pwc-archive/papers-with-abstracts huggingface dataset:
Explainable Automated Coding of Clinical Notes using Hierarchical Label-wise Attention Networks and Label Embedding Initialisation
Authors: Hang Dong, Víctor Suárez-Paniagua, William Whiteley, Honghan Wu
Date: 2020-10-29 00:00:00
Tasks: Diagnostic, Medical Code Prediction, Multi-Label Text Classification

Diagnostic or procedural coding of clinical notes aims to derive a coded summary of disease-related information about patients. Such coding is usually done manually in hospitals but could potentially be automated to improve the efficiency and accuracy of medical coding. Recent studies on deep learning for automated medical coding achieved promising performances. However, the explainability of these models is usually poor, preventing them to be used confidently in supporting clinical practice. Another limitation is that these models mostly assume independence among labels, ignoring the complex correlation among medical codes which can potentially be exploited to improve the performance. We propose a Hierarchical Label-wise Attention Network (HLAN), which aimed to interpret the model by quantifying importance (as attention weights) of words and sentences related to each of the labels. Secondly, we propose to enhance the major deep learning models with a label embedding (LE) initialisation approach, which learns a dense, continuous vector representation and then injects the representation into the final layers and the label-wise attention layers in the models. We evaluated the methods using three settings on the MIMIC-III discharge summaries: full codes, top-50 codes, and the UK NHS COVID-19 shielding codes. Experiments were conducted to compare HLAN and LE initialisation to the state-of-the-art neural network based methods. HLAN achieved the best Micro-level AUC and $F_1$ on the top-50 code prediction and comparable results on the NHS COVID-19 shielding code prediction to other models. By highlighting the most salient words and sentences for each label, HLAN showed more meaningful and comprehensive model interpretation compared to its downgraded baselines and the CNN-based models. LE initialisation consistently boosted most deep learning models for automated medical coding.
Amortized Probabilistic Detection of Communities in Graphs
Authors: Yueqi Wang, Yoonho Lee, Pallab Basu, Juho Lee, Yee Whye Teh, Liam Paninski, Ari Pakman
Date: 2020-10-29 00:00:00
Tasks: Clustering, Community Detection

Learning community structures in graphs has broad applications across scientific domains. While graph neural networks (GNNs) have been successful in encoding graph structures, existing GNN-based methods for community detection are limited by requiring knowledge of the number of communities in advance, in addition to lacking a proper probabilistic formulation to handle uncertainty. We propose a simple framework for amortized community detection, which addresses both of these issues by combining the expressive power of GNNs with recent methods for amortized clustering. Our models consist of a graph representation backbone that extracts structural information and an amortized clustering network that naturally handles variable numbers of clusters. Both components combine into well-defined models of the posterior distribution of graph communities and are jointly optimized given labeled graphs. At inference time, the models yield parallel samples from the posterior of community labels, quantifying uncertainty in a principled way. We evaluate several models from our framework on synthetic and real datasets, and demonstrate improved performance compared to previous methods. As a separate contribution, we extend recent amortized probabilistic clustering architectures by adding attention modules, which yield further improvements on community detection tasks.
Learning interaction kernels in mean-field equations of 1st-order systems of interacting particles
Authors: Quanjun Lang, Fei Lu
Date: 2020-10-29 00:00:00

We introduce a nonparametric algorithm to learn interaction kernels of mean-field equations for 1st-order systems of interacting particles. The data consist of discrete space-time observations of the solution. By least squares with regularization, the algorithm learns the kernel on data-adaptive hypothesis spaces efficiently. A key ingredient is a probabilistic error functional derived from the likelihood of the mean-field equation's diffusion process. The estimator converges, in a reproducing kernel Hilbert space and an L2 space under an identifiability condition, at a rate optimal in the sense that it equals the numerical integrator's order. We demonstrate our algorithm on three typical examples: the opinion dynamics with a piecewise linear kernel, the granular media model with a quadratic kernel, and the aggregation-diffusion with a repulsive-attractive kernel.
Analyzing the tree-layer structure of Deep Forests
Authors: Ludovic Arnould, Claire Boyer, Erwan Scornet, Sorbonne Lpsm
Date: 2020-10-29 00:00:00

Random forests on the one hand, and neural networks on the other hand, have met great success in the machine learning community for their predictive performance. Combinations of both have been proposed in the literature, notably leading to the so-called deep forests (DF) (Zhou \& Feng,2019). In this paper, our aim is not to benchmark DF performances but to investigate instead their underlying mechanisms. Additionally, DF architecture can be generally simplified into more simple and computationally efficient shallow forest networks. Despite some instability, the latter may outperform standard predictive tree-based methods. We exhibit a theoretical framework in which a shallow tree network is shown to enhance the performance of classical decision trees. In such a setting, we provide tight theoretical lower and upper bounds on its excess risk. These theoretical results show the interest of tree-network architectures for well-structured data provided that the first layer, acting as a data encoder, is rich enough.
Learning Deep Interleaved Networks with Asymmetric Co-Attention for Image Restoration
Authors: Feng Li, Runmin Cong, Huihui Bai, Yifan He, Yao Zhao, Ce Zhu
Date: 2020-10-29 00:00:00
Tasks: Deblurring, Image Deblurring, Image Restoration, Image Super-Resolution, Super-Resolution

Recently, convolutional neural network (CNN) has demonstrated significant success for image restoration (IR) tasks (e.g., image super-resolution, image deblurring, rain streak removal, and dehazing). However, existing CNN based models are commonly implemented as a single-path stream to enrich feature representations from low-quality (LQ) input space for final predictions, which fail to fully incorporate preceding low-level contexts into later high-level features within networks, thereby producing inferior results. In this paper, we present a deep interleaved network (DIN) that learns how information at different states should be combined for high-quality (HQ) images reconstruction. The proposed DIN follows a multi-path and multi-branch pattern allowing multiple interconnected branches to interleave and fuse at different states. In this way, the shallow information can guide deep representative features prediction to enhance the feature expression ability. Furthermore, we propose asymmetric co-attention (AsyCA) which is attached at each interleaved node to model the feature dependencies. Such AsyCA can not only adaptively emphasize the informative features from different states, but also improves the discriminative ability of networks. Our presented DIN can be trained end-to-end and applied to various IR tasks. Comprehensive evaluations on public benchmarks and real-world datasets demonstrate that the proposed DIN perform favorably against the state-of-the-art methods quantitatively and qualitatively.
Deep Autofocus for Synthetic Aperture Sonar
Authors: Isaac Gerg, Vishal Monga
Date: 2020-10-29 00:00:00
Tasks: Deblurring, Image Reconstruction

Synthetic aperture sonar (SAS) requires precise positional and environmental information to produce well-focused output during the image reconstruction step. However, errors in these measurements are commonly present resulting in defocused imagery. To overcome these issues, an \emph{autofocus} algorithm is employed as a post-processing step after image reconstruction for the purpose of improving image quality using the image content itself. These algorithms are usually iterative and metric-based in that they seek to optimize an image sharpness metric. In this letter, we demonstrate the potential of machine learning, specifically deep learning, to address the autofocus problem. We formulate the problem as a self-supervised, phase error estimation task using a deep network we call Deep Autofocus. Our formulation has the advantages of being non-iterative (and thus fast) and not requiring ground truth focused-defocused images pairs as often required by other deblurring deep learning methods. We compare our technique against a set of common sharpness metrics optimized using gradient descent over a real-world dataset. Our results demonstrate Deep Autofocus can produce imagery that is perceptually as good as benchmark iterative techniques but at a substantially lower computational cost. We conclude that our proposed Deep Autofocus can provide a more favorable cost-quality trade-off than state-of-the-art alternatives with significant potential of future research.
Maximum a posteriori signal recovery for optical coherence tomography angiography image generation and denoising
Authors: Lennart Husvogt, Stefan B. Ploner, Siyu Chen, Daniel Stromer, Julia Schottenhamml, A. Yasin Alibhai, Eric Moult, Nadia K. Waheed, James G. Fujimoto, Andreas Maier
Date: 2020-10-29 00:00:00
Tasks: Denoising, Image Generation

Optical coherence tomography angiography (OCTA) is a novel and clinically promising imaging modality to image retinal and sub-retinal vasculature. Based on repeated optical coherence tomography (OCT) scans, intensity changes are observed over time and used to compute OCTA image data. OCTA data are prone to noise and artifacts caused by variations in flow speed and patient movement. We propose a novel iterative maximum a posteriori signal recovery algorithm in order to generate OCTA volumes with reduced noise and increased image quality. This algorithm is based on previous work on probabilistic OCTA signal models and maximum likelihood estimates. Reconstruction results using total variation minimization and wavelet shrinkage for regularization were compared against an OCTA ground truth volume, merged from six co-registered single OCTA volumes. The results show a significant improvement in peak signal-to-noise ratio and structural similarity. The presented algorithm brings together OCTA image generation and Bayesian statistics and can be developed into new OCTA image generation and denoising algorithms.
LSTM for Model-Based Anomaly Detection in Cyber-Physical Systems
Authors: Benedikt Eiteneuer, Oliver Niggemann
Date: 2020-10-29 00:00:00
Tasks: Anomaly Detection

Anomaly detection is the task of detecting data which differs from the normal behaviour of a system in a given context. In order to approach this problem, data-driven models can be learned to predict current or future observations. Oftentimes, anomalous behaviour depends on the internal dynamics of the system and looks normal in a static context. To address this problem, the model should also operate depending on state. Long Short-Term Memory (LSTM) neural networks have been shown to be particularly useful to learn time sequences with varying length of temporal dependencies and are therefore an interesting general purpose approach to learn the behaviour of arbitrarily complex Cyber-Physical Systems. In order to perform anomaly detection, we slightly modify the standard norm 2 error to incorporate an estimate of model uncertainty. We analyse the approach on artificial and real data.
Post-selection inference with HSIC-Lasso
Authors: Tobias Freidling, Benjamin Poignard, Héctor Climente-González, Makoto Yamada
Date: 2020-10-29 00:00:00
Tasks: LEMMA, Variable Selection

Detecting influential features in non-linear and/or high-dimensional data is a challenging and increasingly important task in machine learning. Variable selection methods have thus been gaining much attention as well as post-selection inference. Indeed, the selected features can be significantly flawed when the selection procedure is not accounted for. We propose a selective inference procedure using the so-called model-free "HSIC-Lasso" based on the framework of truncated Gaussians combined with the polyhedral lemma. We then develop an algorithm, which allows for low computational costs and provides a selection of the regularisation parameter. The performance of our method is illustrated by both artificial and real-world data based experiments, which emphasise a tight control of the type-I error, even for small sample sizes.
Compressive Sensing and Neural Networks from a Statistical Learning Perspective
Authors: Arash Behboodi, Holger Rauhut, Ekkehard Schnoor
Date: 2020-10-29 00:00:00
Tasks: Compressive Sensing, Dictionary Learning, Generalization Bounds

Various iterative reconstruction algorithms for inverse problems can be unfolded as neural networks. Empirically, this approach has often led to improved results, but theoretical guarantees are still scarce. While some progress on generalization properties of neural networks have been made, great challenges remain. In this chapter, we discuss and combine these topics to present a generalization error analysis for a class of neural networks suitable for sparse reconstruction from few linear measurements. The hypothesis class considered is inspired by the classical iterative soft-thresholding algorithm (ISTA). The neural networks in this class are obtained by unfolding iterations of ISTA and learning some of the weights. Based on training samples, we aim at learning the optimal network parameters via empirical risk minimization and thereby the optimal network that reconstructs signals from their compressive linear measurements. In particular, we may learn a sparsity basis that is shared by all of the iterations/layers and thereby obtain a new approach for dictionary learning. For this class of networks, we present a generalization bound, which is based on bounding the Rademacher complexity of hypothesis classes consisting of such deep networks via Dudley's integral. Remarkably, under realistic conditions, the generalization error scales only logarithmically in the number of layers, and at most linear in number of measurements.
Identification of complex mixtures for Raman spectroscopy using a novel scheme based on a new multi-label deep neural network
Authors: Liangrui Pan, Pronthep Pipitsunthonsan, Chalongrat Daengngam, Mitchai Chongcheawchamnan
Date: 2020-10-29 00:00:00
Tasks: Data Augmentation

With noisy environment caused by fluoresence and additive white noise as well as complicated spectrum fingerprints, the identification of complex mixture materials remains a major challenge in Raman spectroscopy application. In this paper, we propose a new scheme based on a constant wavelet transform (CWT) and a deep network for classifying complex mixture. The scheme first transforms the noisy Raman spectrum to a two-dimensional scale map using CWT. A multi-label deep neural network model (MDNN) is then applied for classifying material. The proposed model accelerates the feature extraction and expands the feature graph using the global averaging pooling layer. The Sigmoid function is implemented in the last layer of the model. The MDNN model was trained, validated and tested with data collected from the samples prepared from substances in palm oil. During training and validating process, data augmentation is applied to overcome the imbalance of data and enrich the diversity of Raman spectra. From the test results, it is found that the MDNN model outperforms previously proposed deep neural network models in terms of Hamming loss, one error, coverage, ranking loss, average precision, F1 macro averaging and F1 micro averaging, respectively. The average detection time obtained from our model is 5.31 s, which is much faster than the detection time of the previously proposed models.
Semi-Supervised Speech Recognition via Graph-based Temporal Classification
Authors: Niko Moritz, Takaaki Hori, Jonathan Le Roux
Date: 2020-10-29 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), Classification, General Classification, Pseudo Label, speech-recognition, Speech Recognition

Semi-supervised learning has demonstrated promising results in automatic speech recognition (ASR) by self-training using a seed ASR model with pseudo-labels generated for unlabeled data. The effectiveness of this approach largely relies on the pseudo-label accuracy, for which typically only the 1-best ASR hypothesis is used. However, alternative ASR hypotheses of an N-best list can provide more accurate labels for an unlabeled speech utterance and also reflect uncertainties of the seed ASR model. In this paper, we propose a generalized form of the connectionist temporal classification (CTC) objective that accepts a graph representation of the training labels. The newly proposed graph-based temporal classification (GTC) objective is applied for self-training with WFST-based supervision, which is generated from an N-best list of pseudo-labels. In this setup, GTC is used to learn not only a temporal alignment, similarly to CTC, but also a label alignment to obtain the optimal pseudo-label sequence from the weighted graph. Results show that this approach can effectively exploit an N-best list of pseudo-labels with associated scores, considerably outperforming standard pseudo-labeling, with ASR results approaching an oracle experiment in which the best hypotheses of the N-best lists are selected manually.
Reliable Graph Neural Networks via Robust Aggregation
Authors: Simon Geisler, Daniel Zügner, Stephan Günnemann
Date: 2020-10-29 00:00:00
Proceeding: NeurIPS 2020 12

Perturbations targeting the graph structure have proven to be extremely effective in reducing the performance of Graph Neural Networks (GNNs), and traditional defenses such as adversarial training do not seem to be able to improve robustness. This work is motivated by the observation that adversarially injected edges effectively can be viewed as additional samples to a node's neighborhood aggregation function, which results in distorted aggregations accumulating over the layers. Conventional GNN aggregation functions, such as a sum or mean, can be distorted arbitrarily by a single outlier. We propose a robust aggregation function motivated by the field of robust statistics. Our approach exhibits the largest possible breakdown point of 0.5, which means that the bias of the aggregation is bounded as long as the fraction of adversarial edges of a node is less than 50\%. Our novel aggregation function, Soft Medoid, is a fully differentiable generalization of the Medoid and therefore lends itself well for end-to-end deep learning. Equipping a GNN with our aggregation improves the robustness with respect to structure perturbations on Cora ML by a factor of 3 (and 5.5 on Citeseer) and by a factor of 8 for low-degree nodes.
Brain Tumor Segmentation Network Using Attention-based Fusion and Spatial Relationship Constraint
Authors: Chenyu Liu, Wangbin Ding, Lei LI, Zhen Zhang, Chenhao Pei, Liqin Huang, Xiahai Zhuang
Date: 2020-10-29 00:00:00
Tasks: Brain Tumor Segmentation, Tumor Segmentation

Delineating the brain tumor from magnetic resonance (MR) images is critical for the treatment of gliomas. However, automatic delineation is challenging due to the complex appearance and ambiguous outlines of tumors. Considering that multi-modal MR images can reflect different tumor biological properties, we develop a novel multi-modal tumor segmentation network (MMTSN) to robustly segment brain tumors based on multi-modal MR images. The MMTSN is composed of three sub-branches and a main branch. Specifically, the sub-branches are used to capture different tumor features from multi-modal images, while in the main branch, we design a spatial-channel fusion block (SCFB) to effectively aggregate multi-modal features. Additionally, inspired by the fact that the spatial relationship between sub-regions of tumor is relatively fixed, e.g., the enhancing tumor is always in the tumor core, we propose a spatial loss to constrain the relationship between different sub-regions of tumor. We evaluate our method on the test set of multi-modal brain tumor segmentation challenge 2020 (BraTs2020). The method achieves 0.8764, 0.8243 and 0.773 dice score for whole tumor, tumor core and enhancing tumor, respectively.
Free-Form Image Inpainting via Contrastive Attention Network
Authors: Xin Ma, Xiaoqiang Zhou, Huaibo Huang, Zhenhua Chai, Xiaolin Wei, Ran He
Date: 2020-10-29 00:00:00
Tasks: Decoder, Form, Image Inpainting

Most deep learning based image inpainting approaches adopt autoencoder or its variants to fill missing regions in images. Encoders are usually utilized to learn powerful representational spaces, which are important for dealing with sophisticated learning tasks. Specifically, in image inpainting tasks, masks with any shapes can appear anywhere in images (i.e., free-form masks) which form complex patterns. It is difficult for encoders to capture such powerful representations under this complex situation. To tackle this problem, we propose a self-supervised Siamese inference network to improve the robustness and generalization. It can encode contextual semantics from full resolution images and obtain more discriminative representations. we further propose a multi-scale decoder with a novel dual attention fusion module (DAF), which can combine both the restored and known regions in a smooth way. This multi-scale architecture is beneficial for decoding discriminative representations learned by encoders into images layer by layer. In this way, unknown regions will be filled naturally from outside to inside. Qualitative and quantitative experiments on multiple datasets, including facial and natural datasets (i.e., Celeb-HQ, Pairs Street View, Places2 and ImageNet), demonstrate that our proposed method outperforms state-of-the-art methods in generating high-quality inpainting results.
Teaching a GAN What Not to Learn
Authors: Siddarth Asokan, Chandra Sekhar Seelamantula
Date: 2020-10-29 00:00:00
Proceeding: NeurIPS 2020 12
Tasks: Philosophy

Generative adversarial networks (GANs) were originally envisioned as unsupervised generative models that learn to follow a target distribution. Variants such as conditional GANs, auxiliary-classifier GANs (ACGANs) project GANs on to supervised and semi-supervised learning frameworks by providing labelled data and using multi-class discriminators. In this paper, we approach the supervised GAN problem from a different perspective, one that is motivated by the philosophy of the famous Persian poet Rumi who said, "The art of knowing is knowing what to ignore." In the GAN framework, we not only provide the GAN positive data that it must learn to model, but also present it with so-called negative samples that it must learn to avoid - we call this "The Rumi Framework." This formulation allows the discriminator to represent the underlying target distribution better by learning to penalize generated samples that are undesirable - we show that this capability accelerates the learning process of the generator. We present a reformulation of the standard GAN (SGAN) and least-squares GAN (LSGAN) within the Rumi setting. The advantage of the reformulation is demonstrated by means of experiments conducted on MNIST, Fashion MNIST, CelebA, and CIFAR-10 datasets. Finally, we consider an application of the proposed formulation to address the important problem of learning an under-represented class in an unbalanced dataset. The Rumi approach results in substantially lower FID scores than the standard GAN frameworks while possessing better generalization capability.