pwc-archive/papers-with-abstracts huggingface dataset:
Statistical Analysis on Brain Surfaces
Authors: Moo K. Chung, Jamie L. Hanson, Seth D. Pollak
Date: 2022-03-13 00:00:00
Tasks: Hippocampus

In this paper, we review widely used statistical analysis frameworks for data defined along cortical and subcortical surfaces that have been developed in last two decades. The cerebral cortex has the topology of a 2D highly convoluted sheet. For data obtained along curved non-Euclidean surfaces, traditional statistical analysis and smoothing techniques based on the Euclidean metric structure are inefficient. To increase the signal-to-noise ratio (SNR) and to boost the sensitivity of the analysis, it is necessary to smooth out noisy surface data. However, this requires smoothing data on curved cortical manifolds and assigning smoothing weights based on the geodesic distance along the surface. Thus, many cortical surface data analysis frameworks are differential geometric in nature. The smoothed surface data is then treated as smooth random fields and statistical inferences can be performed within Keith Worsley's random field theory. The methods described in this paper are illustrated with the hippocampus surface data set. Using this case study, we will determine if there is an effect of family income on the growth of hippocampus in children in detail. There are a total of 124 children and 82 of them have repeat magnetic resonance images (MRI) two years later.
Pareto optimality, economy-effectiveness trade-offs and ion channel degeneracy: Improving population models of neurons
Authors: Peter Jedlicka, Alex Bird, Hermann Cuntz
Date: 2022-03-12 00:00:00

Nerve cells encounter unavoidable evolutionary trade-offs between multiple tasks. They must consume as little energy as possible (be energy-efficient or economical) but at the same time fulfil their functions (be functionally effective). Neurons displaying best performance for such multi-task trade-offs are said to be Pareto optimal. However, it is not understood how ion channel parameters contribute to the Pareto optimal performance of neurons. Ion channel degeneracy implies that multiple combinations of ion channel parameters can lead to functionally similar neuronal behavior. Therefore, to simulate functional behavior, instead of a single model, neuroscientists often use populations of valid models with distinct ion conductance configurations. This approach is called population (also database or ensemble) modeling. It remains unclear, which ion channel parameters in a vast population of functional models are more likely to be found in the brain. Here we propose that Pareto optimality can serve as a guiding principle for addressing this issue. The Pareto optimum concept can help identify the subpopulations of conductance-based models with ion channel configurations that perform best for the trade-off between economy and functional effectiveness. In this way, the high-dimensional parameter space of neuronal models might be reduced to geometrically simple low-dimensional manifolds. Therefore, Pareto optimality is a promising framework for improving population modeling of neurons and their circuits. We also discuss how Pareto inference might help deduce neuronal functions from high-dimensional Patch-seq data. Furthermore, we hypothesize that Pareto optimality might contribute to our understanding of observed ion channel correlations in neurons.
Estimation of the incubation period and generation time of SARS-CoV-2 Alpha and Delta variants from contact tracing data
Authors: Mattia Manica, Maria Litvinova, Alfredo De Bellis, Giorgio Guzzetta, Pamela Mancuso, Massimo Vicentini, Francesco Venturelli, Eufemia Bisaccia, Ana I. Bento, Piero Poletti, Valentina Marziano, Agnese Zardini, Valeria d'Andrea, Filippo Trentini, Antonino Bella, Flavia Riccardo, Patrizio Pezzotti, Marco Ajelli, Paolo Giorgi Rossi, Stefano Merler, the Reggio Emilia COVID-19 Working Group
Date: 2022-03-11 00:00:00
Tasks: Bayesian Inference

Background. During 2021, the COVID-19 pandemic was characterized by the emergence of lineages with increased fitness. For most of these variants, quantitative information is scarce on epidemiological quantities such as the incubation period and generation time, which are critical for both public health decisions and scientific research. Method. We analyzed a dataset collected during contact tracing activities in the province of Reggio Emilia, Italy, throughout 2021. We determined the distributions of the incubation period using information on negative PCR tests and the date of last exposure from 282 symptomatic cases. We estimated the distributions of the intrinsic generation time (the time between the infection dates of an infector and its secondary cases under a fully susceptible population) using a Bayesian inference approach applied to 4,435 SARS-CoV-2 cases clustered in 1,430 households where at least one secondary case was recorded. Results. We estimated a mean incubation period of 4.9 days (95% credible intervals, CrI, 4.4-5.4; 95 percentile of the mean distribution: 1-12) for Alpha and 4.5 days (95%CrI 4.0-5.0; 95 percentile: 1-10) for Delta. The intrinsic generation time was estimated to have a mean of 6.0 days (95% CrI 5.6-6.4; 95 percentile: 1-15) for Alpha and of 6.6 days (95%CrI 6.0-7.3; 95 percentile: 1-18) for Delta. The household serial interval was 2.6 days (95%CrI 2.4-2.7) for Alpha and 2.4 days (95%CrI 2.2-2.6) for Delta, and the estimated proportion of pre-symptomatic transmission was 54-55% for both variants. Conclusions. These results indicate limited differences in the incubation period and intrinsic generation time of SARS-CoV-2 variants Alpha and Delta compared to ancestral lineages.
Using digital traces to build prospective and real-time county-level early warning systems to anticipate COVID-19 outbreaks in the United States
Authors: Lucas M. Stolerman, Leonardo Clemente, Canelle Poirier, Kris V. Parag, Atreyee Majumder, Serge Masyn, Bernd Resch, Mauricio Santillana
Date: 2022-03-12 00:00:00
Tasks: Decision Making

The ongoing COVID-19 pandemic continues to affect communities around the world. To date, almost 6 million people have died as a consequence of COVID-19, and more than one-quarter of a billion people are estimated to have been infected worldwide. The design of appropriate and timely mitigation strategies to curb the effects of this and future disease outbreaks requires close monitoring of their spatio-temporal trajectories. We present machine learning methods to anticipate sharp increases in COVID-19 activity in US counties in real-time. Our methods leverage Internet-based digital traces -- e.g., disease-related Internet search activity from the general population and clinicians, disease-relevant Twitter micro-blogs, and outbreak trajectories from neighboring locations -- to monitor potential changes in population-level health trends. Motivated by the need for finer spatial-resolution epidemiological insights to improve local decision-making, we build upon previous retrospective research efforts originally conceived at the state level and in the early months of the pandemic. Our methods -- tested in real-time and in an out-of-sample manner on a subset of 97 counties distributed across the US -- frequently anticipated sharp increases in COVID-19 activity 1-6 weeks before the onset of local outbreaks (defined as the time when the effective reproduction number $R_t$ becomes larger than 1 consistently). Given the continued emergence of COVID-19 variants of concern -- such as the most recent one, Omicron -- and the fact that multiple countries have not had full access to vaccines, the framework we present, while conceived for the county-level in the US, could be helpful in countries where similar data sources are available.
Determining clinically relevant features in cytometry data using persistent homology
Authors: Soham Mukherjee, Darren Wethington, Tamal K. Dey, Jayajit Das
Date: 2022-03-11 00:00:00
Tasks: Topological Data Analysis

Cytometry experiments yield high-dimensional point cloud data that is difficult to interpret manually. Boolean gating techniques coupled with comparisons of relative abundances of cellular subsets is the current standard for cytometry data analysis. However, this approach is unable to capture more subtle topological features hidden in data, especially if those features are further masked by data transforms or significant batch effects or donor-to-donor variations in clinical data. Analysis of publicly available cytometry data describing non-na\"ive CD8+ T cells in COVID-19 patients and healthy controls shows that systematic structural differences exist between single cell protein expressions in COVID-19 patients and healthy controls. We identify proteins of interest by a decision-tree based classifier, sample points randomly and compute persistence diagrams from these sampled points. The resulting persistence diagrams identify regions in cytometry datasets of varying density and identify protruded structures such as `elbows'. We compute Wasserstein distances between these persistence diagrams for random pairs of healthy controls and COVID-19 patients and find that systematic structural differences exist between COVID-19 patients and healthy controls in the expression data for T-bet, Eomes, and Ki-67. Further analysis shows that expression of T-bet and Eomes are significantly downregulated in COVID-19 patient non-na\"ive CD8+ T cells compared to healthy controls. This counter-intuitive finding may indicate that canonical effector CD8+ T cells are less prevalent in COVID-19 patients than healthy controls. This method is applicable to any cytometry dataset for discovering novel insights through topological data analysis which may be difficult to ascertain otherwise with a standard gating strategy or existing bioinformatic tools.
Regression Monte Carlo for Impulse Control
Authors: Mike Ludkovski
Date: 2022-03-13 00:00:00
Tasks: regression

I develop a numerical algorithm for stochastic impulse control in the spirit of Regression Monte Carlo for optimal stopping. The approach consists in generating statistical surrogates (aka functional approximators) for the continuation function. The surrogates are recursively trained by empirical regression over simulated state trajectories. In parallel, the same surrogates are used to learn the intervention function characterizing the optimal impulse amounts. I discuss appropriate surrogate types for this task, as well as the choice of training sets. Case studies from forest rotation and irreversible investment illustrate the numerical scheme and highlight its flexibility and extensibility. Implementation in \texttt{R} is provided as a publicly available package posted on GitHub.
Bridging the gap between pricing and reserving with an occurrence and development model for non-life insurance claims
Authors: Jonas Crevecoeur, Katrien Antonio, Stijn Desmedt, Alexandre Masquelein
Date: 2022-03-14 00:00:00

Due to the presence of reporting and settlement delay, claim data sets collected by non-life insurance companies are typically incomplete, facing right censored claim count and claim severity observations. Current practice in non-life insurance pricing tackles these right censored data via a two-step procedure. First, best estimates are computed for the number of claims that occurred in past exposure periods and the ultimate claim severities, using the incomplete, historical claim data. Second, pricing actuaries build predictive models to estimate technical, pure premiums for new contracts by treating these best estimates as actual observed outcomes, hereby neglecting their inherent uncertainty. We propose an alternative approach that brings valuable insights for both non-life pricing as well as reserving. As such we effectively bridge these two key actuarial tasks that have traditionally been discussed in silos. Hereto we develop a granular occurrence and development model for non-life claims that tackles reserving and at the same time resolves the inconsistency in traditional pricing techniques between actual observations and imputed best estimates. We illustrate our proposed model on an insurance as well as a reinsurance portfolio. The advantages of our proposed strategy are most compelling in the reinsurance illustration where large uncertainties in the best estimates originate from long reporting and settlement delays, low claim frequencies and heavy (even extreme) claim sizes.
DialMed: A Dataset for Dialogue-based Medication Recommendation
Authors: Zhenfeng He, Yuqiang Han, Zhenqiu Ouyang, Wei Gao, Hongxu Chen, Guandong Xu, Jian Wu
Date: 2022-02-22 00:00:00
Proceeding: COLING 2022 10
Tasks: Graph Attention

Medication recommendation is a crucial task for intelligent healthcare systems. Previous studies mainly recommend medications with electronic health records (EHRs). However, some details of interactions between doctors and patients may be ignored or omitted in EHRs, which are essential for automatic medication recommendation. Therefore, we make the first attempt to recommend medications with the conversations between doctors and patients. In this work, we construct DIALMED, the first high-quality dataset for medical dialogue-based medication recommendation task. It contains 11,996 medical dialogues related to 16 common diseases from 3 departments and 70 corresponding common medications. Furthermore, we propose a Dialogue structure and Disease knowledge aware Network (DDN), where a QA Dialogue Graph mechanism is designed to model the dialogue structure and the knowledge graph is used to introduce external disease knowledge. The extensive experimental results demonstrate that the proposed method is a promising solution to recommend medications with medical dialogues. The dataset and code are available at https://github.com/f-window/DialMed.
One Agent To Rule Them All: Towards Multi-agent Conversational AI
Authors: Christopher Clarke, Joseph Joshua Peper, Karthik Krishnamurthy, Walter Talamonti, Kevin Leach, Walter Lasecki, Yiping Kang, Lingjia Tang, Jason Mars
Date: 2022-03-15 00:00:00
Proceeding: Findings (ACL) 2022 5
Tasks: All, Conversational Response Selection, Multi-agent Integration, Text Classification

The increasing volume of commercially available conversational agents (CAs) on the market has resulted in users being burdened with learning and adopting multiple agents to accomplish their tasks. Though prior work has explored supporting a multitude of domains within the design of a single agent, the interaction experience suffers due to the large action space of desired capabilities. To address these problems, we introduce a new task BBAI: Black-Box Agent Integration, focusing on combining the capabilities of multiple black-box CAs at scale. We explore two techniques: question agent pairing and question response pairing aimed at resolving this task. Leveraging these techniques, we design One For All (OFA), a scalable system that provides a unified interface to interact with multiple CAs. Additionally, we introduce MARS: Multi-Agent Response Selection, a new encoder model for question response pairing that jointly encodes user question and agent response pairs. We demonstrate that OFA is able to automatically and accurately integrate an ensemble of commercially available CAs spanning disparate domains. Specifically, using the MARS encoder we achieve the highest accuracy on our BBAI task, outperforming strong baselines.
Learning What Not to Segment: A New Perspective on Few-Shot Segmentation
Authors: Chunbo Lang, Gong Cheng, Binfei Tu, Junwei Han
Date: 2022-03-15 00:00:00
Proceeding: CVPR 2022 1
Tasks: Few-Shot Semantic Segmentation, Meta-Learning, Semantic Segmentation

Recently few-shot segmentation (FSS) has been extensively developed. Most previous works strive to achieve generalization through the meta-learning framework derived from classification tasks; however, the trained models are biased towards the seen classes instead of being ideally class-agnostic, thus hindering the recognition of new concepts. This paper proposes a fresh and straightforward insight to alleviate the problem. Specifically, we apply an additional branch (base learner) to the conventional FSS model (meta learner) to explicitly identify the targets of base classes, i.e., the regions that do not need to be segmented. Then, the coarse results output by these two learners in parallel are adaptively integrated to yield precise segmentation prediction. Considering the sensitivity of meta learner, we further introduce an adjustment factor to estimate the scene differences between the input image pairs for facilitating the model ensemble forecasting. The substantial performance gains on PASCAL-5i and COCO-20i verify the effectiveness, and surprisingly, our versatile scheme sets a new state-of-the-art even with two plain learners. Moreover, in light of the unique nature of the proposed approach, we also extend it to a more realistic but challenging setting, i.e., generalized FSS, where the pixels of both base and novel classes are required to be determined. The source code is available at github.com/chunbolang/BAM.
Recursive 3D Segmentation of Shoulder Joint with Coarse-scanned MR Image
Authors: Xiaoxiao He, Chaowei Tan, Virak Tan, Kang Li
Date: 2022-03-13 00:00:00

For diagnosis of shoulder illness, it is essential to look at the morphology deviation of scapula and humerus from the medical images that are acquired from Magnetic Resonance (MR) imaging. However, taking high-resolution MR images is time-consuming and costly because the reduction of the physical distance between image slices causes prolonged scanning time. Moreover, due to the lack of training images, images from various sources must be utilized, which creates the issue of high variance across the dataset. Also, there are human errors among the images due to the fact that it is hard to take the spatial relationship into consideration when labeling the 3D image in low resolution. In order to combat all obstacles stated above, we develop a fully automated algorithm for segmenting the humerus and scapula bone from coarsely scanned and low-resolution MR images and a recursive learning framework that iterative utilize the generated labels for reducing the errors among segmentations and increase our dataset set for training the next round network. In this study, 50 MR images are collected from several institutions and divided into five mutually exclusive sets for carrying five-fold cross-validation. Contours that are generated by the proposed method demonstrated a high level of accuracy when compared with ground truth and the traditional method. The proposed neural network and the recursive learning scheme improve the overall quality of the segmentation on humerus and scapula on the low-resolution dataset and reduced incorrect segmentation in the ground truth, which could have a positive impact on finding the cause of shoulder pain and patient's early relief.
Learning Spatio-Temporal Downsampling for Effective Video Upscaling
Authors: Xiaoyu Xiang, Yapeng Tian, Vijay Rengarajan, Lucas Young, Bo Zhu, Rakesh Ranjan
Date: 2022-03-15 00:00:00
Tasks: Quantization

Downsampling is one of the most basic image processing operations. Improper spatio-temporal downsampling applied on videos can cause aliasing issues such as moir\'e patterns in space and the wagon-wheel effect in time. Consequently, the inverse task of upscaling a low-resolution, low frame-rate video in space and time becomes a challenging ill-posed problem due to information loss and aliasing artifacts. In this paper, we aim to solve the space-time aliasing problem by learning a spatio-temporal downsampler. Towards this goal, we propose a neural network framework that jointly learns spatio-temporal downsampling and upsampling. It enables the downsampler to retain the key patterns of the original video and maximizes the reconstruction performance of the upsampler. To make the downsamping results compatible with popular image and video storage formats, the downsampling results are encoded to uint8 with a differentiable quantization layer. To fully utilize the space-time correspondences, we propose two novel modules for explicit temporal propagation and space-time feature rearrangement. Experimental results show that our proposed method significantly boosts the space-time reconstruction quality by preserving spatial textures and motion patterns in both downsampling and upscaling. Moreover, our framework enables a variety of applications, including arbitrary video resampling, blurry frame reconstruction, and efficient video storage.
One Network Doesn't Rule Them All: Moving Beyond Handcrafted Architectures in Self-Supervised Learning
Authors: Sharath Girish, Debadeepta Dey, Neel Joshi, Vibhav Vineet, Shital Shah, Caio Cesar Teodoro Mendes, Abhinav Shrivastava, Yale Song
Date: 2022-03-15 00:00:00
Tasks: All, image-classification, Image Classification, Self-Supervised Learning

The current literature on self-supervised learning (SSL) focuses on developing learning objectives to train neural networks more effectively on unlabeled data. The typical development process involves taking well-established architectures, e.g., ResNet demonstrated on ImageNet, and using them to evaluate newly developed objectives on downstream scenarios. While convenient, this does not take into account the role of architectures which has been shown to be crucial in the supervised learning literature. In this work, we establish extensive empirical evidence showing that a network architecture plays a significant role in SSL. We conduct a large-scale study with over 100 variants of ResNet and MobileNet architectures and evaluate them across 11 downstream scenarios in the SSL setting. We show that there is no one network that performs consistently well across the scenarios. Based on this, we propose to learn not only network weights but also architecture topologies in the SSL regime. We show that "self-supervised architectures" outperform popular handcrafted architectures (ResNet18 and MobileNetV2) while performing competitively with the larger and computationally heavy ResNet50 on major image classification benchmarks (ImageNet-1K, iNat2021, and more). Our results suggest that it is time to consider moving beyond handcrafted architectures in SSL and start thinking about incorporating architecture search into self-supervised learning objectives.
Does Corpus Quality Really Matter for Low-Resource Languages?
Authors: Mikel Artetxe, Itziar Aldabe, Rodrigo Agerri, Olatz Perez-de-Viñaspre, Aitor Soroa
Date: 2022-03-15 00:00:00
Tasks: Representation Learning

The vast majority of non-English corpora are derived from automatically filtered versions of CommonCrawl. While prior work has identified major issues on the quality of these datasets (Kreutzer et al., 2021), it is not clear how this impacts downstream performance. Taking representation learning in Basque as a case study, we explore tailored crawling (manually identifying and scraping websites with high-quality content) as an alternative to filtering CommonCrawl. Our new corpus, called EusCrawl, is similar in size to the Basque portion of popular multilingual corpora like CC100 and mC4, yet it has a much higher quality according to native annotators. For instance, 66% of documents are rated as high-quality for EusCrawl, in contrast with <33% for both mC4 and CC100. Nevertheless, we obtain similar results on downstream NLU tasks regardless of the corpus used for pre-training. Our work suggests that NLU performance in low-resource languages is not primarily constrained by the quality of the data, and other factors like corpus size and domain coverage can play a more important role.