Adversarial Networks (GANs) have shown remarkable success in producing realistic-looking images in the computer vision area. Recently, GAN-based techniques are shown to be promising for spatio-temporal-based applications such as trajectory prediction, events generation and time-series data imputation. While several reviews for GANs in computer vision have been presented, no one has considered addressing the practical applications and challenges relevant to spatio-temporal data. In this paper, we have conducted a comprehensive review of the recent developments of GANs for spatio-temporal data. We summarise the application of popular GAN architectures for spatio-temporal data and the common practices for evaluating the performance of spatio-temporal applications with GANs. Finally, we point out future research directions to benefit researchers in this area.

cs.LG↗

arXiv2021

BiERU: Bidirectional Emotional Recurrent Unit for Conversational Sentiment Analysis

Sentiment analysis in conversations has gained increasing attention in recent years for the growing amount of applications it can serve, e.g., sentiment analysis, recommender systems, and human-robot interaction. The main difference between conversational sentiment analysis and single sentence sentiment analysis is the existence of context information which may influence the sentiment of an utterance in a dialogue. How to effectively encode contextual information in dialogues, however, remains a challenge. Existing approaches employ complicated deep learning structures to distinguish different parties in a conversation and then model the context information. In this paper, we propose a fast, compact and parameter-efficient party-ignorant framework named bidirectional emotional recurrent unit for conversational sentiment analysis. In our system, a generalized neural tensor block followed by a two-channel classifier is designed to perform context compositionality and sentiment classification, respectively. Extensive experiments on three standard datasets demonstrate that our model outperforms the state of the art in most cases.

cs.CL↗

arXiv2021

Weakly Supervised Registration of Prostate MRI and Histopathology Images

The interpretation of prostate MRI suffers from low agreement across radiologists due to the subtle differences between cancer and normal tissue. Image registration addresses this issue by accurately mapping the ground-truth cancer labels from surgical histopathology images onto MRI. Cancer labels achieved by image registration can be used to improve radiologists' interpretation of MRI by training deep learning models for early detection of prostate cancer. A major limitation of current automated registration approaches is that they require manual prostate segmentations, which is a time-consuming task, prone to errors. This paper presents a weakly supervised approach for affine and deformable registration of MRI and histopathology images without requiring prostate segmentations. We used manual prostate segmentations and mono-modal synthetic image pairs to train our registration networks to align prostate boundaries and local prostate features. Although prostate segmentations were used during the training of the network, such segmentations were not needed when registering unseen images at inference time. We trained and validated our registration network with 135 and 10 patients from an internal cohort, respectively. We tested the performance of our method using 16 patients from the internal cohort and 22 patients from an external cohort. The results show that our weakly supervised method has achieved significantly higher registration accuracy than a state-of-the-art method run without prostate segmentations. Our deep learning framework will ease the registration of MRI and histopathology images by obviating the need for prostate segmentations.

eess.IV↗

arXiv2021

Geodesic Density Regression for Correcting 4DCT Pulmonary Respiratory Motion Artifacts

Pulmonary respiratory motion artifacts are common in four-dimensional computed tomography (4DCT) of lungs and are caused by missing, duplicated, and misaligned image data. This paper presents a geodesic density regression (GDR) algorithm to correct motion artifacts in 4DCT by correcting artifacts in one breathing phase with artifact-free data from corresponding regions of other breathing phases. The GDR algorithm estimates an artifact-free lung template image and a smooth, dense, 4D (space plus time) vector field that deforms the template image to each breathing phase to produce an artifact-free 4DCT scan. Correspondences are estimated by accounting for the local tissue density change associated with air entering and leaving the lungs, and using binary artifact masks to exclude regions with artifacts from image regression. The artifact-free lung template image is generated by mapping the artifact-free regions of each phase volume to a common reference coordinate system using the estimated correspondences and then averaging. This procedure generates a fixed view of the lung with an improved signal-to-noise ratio. The GDR algorithm was evaluated and compared to a state-of-the-art geodesic intensity regression (GIR) algorithm using simulated CT time-series and 4DCT scans with clinically observed motion artifacts. The simulation shows that the GDR algorithm has achieved significantly more accurate Jacobian images and sharper template images, and is less sensitive to data dropout than the GIR algorithm. We also demonstrate that the GDR algorithm is more effective than the GIR algorithm for removing clinically observed motion artifacts in treatment planning 4DCT scans. Our code is freely available at https://github.com/Wei-Shao-Reg/GDR.

eess.IV↗

arXiv2021

MoParkeR : Multi-objective Parking Recommendation

Existing parking recommendation solutions mainly focus on finding and suggesting parking spaces based on the unoccupied options only. However, there are other factors associated with parking spaces that can influence someone's choice of parking such as fare, parking rule, walking distance to destination, travel time, likelihood to be unoccupied at a given time. More importantly, these factors may change over time and conflict with each other which makes the recommendations produced by current parking recommender systems ineffective. In this paper, we propose a novel problem called multi-objective parking recommendation. We present a solution by designing a multi-objective parking recommendation engine called MoParkeR that considers various conflicting factors together. Specifically, we utilise a non-dominated sorting technique to calculate a set of Pareto-optimal solutions, consisting of recommended trade-off parking spots. We conduct extensive experiments using two real-world datasets to show the applicability of our multi-objective recommendation methodology.

cs.IR↗

arXiv2021

Predicting Flight Delay with Spatio-Temporal Trajectory Convolutional Network and Airport Situational Awareness Map

To model and forecast flight delays accurately, it is crucial to harness various vehicle trajectory and contextual sensor data on airport tarmac areas. These heterogeneous sensor data, if modelled correctly, can be used to generate a situational awareness map. Existing techniques apply traditional supervised learning methods onto historical data, contextual features and route information among different airports to predict flight delay are inaccurate and only predict arrival delay but not departure delay, which is essential to airlines. In this paper, we propose a vision-based solution to achieve a high forecasting accuracy, applicable to the airport. Our solution leverages a snapshot of the airport situational awareness map, which contains various trajectories of aircraft and contextual features such as weather and airline schedules. We propose an end-to-end deep learning architecture, TrajCNN, which captures both the spatial and temporal information from the situational awareness map. Additionally, we reveal that the situational awareness map of the airport has a vital impact on estimating flight departure delay. Our proposed framework obtained a good result (around 18 minutes error) for predicting flight departure delay at Los Angeles International Airport.

cs.LG↗

arXiv2021

FADACS: A Few-shot Adversarial Domain Adaptation Architecture for Context-Aware Parking Availability Sensing

Existing research on parking availability sensing mainly relies on extensive contextual and historical information. In practice, the availability of such information is a challenge as it requires continuous collection of sensory signals. In this study, we design an end-to-end transfer learning framework for parking availability sensing to predict parking occupancy in areas in which the parking data is insufficient to feed into data-hungry models. This framework overcomes two main challenges: 1) many real-world cases cannot provide enough data for most existing data-driven models, and 2) it is difficult to merge sensor data and heterogeneous contextual information due to the differing urban fabric and spatial characteristics. Our work adopts a widely-used concept, adversarial domain adaptation, to predict the parking occupancy in an area without abundant sensor data by leveraging data from other areas with similar features. In this paper, we utilise more than 35 million parking data records from sensors placed in two different cities, one a city centre and the other a coastal tourist town. We also utilise heterogeneous spatio-temporal contextual information from external resources, including weather and points of interest. We quantify the strength of our proposed framework in different cases and compare it to the existing data-driven approaches. The results show that the proposed framework is comparable to existing state-of-the-art methods and also provide some valuable insights on parking availability prediction.

cs.LG↗

arXiv2020

ProsRegNet: A Deep Learning Framework for Registration of MRI and Histopathology Images of the Prostate

Magnetic resonance imaging (MRI) is an increasingly important tool for the diagnosis and treatment of prostate cancer. However, interpretation of MRI suffers from high inter-observer variability across radiologists, thereby contributing to missed clinically significant cancers, overdiagnosed low-risk cancers, and frequent false positives. Interpretation of MRI could be greatly improved by providing radiologists with an answer key that clearly shows cancer locations on MRI. Registration of histopathology images from patients who had radical prostatectomy to pre-operative MRI allows such mapping of ground truth cancer labels onto MRI. However, traditional MRI-histopathology registration approaches are computationally expensive and require careful choices of the cost function and registration hyperparameters. This paper presents ProsRegNet, a deep learning-based pipeline to accelerate and simplify MRI-histopathology image registration in prostate cancer. Our pipeline consists of image preprocessing, estimation of affine and deformable transformations by deep neural networks, and mapping cancer labels from histopathology images onto MRI using estimated transformations. We trained our neural network using MR and histopathology images of 99 patients from our internal cohort (Cohort 1) and evaluated its performance using 53 patients from three different cohorts (an additional 12 from Cohort 1 and 41 from two public cohorts). Results show that our deep learning pipeline has achieved more accurate registration results and is at least 20 times faster than a state-of-the-art registration algorithm. This important advance will provide radiologists with highly accurate prostate MRI answer keys, thereby facilitating improvements in the detection of prostate cancer on MRI. Our code is freely available at https://github.com/pimed//ProsRegNet.

eess.IV↗

arXiv2020

Towards Fair Cross-Domain Adaptation via Generative Learning

Domain Adaptation (DA) targets at adapting a model trained over the well-labeled source domain to the unlabeled target domain lying in different distributions. Existing DA normally assumes the well-labeled source domain is class-wise balanced, which means the size per source class is relatively similar. However, in real-world applications, labeled samples for some categories in the source domain could be extremely few due to the difficulty of data collection and annotation, which leads to decreasing performance over target domain on those few-shot categories. To perform fair cross-domain adaptation and boost the performance on these minority categories, we develop a novel Generative Few-shot Cross-domain Adaptation (GFCA) algorithm for fair cross-domain classification. Specifically, generative feature augmentation is explored to synthesize effective training data for few-shot source classes, while effective cross-domain alignment aims to adapt knowledge from source to facilitate the target learning. Experimental results on two large cross-domain visual datasets demonstrate the effectiveness of our proposed method on improving both few-shot and overall classification accuracy comparing with the state-of-the-art DA approaches.

cs.CV↗

arXiv2020

Transfer Learning for Thermal Comfort Prediction in Multiple Cities

HVAC (Heating, Ventilation and Air Conditioning) system is an important part of a building, which constitutes up to 40% of building energy usage. The main purpose of HVAC, maintaining appropriate thermal comfort, is crucial for the best utilisation of energy usage. Besides, thermal comfort is also crucial for well-being, health, and work productivity. Recently, data-driven thermal comfort models have got better performance than traditional knowledge-based methods (e.g. Predicted Mean Vote Model). An accurate thermal comfort model requires a large amount of self-reported thermal comfort data from indoor occupants which undoubtedly remains a challenge for researchers. In this research, we aim to tackle this data-shortage problem and boost the performance of thermal comfort prediction. We utilise sensor data from multiple cities in the same climate zone to learn thermal comfort patterns. We present a transfer learning based multilayer perceptron model from the same climate zone (TL-MLP-C*) for accurate thermal comfort prediction. Extensive experimental results on ASHRAE RP-884, the Scales Project and Medium US Office datasets show that the performance of the proposed TL-MLP-C* exceeds the state-of-the-art methods in accuracy, precision and F1-score.

cs.LG↗

arXiv2020

Low-Rank Reorganization via Proportional Hazards Non-negative Matrix Factorization Unveils Survival Associated Gene Clusters

One of the central goals in precision health is the understanding and interpretation of high-dimensional biological data to identify genes and markers associated with disease initiation, development, and outcomes. Though significant effort has been committed to harness gene expression data for multiple analyses while accounting for time-to-event modeling by including survival times, many traditional analyses have focused separately on non-negative matrix factorization (NMF) of the gene expression data matrix and survival regression with Cox proportional hazards model. In this work, Cox proportional hazards regression is integrated with NMF by imposing survival constraints. This is accomplished by jointly optimizing the Frobenius norm and partial log likelihood for events such as death or relapse. Simulation results on synthetic data demonstrated the superiority of the proposed method, when compared to other algorithms, in finding survival associated gene clusters. In addition, using human cancer gene expression data, the proposed technique can unravel critical clusters of cancer genes. The discovered gene clusters reflect rich biological implications and can help identify survival-related biomarkers. Towards the goal of precision health and cancer treatments, the proposed algorithm can help understand and interpret high-dimensional heterogeneous genomics data with accurate identification of survival-associated gene clusters.

q-bio.QM↗

arXiv2020

CorrSigNet: Learning CORRelated Prostate Cancer SIGnatures from Radiology and Pathology Images for Improved Computer Aided Diagnosis

Magnetic Resonance Imaging (MRI) is widely used for screening and staging prostate cancer. However, many prostate cancers have subtle features which are not easily identifiable on MRI, resulting in missed diagnoses and alarming variability in radiologist interpretation. Machine learning models have been developed in an effort to improve cancer identification, but current models localize cancer using MRI-derived features, while failing to consider the disease pathology characteristics observed on resected tissue. In this paper, we propose CorrSigNet, an automated two-step model that localizes prostate cancer on MRI by capturing the pathology features of cancer. First, the model learns MRI signatures of cancer that are correlated with corresponding histopathology features using Common Representation Learning. Second, the model uses the learned correlated MRI features to train a Convolutional Neural Network to localize prostate cancer. The histopathology images are used only in the first step to learn the correlated features. Once learned, these correlated features can be extracted from MRI of new patients (without histopathology or surgery) to localize cancer. We trained and validated our framework on a unique dataset of 75 patients with 806 slices who underwent MRI followed by prostatectomy surgery. We tested our method on an independent test set of 20 prostatectomy patients (139 slices, 24 cancerous lesions, 1.12M pixels) and achieved a per-pixel sensitivity of 0.81, specificity of 0.71, AUC of 0.86 and a per-lesion AUC of $0.96 \pm 0.07$, outperforming the current state-of-the-art accuracy in predicting prostate cancer using MRI.

eess.IV↗

arXiv2020

G-CREWE: Graph CompREssion With Embedding for Network Alignment

Network alignment is useful for multiple applications that require increasingly large graphs to be processed. Existing research approaches this as an optimization problem or computes the similarity based on node representations. However, the process of aligning every pair of nodes between relatively large networks is time-consuming and resource-intensive. In this paper, we propose a framework, called G-CREWE (Graph CompREssion With Embedding) to solve the network alignment problem. G-CREWE uses node embeddings to align the networks on two levels of resolution, a fine resolution given by the original network and a coarse resolution given by a compressed version, to achieve an efficient and effective network alignment. The framework first extracts node features and learns the node embedding via a Graph Convolutional Network (GCN). Then, node embedding helps to guide the process of graph compression and finally improve the alignment performance. As part of G-CREWE, we also propose a new compression mechanism called MERGE (Minimum dEgRee neiGhbors comprEssion) to reduce the size of the input networks while preserving the consistency in their topological structure. Experiments on all real networks show that our method is more than twice as fast as the most competitive existing methods while maintaining high accuracy.

cs.SI↗

arXiv2020

n-Gage: Predicting in-class Emotional, Behavioural and Cognitive Engagement in the Wild

The study of student engagement has attracted growing interests to address problems such as low academic performance, disaffection, and high dropout rates. Existing approaches to measuring student engagement typically rely on survey-based instruments. While effective, those approaches are time-consuming and labour-intensive. Meanwhile, both the response rate and quality of the survey are usually poor. As an alternative, in this paper, we investigate whether we can infer and predict engagement at multiple dimensions, just using sensors. We hypothesize that multidimensional student engagement can be translated into physiological responses and activity changes during the class, and also be affected by the environmental changes. Therefore, we aim to explore the following questions: Can we measure the multiple dimensions of high school student's learning engagement including emotional, behavioural and cognitive engagement with sensing data in the wild? Can we derive the activity, physiological, and environmental factors contributing to the different dimensions of student engagement? If yes, which sensors are the most useful in differentiating each dimension of the engagement? Then, we conduct an in-situ study in a high school from 23 students and 6 teachers in 144 classes over 11 courses for 4 weeks. We present the n-Gage, a student engagement sensing system using a combination of sensors from wearables and environments to automatically detect student in-class multidimensional learning engagement. Experiment results show that n-Gage can accurately predict multidimensional student engagement in real-world scenarios with an average MAE of 0.788 and RMSE of 0.975 using all the sensors. We also show a set of interesting findings of how different factors (e.g., combinations of sensors, school subjects, CO2 level) affect each dimension of the student learning engagement.

cs.HC↗

arXiv2020

Adaptive Feature Selection Guided Deep Forest for COVID-19 Classification with Chest CT

Chest computed tomography (CT) becomes an effective tool to assist the diagnosis of coronavirus disease-19 (COVID-19). Due to the outbreak of COVID-19 worldwide, using the computed-aided diagnosis technique for COVID-19 classification based on CT images could largely alleviate the burden of clinicians. In this paper, we propose an Adaptive Feature Selection guided Deep Forest (AFS-DF) for COVID-19 classification based on chest CT images. Specifically, we first extract location-specific features from CT images. Then, in order to capture the high-level representation of these features with the relatively small-scale data, we leverage a deep forest model to learn high-level representation of the features. Moreover, we propose a feature selection method based on the trained deep forest model to reduce the redundancy of features, where the feature selection could be adaptively incorporated with the COVID-19 classification model. We evaluated our proposed AFS-DF on COVID-19 dataset with 1495 patients of COVID-19 and 1027 patients of community acquired pneumonia (CAP). The accuracy (ACC), sensitivity (SEN), specificity (SPE) and AUC achieved by our method are 91.79%, 93.05%, 89.95% and 96.35%, respectively. Experimental results on the COVID-19 dataset suggest that the proposed AFS-DF achieves superior performance in COVID-19 vs. CAP classification, compared with 4 widely used machine learning methods.

eess.IV↗