pwc-archive/papers-with-abstracts huggingface dataset:
Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain
Authors: B.B.Avants, C.L.Epstein, M.Grossman, J.C.Gee
Date: 2008-02-01 00:00:00
Proceeding: Medical Image Analysis 2008 2
Tasks: BIRL, Diffeomorphic Medical Image Registration, Image Registration

One of the most challenging problems in modern neuroimaging is detailed characterization of neurodegeneration. Quantifying spatial and longitudinal atrophy patterns is an important component of this process. These spatiotemporal signals will aid in discriminating between related diseases, such as frontotemporal dementia (FTD) and Alzheimer's disease (AD), which manifest themselves in the same at-risk population. Here, we develop a novel symmetric image normalization method (SyN) for maximizing the cross-correlation within the space of diffeomorphic maps and provide the Euler-Lagrange equations necessary for this optimization. We then turn to a careful evaluation of our method. Our evaluation uses gold standard, human cortical segmentation to contrast SyN's performance with a related elastic method and with the standard ITK implementation of Thirion's Demons algorithm. The new method compares favorably with both approaches, in particular when the distance between the template brain and the target brain is large. We then report the correlation of volumes gained by algorithmic cortical labelings of FTD and control subjects with those gained by the manual rater. This comparison shows that, of the three methods tested, SyN's volume measurements are the most strongly correlated with volume measurements gained by expert labeling. This study indicates that SyN, with cross-correlation, is a reliable method for normalizing and making anatomical measurements in volumetric MRI of patients and at-risk elderly individuals.
Generative diffeomorphic modelling of large MRI data sets for probabilistic template construction
Authors: Claudia Blaiotta, Patrick Freund, M. Jorge Cardoso, John Ashburner
Date: 2018-02-01 00:00:00
Proceeding: NeuroImage 2018 2
Tasks: Diffeomorphic Medical Image Registration, Image Registration, Medical Image Registration

In this paper we present a hierarchical generative model of medical image data, which can capture simultaneously the variability of both signal intensity and anatomical shapes across large populations. Such a model has a direct application for learning average-shaped probabilistic tissue templates in a fully automated manner. While in principle the generality of the proposed Bayesian approach makes it suitable to address a wide range of medical image computing problems, our work focuses primarily on neuroimaging applications. In particular we validate the proposed method on both real and synthetic brain MR scans including the cervical cord and demonstrate that it yields accurate alignment of brain and spinal cord structures, as compared to state-of-the-art tools for medical image registration. At the same time we illustrate how the resulting tissue probability maps can readily be used to segment, bias correct and spatially normalise unseen data, which are all crucial pre-processing steps for MR imaging studies.
Diffeomorphic registration with intensity transformation and missing data: Application to 3D digital pathology of Alzheimer’s disease
Authors: Daniel Tward, Timothy Brown, Yusuke Kageyama, Jaymin Patel, Zhipeng Hou, Susumu Mori, Marilyn Albert, Juan Troncoso, Michael Miller
Date: 2019-01-04 00:00:00
Proceeding: bioRxiv 2019 1
Tasks: 3D Reconstruction, Deformable Medical Image Registration, Diffeomorphic Medical Image Registration, Image Registration

This paper examines the problem of diffeomorphic image mapping in the presence of differing image intensity profiles and missing data. Our motivation comes from the problem of aligning 3D brain MRI with 100 micron isotropic resolution, to histology sections with 1 micron in plane resolution. Multiple stains, as well as damaged, folded, or missing tissue are common in this situation. We overcome these challenges by introducing two new concepts. Cross modality image matching is achieved by jointly estimating polynomial transformations of the atlas intensity, together with pose and deformation parameters. Missing data is accommodated via a multiple atlas selection procedure where several atlases may be of homogeneous intensity and correspond to “background” or “artifact”. The two concepts are combined within an Expectation Maximization algorithm, where atlas selection posteriors and deformation parameters are updated iteratively, and polynomial coefficients are computed in closed form. We show results for 3D reconstruction of digital pathology and MRI in standard atlas coordinates. In conjunction with convolutional neural networks, we quantify the 3D density distribution of tauopathy throughout the medial temporal lobe of an Alzheimer’s disease postmortem specimen.

Author summary Our work in Alzheimer’s disease (AD) is attempting to connect histopathology at autopsy and longitudinal clinical magnetic resonance imaging (MRI), combining the strengths of each modality in a common coordinate system. We are bridging this gap by using post mortem high resolution MRI to reconstruct digital pathology in 3D. This image registration problem is challenging because it combines images from different modalities in the presence of missing tissue and artifacts. We overcome this challenge by developing a new registration technique that simultaneously classifies each pixel as “good data” / “missing tissue” / “artifact”, learns a contrast transformation between modalities, and computes deformation parameters. We name this technique “(D)eformable (R)egistration and (I)ntensity (T)ransformation with (M)issing (D)ata”, pronounced as “Dr. It, M.D.”. In conjunction with convolutional neural networks, we use this technique to map the three dimensional distribution of tau tangles in the medial temporal lobe of an AD postmortem specimen.
Spectral backtests of forecast distributions with application to risk management
Authors: Michael B. Gordy, Alexander J. McNeil
Date: 2017-08-04 00:00:00
Tasks: Management

We study a class of backtests for forecast distributions in which the test statistic depends on a spectral transformation that weights exceedance events by a function of the modeled probability level. The weighting scheme is specified by a kernel measure which makes explicit the user's priorities for model performance. The class of spectral backtests includes tests of unconditional coverage and tests of conditional coverage. We show how the class embeds a wide variety of backtests in the existing literature, and further propose novel variants which are easily implemented, well-sized and have good power. In an empirical application, we backtest forecast distributions for the overnight P&L of ten bank trading portfolios. For some portfolios, test results depend materially on the choice of kernel.
RSS-Based Q-Learning for Indoor UAV Navigation
Authors: Md Moin Uddin Chowdhury, Fatih Erden, Ismail Guvenc
Date: 2019-05-31 00:00:00
Tasks: Q-Learning

In this paper, we focus on the potential use of unmanned aerial vehicles (UAVs) for search and rescue (SAR) missions in GPS-denied indoor environments. We consider the problem of navigating a UAV to a wireless signal source, e.g., a smartphone or watch owned by a victim. We assume that the source periodically transmits RF signals to nearby wireless access points. Received signal strength (RSS) at the UAV, which is a function of the UAV and source positions, is fed to a Q-learning algorithm and the UAV is navigated to the vicinity of the source. Unlike the traditional location-based Q-learning approach that uses the GPS coordinates of the agent, our method uses the RSS to define the states and rewards of the algorithm. It does not require any a priori information about the environment. These, in turn, make it possible to use the UAVs in indoor SAR operations. Two indoor scenarios with different dimensions are created using a ray tracing software. Then, the corresponding heat maps that show the RSS at each possible UAV location are extracted for more realistic analysis. Performance of the RSS-based Q-learning algorithm is compared with the baseline (location-based) Q-learning algorithm in terms of convergence speed, average number of steps per episode, and the total length of the final trajectory. Our results show that the RSS-based Q-learning provides competitive performance with the location-based Q-learning.
Neural Network Applications in Earthquake Prediction (1994-2019): Meta-Analytic Insight on their Limitations
Authors: Arnaud Mignan, Marco Broccardo
Date: 2019-10-02 00:00:00
Tasks: Articles, Deep Learning, Earthquake prediction

In the last few years, deep learning has solved seemingly intractable problems, boosting the hope to find approximate solutions to problems that now are considered unsolvable. Earthquake prediction, the Grail of Seismology, is, in this context of continuous exciting discoveries, an obvious choice for deep learning exploration. We review the entire literature of artificial neural network (ANN) applications for earthquake prediction (77 articles, 1994-2019 period) and find two emerging trends: an increasing interest in this domain, and a complexification of ANN models over time, towards deep learning. Despite apparent positive results observed in this corpus, we demonstrate that simpler models seem to offer similar predictive powers, if not better ones. Due to the structured, tabulated nature of earthquake catalogues, and the limited number of features so far considered, simpler and more transparent machine learning models seem preferable at the present stage of research. Those baseline models follow first physical principles and are consistent with the known empirical laws of Statistical Seismology, which have minimal abilities to predict large earthquakes.
A Hybrid Cooperative Co-evolution Algorithm Framework for Optimising Power Take Off and Placements of Wave Energy Converters
Authors: Mehdi Neshat, Bradley Alexander, Markus Wagner
Date: 2019-10-03 00:00:00
Tasks: Evolutionary Algorithms

Wave energy technologies have the potential to play a significant role in the supply of renewable energy on a world scale. One of the most promising designs for wave energy converters (WECs) are fully submerged buoys. In this work, we explore the optimisation of WEC arrays consisting of a three-tether buoy model called CETO. Such arrays can be optimised for total energy output by adjusting both the relative positions of buoys in farms and also the power-take-off (PTO) parameters for each buoy. The search space for these parameters is complex and multi-modal. Moreover, the evaluation of each parameter setting is computationally expensive -- limiting the number of full model evaluations that can be made. To handle this problem, we propose a new hybrid cooperative co-evolution algorithm (HCCA). HCCA consists of a symmetric local search plus Nelder-Mead and a cooperative co-evolution algorithm (CC) with a backtracking strategy for optimising the positions and PTO settings of WECs, respectively. Moreover, a new adaptive scenario is proposed for tuning grey wolf optimiser (AGWO) hyper-parameter. AGWO participates notably with other applied optimisers in HCCA. For assessing the effectiveness of the proposed approach five popular Evolutionary Algorithms (EAs), four alternating optimisation methods and two modern hybrid ideas (LS-NM and SLS-NM-B) are carefully compared in four real wave situations (Adelaide, Tasmania, Sydney and Perth) with two wave farm sizes (4 and 16). According to the experimental outcomes, the hybrid cooperative framework exhibits better performance in terms of both runtime and quality of obtained solutions.
ES-MAML: Simple Hessian-Free Meta Learning
Authors: Xingyou Song, Wenbo Gao, Yuxiang Yang, Krzysztof Choromanski, Aldo Pacchiano, Yunhao Tang
Date: 2019-09-25 00:00:00
Proceeding: ICLR 2020 1
Tasks: Meta-Learning

We introduce ES-MAML, a new framework for solving the model agnostic meta learning (MAML) problem based on Evolution Strategies (ES). Existing algorithms for MAML are based on policy gradients, and incur significant difficulties when attempting to estimate second derivatives using backpropagation on stochastic policies. We show how ES can be applied to MAML to obtain an algorithm which avoids the problem of estimating second derivatives, and is also conceptually simple and easy to implement. Moreover, ES-MAML can handle new types of nonsmooth adaptation operators, and other techniques for improving performance and estimation of ES methods become applicable. We show empirically that ES-MAML is competitive with existing methods and often yields better adaptation with fewer queries.
YOLO Nano: a Highly Compact You Only Look Once Convolutional Neural Network for Object Detection
Authors: Alexander Wong, Mahmoud Famuori, Mohammad Javad Shafiee, Francis Li, Brendan Chwyl, Jonathan Chung
Date: 2019-10-03 00:00:00
Tasks: Object, object-detection, Object Detection

Object detection remains an active area of research in the field of computer vision, and considerable advances and successes has been achieved in this area through the design of deep convolutional neural networks for tackling object detection. Despite these successes, one of the biggest challenges to widespread deployment of such object detection networks on edge and mobile scenarios is the high computational and memory requirements. As such, there has been growing research interest in the design of efficient deep neural network architectures catered for edge and mobile usage. In this study, we introduce YOLO Nano, a highly compact deep convolutional neural network for the task of object detection. A human-machine collaborative design strategy is leveraged to create YOLO Nano, where principled network design prototyping, based on design principles from the YOLO family of single-shot object detection network architectures, is coupled with machine-driven design exploration to create a compact network with highly customized module-level macroarchitecture and microarchitecture designs tailored for the task of embedded object detection. The proposed YOLO Nano possesses a model size of ~4.0MB (>15.1x and >8.3x smaller than Tiny YOLOv2 and Tiny YOLOv3, respectively) and requires 4.57B operations for inference (>34% and ~17% lower than Tiny YOLOv2 and Tiny YOLOv3, respectively) while still achieving an mAP of ~69.1% on the VOC 2007 dataset (~12% and ~10.7% higher than Tiny YOLOv2 and Tiny YOLOv3, respectively). Experiments on inference speed and power efficiency on a Jetson AGX Xavier embedded module at different power budgets further demonstrate the efficacy of YOLO Nano for embedded scenarios.
Extracting UMLS Concepts from Medical Text Using General and Domain-Specific Deep Learning Models
Authors: Kathleen C. Fraser, Isar Nejadgholi, Berry de Bruijn, Muqun Li, Astha LaPlante, Khaldoun Zine El Abidine
Date: 2019-10-03 00:00:00
Tasks: Entity Linking, Relation Extraction, Unsupervised Pre-training, Word Embeddings

Entity recognition is a critical first step to a number of clinical NLP applications, such as entity linking and relation extraction. We present the first attempt to apply state-of-the-art entity recognition approaches on a newly released dataset, MedMentions. This dataset contains over 4000 biomedical abstracts, annotated for UMLS semantic types. In comparison to existing datasets, MedMentions contains a far greater number of entity types, and thus represents a more challenging but realistic scenario in a real-world setting. We explore a number of relevant dimensions, including the use of contextual versus non-contextual word embeddings, general versus domain-specific unsupervised pre-training, and different deep learning architectures. We contrast our results against the well-known i2b2 2010 entity recognition dataset, and propose a new method to combine general and domain-specific information. While producing a state-of-the-art result for the i2b2 2010 task (F1 = 0.90), our results on MedMentions are significantly lower (F1 = 0.63), suggesting there is still plenty of opportunity for improvement on this new data.
Blood lactate concentration prediction in critical care patients: handling missing values
Authors: Behrooz Mamandipoor, Mahshid Majd, Monica Moz, Venet Osmani
Date: 2019-10-03 00:00:00
Tasks: Decision Making, Imputation, Missing Values, Prediction

Blood lactate concentration is a strong indicator of mortality risk in critically ill patients. While frequent lactate measurements are necessary to assess patient's health state, the measurement is an invasive procedure that can increase risk of hospital-acquired infections. For this reason we formally define the problem of lactate prediction as a clinically relevant benchmark problem for machine learning community so as to assist clinical decision making in blood lactate testing. Accordingly, we demonstrate the relevant challenges of the problem and its data in addition to the adopted solutions. Also, we evaluate the performance of different prediction algorithms on a large dataset of ICU patients from the multi-centre eICU database. More specifically, we focus on investigating the impact of missing value imputation methods in lactate prediction for each algorithm. The experimental analysis shows promising prediction results that encourages further investigation of this problem.
Cracking the Contextual Commonsense Code: Understanding Commonsense Reasoning Aptitude of Deep Contextual Representations
Authors: Jeff Da, Jungo Kasai
Date: 2019-10-02 00:00:00
Proceeding: WS 2019 11
Tasks: Knowledge Graphs

Pretrained deep contextual representations have advanced the state-of-the-art on various commonsense NLP tasks, but we lack a concrete understanding of the capability of these models. Thus, we investigate and challenge several aspects of BERT's commonsense representation abilities. First, we probe BERT's ability to classify various object attributes, demonstrating that BERT shows a strong ability in encoding various commonsense features in its embedding space, but is still deficient in many areas. Next, we show that, by augmenting BERT's pretraining data with additional data related to the deficient attributes, we are able to improve performance on a downstream commonsense reasoning task while using a minimal amount of data. Finally, we develop a method of fine-tuning knowledge graphs embeddings alongside BERT and show the continued importance of explicit knowledge graphs.
Identifying Nuances in Fake News vs. Satire: Using Semantic and Linguistic Cues
Authors: Or Levi, Pedram Hosseini, Mona Diab, David A. Broniatowski
Date: 2019-10-02 00:00:00
Proceeding: WS 2019 11
Tasks: Language Modelling, Misinformation

The blurry line between nefarious fake news and protected-speech satire has been a notorious struggle for social media platforms. Further to the efforts of reducing exposure to misinformation on social media, purveyors of fake news have begun to masquerade as satire sites to avoid being demoted. In this work, we address the challenge of automatically classifying fake news versus satire. Previous work have studied whether fake news and satire can be distinguished based on language differences. Contrary to fake news, satire stories are usually humorous and carry some political or social message. We hypothesize that these nuances could be identified using semantic and linguistic cues. Consequently, we train a machine learning method using semantic representation, with a state-of-the-art contextual language model, and with linguistic features based on textual coherence metrics. Empirical evaluation attests to the merits of our approach compared to the language-based baseline and sheds light on the nuances between fake news and satire. As avenues for future work, we consider studying additional linguistic features related to the humor aspect, and enriching the data with current news events, to help identify a political or social message.
Linking artificial and human neural representations of language
Authors: Jon Gauthier, Roger Levy
Date: 2019-10-02 00:00:00
Proceeding: IJCNLP 2019 11
Tasks: Brain Decoding, Natural Language Understanding, Sentence

What information from an act of sentence understanding is robustly represented in the human brain? We investigate this question by comparing sentence encoding models on a brain decoding task, where the sentence that an experimental participant has seen must be predicted from the fMRI signal evoked by the sentence. We take a pre-trained BERT architecture as a baseline sentence encoding model and fine-tune it on a variety of natural language understanding (NLU) tasks, asking which lead to improvements in brain-decoding performance. We find that none of the sentence encoding tasks tested yield significant increases in brain decoding performance. Through further task ablations and representational analyses, we find that tasks which produce syntax-light representations yield significant improvements in brain decoding performance. Our results constrain the space of NLU models that could best account for human neural representations of language, but also suggest limits on the possibility of decoding fine-grained syntactic information from fMRI human neuroimaging.
Neural Zero-Inflated Quality Estimation Model For Automatic Speech Recognition System
Authors: Kai Fan, Jiayi Wang, Bo Li, Shiliang Zhang, Boxing Chen, Niyu Ge, Zhijie Yan
Date: 2019-10-03 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), Language Modeling, Language Modelling, Machine Translation, speech-recognition, Speech Recognition, Translation

The performances of automatic speech recognition (ASR) systems are usually evaluated by the metric word error rate (WER) when the manually transcribed data are provided, which are, however, expensively available in the real scenario. In addition, the empirical distribution of WER for most ASR systems usually tends to put a significant mass near zero, making it difficult to simulate with a single continuous distribution. In order to address the two issues of ASR quality estimation (QE), we propose a novel neural zero-inflated model to predict the WER of the ASR result without transcripts. We design a neural zero-inflated beta regression on top of a bidirectional transformer language model conditional on speech features (speech-BERT). We adopt the pre-training strategy of token level mask language modeling for speech-BERT as well, and further fine-tune with our zero-inflated layer for the mixture of discrete and continuous outputs. The experimental results show that our approach achieves better performance on WER prediction in the metrics of Pearson and MAE, compared with most existed quality estimation algorithms for ASR or machine translation.
Hitachi at MRP 2019: Unified Encoder-to-Biaffine Network for Cross-Framework Meaning Representation Parsing
Authors: Yuta Koreeda, Gaku Morio, Terufumi Morishita, Hiroaki Ozaki, Kohsuke Yanai
Date: 2019-10-03 00:00:00
Proceeding: CONLL 2019 11
Tasks: Decoder, Multi-Task Learning

This paper describes the proposed system of the Hitachi team for the Cross-Framework Meaning Representation Parsing (MRP 2019) shared task. In this shared task, the participating systems were asked to predict nodes, edges and their attributes for five frameworks, each with different order of "abstraction" from input tokens. We proposed a unified encoder-to-biaffine network for all five frameworks, which effectively incorporates a shared encoder to extract rich input features, decoder networks to generate anchorless nodes in UCCA and AMR, and biaffine networks to predict edges. Our system was ranked fifth with the macro-averaged MRP F1 score of 0.7604, and outperformed the baseline unified transition-based MRP. Furthermore, post-evaluation experiments showed that we can boost the performance of the proposed system by incorporating multi-task learning, whereas the baseline could not. These imply efficacy of incorporating the biaffine network to the shared architecture for MRP and that learning heterogeneous meaning representations at once can boost the system performance.