pwc-archive/papers-with-abstracts huggingface dataset:
Quantifying the effect of image compression on supervised learning applications in optical microscopy
Authors: Enrico Pomarico, Cédric Schmidt, Florian Chays, David Nguyen, Arielle Planchette, Audrey Tissot, Adrien Roux, Stéphane Pagès, Laura Batti, Christoph Clausen, Theo Lasser, Aleksandra Radenovic, Bruno Sanguinetti, Jérôme Extermann
Date: 2020-09-26 00:00:00
Tasks: Cell Segmentation, Data Compression, Image Compression

The impressive growth of data throughput in optical microscopy has triggered a widespread use of supervised learning (SL) models running on compressed image datasets for efficient automated analysis. However, since lossy image compression risks to produce unpredictable artifacts, quantifying the effect of data compression on SL applications is of pivotal importance to assess their reliability, especially for clinical use. We propose an experimental method to evaluate the tolerability of image compression distortions in 2D and 3D cell segmentation SL tasks: predictions on compressed data are compared to the raw predictive uncertainty, which is numerically estimated from the raw noise statistics measured through sensor calibration. We show that predictions on object- and image-specific segmentation parameters can be altered by up to 15% and more than 10 standard deviations after 16-to-8 bits downsampling or JPEG compression. In contrast, a recently developed lossless compression algorithm provides a prediction spread which is statistically equivalent to that stemming from raw noise, while providing a compression ratio of up to 10:1. By setting a lower bound to the SL predictive uncertainty, our technique can be generalized to validate a variety of data analysis pipelines in SL-assisted fields.
Physics-Guided Recurrent Graph Networks for Predicting Flow and Temperature in River Networks
Authors: Xiaowei Jia, Jacob Zwart, Jeffrey Sadler, Alison Appling, Samantha Oliver, Steven Markstrom, Jared Willard, Shaoming Xu, Michael Steinbach, Jordan Read, Vipin Kumar
Date: 2020-09-26 00:00:00
Tasks: BIG-bench Machine Learning

This paper proposes a physics-guided machine learning approach that combines advanced machine learning models and physics-based models to improve the prediction of water flow and temperature in river networks. We first build a recurrent graph network model to capture the interactions among multiple segments in the river network. Then we present a pre-training technique which transfers knowledge from physics-based models to initialize the machine learning model and learn the physics of streamflow and thermodynamics. We also propose a new loss function that balances the performance over different river segments. We demonstrate the effectiveness of the proposed method in predicting temperature and streamflow in a subset of the Delaware River Basin. In particular, we show that the proposed method brings a 33\%/14\% improvement over the state-of-the-art physics-based model and 24\%/14\% over traditional machine learning models (e.g., Long-Short Term Memory Neural Network) in temperature/streamflow prediction using very sparse (0.1\%) observation data for training. The proposed method has also been shown to produce better performance when generalized to different seasons or river segments with different streamflow ranges.
ProDOMA: improve PROtein DOMAin classification for third-generation sequencing reads using deep learning
Authors: Du Nan, Jiayu Shang, Yanni Sun
Date: 2020-09-26 00:00:00
Tasks: domain classification, General Classification

Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce important insights into the biological functions of the underlying data. However, the high error rate in third-generation sequencing data raises a new challenge to established domain analysis pipelines. The state-of-the-art methods are not optimized for noisy reads and have shown unsatisfactory accuracy of domain classification in third-generation sequencing data. New computational methods are still needed to improve the performance of domain prediction in long noisy reads. Results: In this work, we introduce ProDOMA, a deep learning model that conducts domain classification for third-generation sequencing reads. It uses deep neural networks with 3-frame translation encoding to learn conserved features from partially correct translations. In addition, we formulate our problem as an open-set problem and thus our model can reject unrelated DNA reads such as those from noncoding regions. In the experiments on simulated reads of protein coding sequences and real reads from the human genome, our model outperforms HMMER and DeepFam on protein domain classification. In summary, ProDOMA is a useful end-to-end protein domain analysis tool for long noisy reads without relying on error correction. Availability: The source code and the trained model are freely available at https://github.com/strideradu/ProDOMA. Contact: yannisun@cityu.edu.hk
fMRI Multiple Missing Values Imputation Regularized by a Recurrent Denoiser
Authors: David Calhas, Rui Henriques
Date: 2020-09-26 00:00:00
Tasks: Imputation, Missing Values

Functional Magnetic Resonance Imaging (fMRI) is a neuroimaging technique with pivotal importance due to its scientific and clinical applications. As with any widely used imaging modality, there is a need to ensure the quality of the same, with missing values being highly frequent due to the presence of artifacts or sub-optimal imaging resolutions. Our work focus on missing values imputation on multivariate signal data. To do so, a new imputation method is proposed consisting on two major steps: spatial-dependent signal imputation and time-dependent regularization of the imputed signal. A novel layer, to be used in deep learning architectures, is proposed in this work, bringing back the concept of chained equations for multiple imputation. Finally, a recurrent layer is applied to tune the signal, such that it captures its true patterns. Both operations yield an improved robustness against state-of-the-art alternatives.
Deep Learning-based Four-region Lung Segmentation in Chest Radiography for COVID-19 Diagnosis
Authors: Young-Gon Kim, Kyungsang Kim, Dufan Wu, Hui Ren, Won Young Tak, Soo Young Park, Yu Rim Lee, Min Kyu Kang, Jung Gil Park, Byung Seok Kim, Woo Jin Chung, Mannudeep K. Kalra, Quanzheng Li
Date: 2020-09-26 00:00:00
Tasks: COVID-19 Diagnosis, Segmentation

Purpose. Imaging plays an important role in assessing severity of COVID 19 pneumonia. However, semantic interpretation of chest radiography (CXR) findings does not include quantitative description of radiographic opacities. Most current AI assisted CXR image analysis framework do not quantify for regional variations of disease. To address these, we proposed a four region lung segmentation method to assist accurate quantification of COVID 19 pneumonia. Methods. A segmentation model to separate left and right lung is firstly applied, and then a carina and left hilum detection network is used, which are the clinical landmarks to separate the upper and lower lungs. To improve the segmentation performance of COVID 19 images, ensemble strategy incorporating five models is exploited. Using each region, we evaluated the clinical relevance of the proposed method with the Radiographic Assessment of the Quality of Lung Edema (RALE). Results. The proposed ensemble strategy showed dice score of 0.900, which is significantly higher than conventional methods (0.854 0.889). Mean intensities of segmented four regions indicate positive correlation to the extent and density scores of pulmonary opacities under the RALE framework. Conclusion. A deep learning based model in CXR can accurately segment and quantify regional distribution of pulmonary opacities in patients with COVID 19 pneumonia.
Automatic Arabic Dialect Identification Systems for Written Texts: A Survey
Authors: Maha J. Althobaiti
Date: 2020-09-26 00:00:00
Tasks: Dialect Identification, Machine Translation, Sentence, Speech Synthesis, Survey, Text Generation, text-to-speech, Text to Speech, Text-To-Speech Synthesis, Translation

Arabic dialect identification is a specific task of natural language processing, aiming to automatically predict the Arabic dialect of a given text. Arabic dialect identification is the first step in various natural language processing applications such as machine translation, multilingual text-to-speech synthesis, and cross-language text generation. Therefore, in the last decade, interest has increased in addressing the problem of Arabic dialect identification. In this paper, we present a comprehensive survey of Arabic dialect identification research in written texts. We first define the problem and its challenges. Then, the survey extensively discusses in a critical manner many aspects related to Arabic dialect identification task. So, we review the traditional machine learning methods, deep learning architectures, and complex learning approaches to Arabic dialect identification. We also detail the features and techniques for feature representations used to train the proposed systems. Moreover, we illustrate the taxonomy of Arabic dialects studied in the literature, the various levels of text processing at which Arabic dialect identification are conducted (e.g., token, sentence, and document level), as well as the available annotated resources, including evaluation benchmark corpora. Open challenges and issues are discussed at the end of the survey.
Topology Learning of unknown Networked Linear Dynamical System excited by Cyclostationary inputs
Authors: Harish Doddi, Deepjyoti Deka, Murti Salapaka
Date: 2020-09-26 00:00:00
Tasks: Decision Making

Topology learning of networked dynamical systems is an important problem with implications to optimal control, decision-making over networks, cybersecurity and safety. The majority of prior work in consistent topology estimation relies on dynamical systems excited by temporally uncorrelated processes. In this article, we present a novel algorithm for guaranteed topology learning of networks that are excited by temporally (colored) cyclostationary processes, which encompasses a wide range of temporal correlation including wide-sense stationarity. Furthermore, unlike prior work, the framework applies to linear dynamic system with complex valued dependencies, and leverages group lasso regularization for effective learning of the network structure. In the second part of the article, we analyze conditions for consistent topology learning for bidirected tree networks when a subset of the network is unobserved. Here, the full topology along with unobserved nodes are recovered from observed node's time-series alone. Our theoretical contributions are validated on simulated data as well as on real-world climate data.
Clustering-based Unsupervised Generative Relation Extraction
Authors: Chenhan Yuan, Ryan Rossi, Andrew Katz, Hoda Eldardiry
Date: 2020-09-26 00:00:00
Tasks: Clustering, Decoder, Relation, Relation Extraction, Self-Supervised Learning, Sentence

This paper focuses on the problem of unsupervised relation extraction. Existing probabilistic generative model-based relation extraction methods work by extracting sentence features and using these features as inputs to train a generative model. This model is then used to cluster similar relations. However, these methods do not consider correlations between sentences with the same entity pair during training, which can negatively impact model performance. To address this issue, we propose a Clustering-based Unsupervised generative Relation Extraction (CURE) framework that leverages an "Encoder-Decoder" architecture to perform self-supervised learning so the encoder can extract relation information. Given multiple sentences with the same entity pair as inputs, self-supervised learning is deployed by predicting the shortest path between entity pairs on the dependency graph of one of the sentences. After that, we extract the relation information using the well-trained encoder. Then, entity pairs that share the same relation are clustered based on their corresponding relation information. Each cluster is labeled with a few words based on the words in the shortest paths corresponding to the entity pairs in each cluster. These cluster labels also describe the meaning of these relation clusters. We compare the triplets extracted by our proposed framework (CURE) and baseline methods with a ground-truth Knowledge Base. Experimental results show that our model performs better than state-of-the-art models on both New York Times (NYT) and United Nations Parallel Corpus (UNPC) standard datasets.
MicroAnalyzer: A Python Tool for Automated Bacterial Analysis with Fluorescence Microscopy
Authors: Jonathan Reiner, Guy Azran, Gal Hyams
Date: 2020-09-26 00:00:00
Tasks: Segmentation

Fluorescence microscopy is a widely used method among cell biologists for studying the localization and co-localization of fluorescent protein. For microbial cell biologists, these studies often include tedious and time-consuming manual segmentation of bacteria and of the fluorescence clusters or working with multiple programs. Here, we present MicroAnalyzer - a tool that automates these tasks by providing an end-to-end platform for microscope image analysis. While such tools do exist, they are costly, black-boxed programs. Microanalyzer offers an open-source alternative to these tools, allowing flexibility and expandability by advanced users. MicroAnalyzer provides accurate cell and fluorescence cluster segmentation based on state-of-the-art deep-learning segmentation models, combined with ad-hoc post-processing and Colicoords - an open-source cell image analysis tool for calculating general cell and fluorescence measurements. Using these methods, it performs better than generic approaches since the dynamic nature of neural networks allows for a quick adaptation to experiment restrictions and assumptions. Other existing tools do not consider experiment assumptions, nor do they provide fluorescence cluster detection without the need for any specialized equipment. The key goal of MicroAnalyzer is to automate the entire process of cell and fluorescence image analysis "from microscope to database", meaning it does not require any further input from the researcher except for the initial deep-learning model training. In this fashion, it allows the researchers to concentrate on the bigger picture instead of granular, eye-straining labor
COVID-19 Infection Map Generation and Detection from Chest X-Ray Images
Authors: Aysen Degerli, Mete Ahishali, Mehmet Yamac, Serkan Kiranyaz, Muhammad E. H. Chowdhury, Khalid Hameed, Tahir Hamid, Rashid Mazhar, Moncef Gabbouj
Date: 2020-09-26 00:00:00
Tasks: COVID-19 Diagnosis, Segmentation, Specificity

Computer-aided diagnosis has become a necessity for accurate and immediate coronavirus disease 2019 (COVID-19) detection to aid treatment and prevent the spread of the virus. Numerous studies have proposed to use Deep Learning techniques for COVID-19 diagnosis. However, they have used very limited chest X-ray (CXR) image repositories for evaluation with a small number, a few hundreds, of COVID-19 samples. Moreover, these methods can neither localize nor grade the severity of COVID-19 infection. For this purpose, recent studies proposed to explore the activation maps of deep networks. However, they remain inaccurate for localizing the actual infestation making them unreliable for clinical use. This study proposes a novel method for the joint localization, severity grading, and detection of COVID-19 from CXR images by generating the so-called infection maps. To accomplish this, we have compiled the largest dataset with 119,316 CXR images including 2951 COVID-19 samples, where the annotation of the ground-truth segmentation masks is performed on CXRs by a novel collaborative human-machine approach. Furthermore, we publicly release the first CXR dataset with the ground-truth segmentation masks of the COVID-19 infected regions. A detailed set of experiments show that state-of-the-art segmentation networks can learn to localize COVID-19 infection with an F1-score of 83.20%, which is significantly superior to the activation maps created by the previous methods. Finally, the proposed approach achieved a COVID-19 detection performance with 94.96% sensitivity and 99.88% specificity.
Neural Proof Nets
Authors: Konstantinos Kogkalidis, Michael Moortgat, Richard Moot
Date: 2020-09-26 00:00:00
Proceeding: CONLL 2020

Linear logic and the linear {\lambda}-calculus have a long standing tradition in the study of natural language form and meaning. Among the proof calculi of linear logic, proof nets are of particular interest, offering an attractive geometric representation of derivations that is unburdened by the bureaucratic complications of conventional prooftheoretic formats. Building on recent advances in set-theoretic learning, we propose a neural variant of proof nets based on Sinkhorn networks, which allows us to translate parsing as the problem of extracting syntactic primitives and permuting them into alignment. Our methodology induces a batch-efficient, end-to-end differentiable architecture that actualizes a formally grounded yet highly efficient neuro-symbolic parser. We test our approach on {\AE}Thel, a dataset of type-logical derivations for written Dutch, where it manages to correctly transcribe raw text sentences into proofs and terms of the linear {\lambda}-calculus with an accuracy of as high as 70%.
Local and non-local dependency learning and emergence of rule-like representations in speech data by Deep Convolutional Generative Adversarial Networks
Authors: Gašper Beguš
Date: 2020-09-27 00:00:00
Tasks: Language Acquisition

This paper argues that training GANs on local and non-local dependencies in speech data offers insights into how deep neural networks discretize continuous data and how symbolic-like rule-based morphophonological processes emerge in a deep convolutional architecture. Acquisition of speech has recently been modeled as a dependency between latent space and data generated by GANs in Begu\v{s} (2020b; arXiv:2006.03965), who models learning of a simple local allophonic distribution. We extend this approach to test learning of local and non-local phonological processes that include approximations of morphological processes. We further parallel outputs of the model to results of a behavioral experiment where human subjects are trained on the data used for training the GAN network. Four main conclusions emerge: (i) the networks provide useful information for computational models of speech acquisition even if trained on a comparatively small dataset of an artificial grammar learning experiment; (ii) local processes are easier to learn than non-local processes, which matches both behavioral data in human subjects and typology in the world's languages. This paper also proposes (iii) how we can actively observe the network's progress in learning and explore the effect of training steps on learning representations by keeping latent space constant across different training steps. Finally, this paper shows that (iv) the network learns to encode the presence of a prefix with a single latent variable; by interpolating this variable, we can actively observe the operation of a non-local phonological process. The proposed technique for retrieving learning representations has general implications for our understanding of how GANs discretize continuous speech data and suggests that rule-like generalizations in the training data are represented as an interaction between variables in the network's latent space.
Multi-timescale Representation Learning in LSTM Language Models
Authors: Shivangi Mahto, Vy A. Vo, Javier S. Turek, Alexander G. Huth
Date: 2020-09-27 00:00:00
Proceeding: ICLR 2021 1
Tasks: Language Modeling, Language Modelling, Representation Learning

Language models must capture statistical dependencies between words at timescales ranging from very short to very long. Earlier work has demonstrated that dependencies in natural language tend to decay with distance between words according to a power law. However, it is unclear how this knowledge can be used for analyzing or designing neural network language models. In this work, we derived a theory for how the memory gating mechanism in long short-term memory (LSTM) language models can capture power law decay. We found that unit timescales within an LSTM, which are determined by the forget gate bias, should follow an Inverse Gamma distribution. Experiments then showed that LSTM language models trained on natural English text learn to approximate this theoretical distribution. Further, we found that explicitly imposing the theoretical distribution upon the model during training yielded better language model perplexity overall, with particular improvements for predicting low-frequency (rare) words. Moreover, the explicit multi-timescale model selectively routes information about different types of words through units with different timescales, potentially improving model interpretability. These results demonstrate the importance of careful, theoretically-motivated analysis of memory and timescale in language models.
Modeling Topical Relevance for Multi-Turn Dialogue Generation
Authors: Hainan Zhang, Yanyan Lan, Liang Pang, Hongshen Chen, Zhuoye Ding, Dawei Yin
Date: 2020-09-27 00:00:00
Tasks: Dialogue Generation, Sentence

Topic drift is a common phenomenon in multi-turn dialogue. Therefore, an ideal dialogue generation models should be able to capture the topic information of each context, detect the relevant context, and produce appropriate responses accordingly. However, existing models usually use word or sentence level similarities to detect the relevant contexts, which fail to well capture the topical level relevance. In this paper, we propose a new model, named STAR-BTM, to tackle this problem. Firstly, the Biterm Topic Model is pre-trained on the whole training dataset. Then, the topic level attention weights are computed based on the topic representation of each context. Finally, the attention weights and the topic distribution are utilized in the decoding process to generate the corresponding responses. Experimental results on both Chinese customer services data and English Ubuntu dialogue data show that STAR-BTM significantly outperforms several state-of-the-art methods, in terms of both metric-based and human evaluations.
Faster Biological Gradient Descent Learning
Authors: Ho Ling Li
Date: 2020-09-27 00:00:00

Back-propagation is a popular machine learning algorithm that uses gradient descent in training neural networks for supervised learning, but can be very slow. A number of algorithms have been developed to speed up convergence and improve robustness of the learning. However, they are complicated to implement biologically as they require information from previous updates. Inspired by synaptic competition in biology, we have come up with a simple and local gradient descent optimization algorithm that can reduce training time, with no demand on past details. Our algorithm, named dynamic learning rate (DLR), works similarly to the traditional gradient descent used in back-propagation, except that instead of having a uniform learning rate across all synapses, the learning rate depends on the current neuronal connection weights. Our algorithm is found to speed up learning, particularly for small networks.