pwc-archive/papers-with-abstracts huggingface dataset:
Deep learning for prediction of hepatocellular carcinoma recurrence after resection or liver transplantation: a discovery and validation study
Authors: Zhikun Liu, Yuanpeng Liu, Yuan Hong, Jinwen Meng, Jianguo Wang, Shusen Zheng, Xiao Xu
Date: 2021-05-31 00:00:00
Tasks: Management, Prognosis

This study aimed to develop a classifier of prognosis after resection or liver transplantation (LT) for HCC by directly analysing the ubiquitously available histological images using deep learning based neural networks. Nucleus map set was used to train U-net to capture the nuclear architectural information. Train set included the patients with HCC treated by resection and has a distinct outcome. LT set contained patients with HCC treated by LT. Train set and its nuclear architectural information extracted by U-net were used to train MobileNet V2 based classifier (MobileNetV2_HCC_Class), purpose-built for classifying supersized heterogeneous images. The MobileNetV2_HCC_Class maintained relative higher discriminatory power than the other factors after HCC resection or LT in the independent validation set. Pathological review showed that the tumoral areas most predictive of recurrence were characterized by presence of stroma, high degree of cytological atypia, nuclear hyperchomasia, and a lack of immune infiltration. A clinically useful prognostic classifier was developed using deep learning allied to histological slides. The classifier has been extensively evaluated in independent patient populations with different treatment, and gives consistent excellent results across the classical clinical, biological and pathological features. The classifier assists in refining the prognostic prediction of HCC patients and identifying patients who would benefit from more intensive management.
Closer Look at the Uncertainty Estimation in Semantic Segmentation under Distributional Shift
Authors: Sebastian Cygert, Bartłomiej Wróblewski, Karol Woźniak, Radosław Słowiński, Andrzej Czyżewski
Date: 2021-05-31 00:00:00
Tasks: Data Augmentation, Semantic Segmentation, Style Transfer

While recent computer vision algorithms achieve impressive performance on many benchmarks, they lack robustness - presented with an image from a different distribution, (e.g. weather or lighting conditions not considered during training), they may produce an erroneous prediction. Therefore, it is desired that such a model will be able to reliably predict its confidence measure. In this work, uncertainty estimation for the task of semantic segmentation is evaluated under a varying level of domain shift: in a cross-dataset setting and when adapting a model trained on data from the simulation. It was shown that simple color transformations already provide a strong baseline, comparable to using more sophisticated style-transfer data augmentation. Further, by constructing an ensemble consisting of models using different backbones and/or augmentation methods, it was possible to improve significantly model performance in terms of overall accuracy and uncertainty estimation under the domain shift setting. The Expected Calibration Error (ECE) on challenging GTA to Cityscapes adaptation was reduced from 4.05 to the competitive value of 1.1. Further, an ensemble of models was utilized in the self-training setting to improve the pseudo-labels generation, which resulted in a significant gain in the final model accuracy, compared to the standard fine-tuning (without ensemble).
Continual 3D Convolutional Neural Networks for Real-time Processing of Videos
Authors: Lukas Hedegaard, Alexandros Iosifidis
Date: 2021-05-31 00:00:00
Tasks: Action Classification, Video Recognition

We introduce Continual 3D Convolutional Neural Networks (Co3D CNNs), a new computational formulation of spatio-temporal 3D CNNs, in which videos are processed frame-by-frame rather than by clip. In online tasks demanding frame-wise predictions, Co3D CNNs dispense with the computational redundancies of regular 3D CNNs, namely the repeated convolutions over frames, which appear in overlapping clips. We show that Continual 3D CNNs can reuse preexisting 3D-CNN weights to reduce the per-prediction floating point operations (FLOPs) in proportion to the temporal receptive field while retaining similar memory requirements and accuracy. This is validated with multiple models on Kinetics-400 and Charades with remarkable results: CoX3D models attain state-of-the-art complexity/accuracy trade-offs on Kinetics-400 with 12.1-15.3x reductions of FLOPs and 2.3-3.8% improvements in accuracy compared to regular X3D models while reducing peak memory consumption by up to 48%. Moreover, we investigate the transient response of Co3D CNNs at start-up and perform extensive benchmarks of on-hardware processing characteristics for publicly available 3D CNNs.
Unsupervised detection of mouse behavioural anomalies using two-stream convolutional autoencoders
Authors: Ezechukwu I Nwokedi, Rasneer S Bains, Luc Bidaut, Sara Wells, Xujiong Ye, James M Brown
Date: 2021-05-28 00:00:00
Tasks: Vocal Bursts Valence Prediction

This paper explores the application of unsupervised learning to detecting anomalies in mouse video data. The two models presented in this paper are a dual-stream, 3D convolutional autoencoder (with residual connections) and a dual-stream, 2D convolutional autoencoder. The publicly available dataset used here contains twelve videos of single home-caged mice alongside frame-level annotations. Under the pretext that the autoencoder only sees normal events, the video data was handcrafted to treat each behaviour as a pseudo-anomaly thereby eliminating them from the others during training. The results are presented for one conspicuous behaviour (hang) and one inconspicuous behaviour (groom). The performance of these models is compared to a single stream autoencoder and a supervised learning model, which are both based on the custom CAE. Both models are also tested on the CUHK Avenue dataset were found to perform as well as some state-of-the-art architectures.
KVT: k-NN Attention for Boosting Vision Transformers
Authors: Pichao Wang, Xue Wang, Fan Wang, Ming Lin, Shuning Chang, Hao Li, Rong Jin
Date: 2021-05-28 00:00:00

Convolutional Neural Networks (CNNs) have dominated computer vision for years, due to its ability in capturing locality and translation invariance. Recently, many vision transformer architectures have been proposed and they show promising performance. A key component in vision transformers is the fully-connected self-attention which is more powerful than CNNs in modelling long range dependencies. However, since the current dense self-attention uses all image patches (tokens) to compute attention matrix, it may neglect locality of images patches and involve noisy tokens (e.g., clutter background and occlusion), leading to a slow training process and potential degradation of performance. To address these problems, we propose the $k$-NN attention for boosting vision transformers. Specifically, instead of involving all the tokens for attention matrix calculation, we only select the top-$k$ similar tokens from the keys for each query to compute the attention map. The proposed $k$-NN attention naturally inherits the local bias of CNNs without introducing convolutional operations, as nearby tokens tend to be more similar than others. In addition, the $k$-NN attention allows for the exploration of long range correlation and at the same time filters out irrelevant tokens by choosing the most similar tokens from the entire image. Despite its simplicity, we verify, both theoretically and empirically, that $k$-NN attention is powerful in speeding up training and distilling noise from input tokens. Extensive experiments are conducted by using 11 different vision transformer architectures to verify that the proposed $k$-NN attention can work with any existing transformer architectures to improve its prediction performance. The codes are available at \url{https://github.com/damo-cv/KVT}.
Towards Interpretable Attention Networks for Cervical Cancer Analysis
Authors: Ruiqi Wang, Mohammad Ali Armin, Simon Denman, Lars Petersson, David Ahmedt-Aristizabal
Date: 2021-05-27 00:00:00
Tasks: Classification, Deep Learning

Recent advances in deep learning have enabled the development of automated frameworks for analysing medical images and signals, including analysis of cervical cancer. Many previous works focus on the analysis of isolated cervical cells, or do not offer sufficient methods to explain and understand how the proposed models reach their classification decisions on multi-cell images. Here, we evaluate various state-of-the-art deep learning models and attention-based frameworks for the classification of images of multiple cervical cells. As we aim to provide interpretable deep learning models to address this task, we also compare their explainability through the visualization of their gradients. We demonstrate the importance of using images that contain multiple cells over using isolated single-cell images. We show the effectiveness of the residual channel attention model for extracting important features from a group of cells, and demonstrate this model's efficiency for this classification task. This work highlights the benefits of channel attention mechanisms in analyzing multiple-cell images for potential relations and distributions within a group of cells. It also provides interpretable models to address the classification of cervical cells.
Validating GAN-BioBERT: A Methodology For Assessing Reporting Trends In Clinical Trials
Authors: Joshua J Myszewski, Emily Klossowski, Patrick Meyer, Kristin Bevil, Lisa Klesius, Kristopher M Schroeder
Date: 2021-06-01 00:00:00
Tasks: Classification, Sentiment Analysis, Sentiment Classification

In the past decade, there has been much discussion about the issue of biased reporting in clinical research. Despite this attention, there have been limited tools developed for the systematic assessment of qualitative statements made in clinical research, with most studies assessing qualitative statements relying on the use of manual expert raters, which limits their size. Also, previous attempts to develop larger scale tools, such as those using natural language processing, were limited by both their accuracy and the number of categories used for the classification of their findings. With these limitations in mind, this study's goal was to develop a classification algorithm that was both suitably accurate and finely grained to be applied on a large scale for assessing the qualitative sentiment expressed in clinical trial abstracts. Additionally, this study seeks to compare the performance of the proposed algorithm, GAN-BioBERT, to previous studies as well as to expert manual rating of clinical trial abstracts. This study develops a three-class sentiment classification algorithm for clinical trial abstracts using a semi-supervised natural language process model based on the Bidirectional Encoder Representation from Transformers (BERT) model, from a series of clinical trial abstracts annotated by a group of experts in academic medicine. Results: The use of this algorithm was found to have a classification accuracy of 91.3%, with a macro F1-Score of 0.92, which is a significant improvement in accuracy when compared to previous methods and expert ratings, while also making the sentiment classification finer grained than previous studies. The proposed algorithm, GAN-BioBERT, is a suitable classification model for the large-scale assessment of qualitative statements in clinical trial literature, providing an accurate, reproducible tool for the large-scale study of clinical publication trends.
A reinforcement learning approach to improve communication performance and energy utilization in fog-based IoT
Authors: Babatunji Omoniwa, Maxime Gueriau, Ivana Dusparic
Date: 2021-06-01 00:00:00
Tasks: Industrial Robots, Q-Learning

Recent research has shown the potential of using available mobile fog devices (such as smartphones, drones, domestic and industrial robots) as relays to minimize communication outages between sensors and destination devices, where localized Internet-of-Things services (e.g., manufacturing process control, health and security monitoring) are delivered. However, these mobile relays deplete energy when they move and transmit to distant destinations. As such, power-control mechanisms and intelligent mobility of the relay devices are critical in improving communication performance and energy utilization. In this paper, we propose a Q-learning-based decentralized approach where each mobile fog relay agent (MFRA) is controlled by an autonomous agent which uses reinforcement learning to simultaneously improve communication performance and energy utilization. Each autonomous agent learns based on the feedback from the destination and its own energy levels whether to remain active and forward the message, or become passive for that transmission phase. We evaluate the approach by comparing with the centralized approach, and observe that with lesser number of MFRAs, our approach is able to ensure reliable delivery of data and reduce overall energy cost by 56.76\% -- 88.03\%.
Asymptotics of representation learning in finite Bayesian neural networks
Authors: Jacob A. Zavatone-Veth, Abdulkadir Canatar, Benjamin S. Ruben, Cengiz Pehlevan
Date: 2021-06-01 00:00:00
Proceeding: NeurIPS 2021 12
Tasks: Representation Learning

Recent works have suggested that finite Bayesian neural networks may sometimes outperform their infinite cousins because finite networks can flexibly adapt their internal representations. However, our theoretical understanding of how the learned hidden layer representations of finite networks differ from the fixed representations of infinite networks remains incomplete. Perturbative finite-width corrections to the network prior and posterior have been studied, but the asymptotics of learned features have not been fully characterized. Here, we argue that the leading finite-width corrections to the average feature kernels for any Bayesian network with linear readout and Gaussian likelihood have a largely universal form. We illustrate this explicitly for three tractable network architectures: deep linear fully-connected and convolutional networks, and networks with a single nonlinear hidden layer. Our results begin to elucidate how task-relevant learning signals shape the hidden layer representations of wide Bayesian neural networks.
A survey of machine learning-based physics event generation
Authors: Yasir Alanazi, N. Sato, Pawel Ambrozewicz, Astrid N. Hiller Blin, W. Melnitchouk, Marco Battaglieri, Tianbo Liu, Yaohang Li
Date: 2021-06-01 00:00:00
Tasks: BIG-bench Machine Learning, Super-Resolution, Survey

Event generators in high-energy nuclear and particle physics play an important role in facilitating studies of particle reactions. We survey the state-of-the-art of machine learning (ML) efforts at building physics event generators. We review ML generative models used in ML-based event generators and their specific challenges, and discuss various approaches of incorporating physics into the ML model designs to overcome these challenges. Finally, we explore some open questions related to super-resolution, fidelity, and extrapolation for physics event generation based on ML technology.
Detection of preventable fetal distress during labor from scanned cardiotocogram tracings using deep learning
Authors: Martin G. Frasch, Shadrian B. Strong, David Nilosek, Joshua Leaverton, Barry S. Schifrin
Date: 2021-06-01 00:00:00

Despite broad application during labor and delivery, there remains considerable debate about the value of electronic fetal monitoring (EFM). EFM includes the surveillance of the fetal heart rate (FHR) patterns in conjunction with the maternal uterine contractions providing a wealth of data about fetal behavior and the threat of diminished oxygenation and perfusion. Adverse outcomes universally associate a fetal injury with the failure to timely respond to FHR pattern information. Historically, the EFM data, stored digitally, are available only as rasterized pdf images for contemporary or historical discussion and examination. In reality, however, they are rarely reviewed systematically. Using a unique archive of EFM collected over 50 years of practice in conjunction with adverse outcomes, we present a deep learning framework for training and detection of incipient or past fetal injury. We report 94% accuracy in identifying early, preventable fetal injury intrapartum. This framework is suited for automating an early warning and decision support system for maintaining fetal well-being during the stresses of labor. Ultimately, such a system could enable a physician to timely respond during labor and prevent adverse outcomes. When adverse outcomes cannot be avoided, they can provide guidance to the early neuroprotective treatment of the newborn.
Fair Clustering Using Antidote Data
Authors: Anshuman Chhabra, Adish Singla, Prasant Mohapatra
Date: 2021-06-01 00:00:00
Tasks: Clustering, Fairness

Clustering algorithms are widely utilized for many modern data science applications. This motivates the need to make outputs of clustering algorithms fair. Traditionally, new fair algorithmic variants to clustering algorithms are developed for specific notions of fairness. However, depending on the application context, different definitions of fairness might need to be employed. As a result, new algorithms and analysis need to be proposed for each combination of clustering algorithm and fairness definition. Additionally, each new algorithm would need to be reimplemented for deployment in a real-world system. Hence, we propose an alternate approach to fairness in clustering where we augment the original dataset with a small number of data points, called antidote data. When clustering is undertaken on this new dataset, the output is fair, for the chosen clustering algorithm and fairness definition. We formulate this as a general bi-level optimization problem which can accommodate any center-based clustering algorithms and fairness notions. We then categorize approaches for solving this bi-level optimization for different problem settings. Extensive experiments on different clustering algorithms and fairness notions show that our algorithms can achieve desired levels of fairness on many real-world datasets with a very small percentage of antidote data added. We also find that our algorithms achieve lower fairness costs and competitive clustering performance compared to other state-of-the-art fair clustering algorithms.
ClustML: A Measure of Cluster Pattern Complexity in Scatterplots Learnt from Human-labeled Groupings
Authors: Mostafa M. Abbas, Ehsan Ullah, Abdelkader Baggag, Halima Bensmail, Michael Sedlmair, Michaël Aupetit
Date: 2021-06-01 00:00:00

Visual quality measures (VQMs) are designed to support analysts by automatically detecting and quantifying patterns in visualizations. We propose a new VQM for visual grouping patterns in scatterplots, called ClustML, which is trained on previously collected human subject judgments. Our model encodes scatterplots in the parametric space of a Gaussian Mixture Model and uses a classifier trained on human judgment data to estimate the perceptual complexity of grouping patterns. The numbers of initial mixture components and final combined groups. It improves on existing VQMs, first, by better estimating human judgments on two-Gaussian cluster patterns and, second, by giving higher accuracy when ranking general cluster patterns in scatterplots. We use it to analyze kinship data for genome-wide association studies, in which experts rely on the visual analysis of large sets of scatterplots. We make the benchmark datasets and the new VQM available for practical use and further improvements.
NewsEmbed: Modeling News through Pre-trained Document Representations
Authors: Jialu Liu, Tianqi Liu, Cong Yu
Date: 2021-06-01 00:00:00
Tasks: Articles, Contrastive Learning, Multi-Label Classification, MUlTI-LABEL-ClASSIFICATION, Natural Language Understanding

Effectively modeling text-rich fresh content such as news articles at document-level is a challenging problem. To ensure a content-based model generalize well to a broad range of applications, it is critical to have a training dataset that is large beyond the scale of human labels while achieving desired quality. In this work, we address those two challenges by proposing a novel approach to mine semantically-relevant fresh documents, and their topic labels, with little human supervision. Meanwhile, we design a multitask model called NewsEmbed that alternatively trains a contrastive learning with a multi-label classification to derive a universal document encoder. We show that the proposed approach can provide billions of high quality organic training examples and can be naturally extended to multilingual setting where texts in different languages are encoded in the same semantic space. We experimentally demonstrate NewsEmbed's competitive performance across multiple natural language understanding tasks, both supervised and unsupervised.
Improving Long-Term Metrics in Recommendation Systems using Short-Horizon Reinforcement Learning
Authors: Bogdan Mazoure, Paul Mineiro, Pavithra Srinath, Reza Sharifi Sedeh, Doina Precup, Adith Swaminathan
Date: 2021-06-01 00:00:00
Tasks: Offline RL, Recommendation Systems, reinforcement-learning, Reinforcement Learning (RL), Session-Based Recommendations

We study session-based recommendation scenarios where we want to recommend items to users during sequential interactions to improve their long-term utility. Optimizing a long-term metric is challenging because the learning signal (whether the recommendations achieved their desired goals) is delayed and confounded by other user interactions with the system. Targeting immediately measurable proxies such as clicks can lead to suboptimal recommendations due to misalignment with the long-term metric. We develop a new reinforcement learning algorithm called Short Horizon Policy Improvement (SHPI) that approximates policy-induced drift in user behavior across sessions. SHPI is a straightforward modification of episodic RL algorithms for session-based recommendation, that additionally gives an appropriate termination bonus in each session. Empirical results on four recommendation tasks show that SHPI can outperform state-of-the-art recommendation techniques like matrix factorization with offline proxy signals, bandits with myopic online proxies, and RL baselines with limited amounts of user interaction.
Wireless Federated Learning with Limited Communication and Differential Privacy
Authors: Amir Sonee, Stefano Rini, Yu-Chih Huang
Date: 2021-06-01 00:00:00
Tasks: Dimensionality Reduction, Federated Learning

This paper investigates the role of dimensionality reduction in efficient communication and differential privacy (DP) of the local datasets at the remote users for over-the-air computation (AirComp)-based federated learning (FL) model. More precisely, we consider the FL setting in which clients are prompted to train a machine learning model by simultaneous channel-aware and limited communications with a parameter server (PS) over a Gaussian multiple-access channel (GMAC), so that transmissions sum coherently at the PS globally aware of the channel coefficients. For this setting, an algorithm is proposed based on applying federated stochastic gradient descent (FedSGD) for training the minimum of a given loss function based on the local gradients, Johnson-Lindenstrauss (JL) random projection for reducing the dimension of the local updates, and artificial noise to further aid user's privacy. For this scheme, our results show that the local DP performance is mainly improved due to injecting noise of greater variance on each dimension while keeping the sensitivity of the projected vectors unchanged. This is while the convergence rate is slowed down compared to the case without dimensionality reduction. As the performance outweighs for the slower convergence, the trade-off between privacy and convergence is higher but is shown to lessen in high-dimensional regime yielding almost the same trade-off with much less communication cost.