pwc-archive/papers-with-abstracts huggingface dataset:
Multi-layer Trajectory Clustering: A Network Algorithm for Disease Subtyping
Authors: Sanjukta Krishnagopal
Date: 2020-05-29 00:00:00
Tasks: Clustering, Prognosis, Trajectory Clustering, Trajectory Modeling

Many diseases display heterogeneity in clinical features and their progression, indicative of the existence of disease subtypes. Extracting patterns of disease variable progression for subtypes has tremendous application in medicine, for example, in early prognosis and personalized medical therapy. This work present a novel, data-driven, network-based Trajectory Clustering (TC) algorithm for identifying Parkinson's subtypes based on disease trajectory. Modeling patient-variable interactions as a bipartite network, TC first extracts communities of co-expressing disease variables at different stages of progression. Then, it identifies Parkinson's subtypes by clustering similar patient trajectories that are characterized by severity of disease variables through a multi-layer network. Determination of trajectory similarity accounts for direct overlaps between trajectories as well as second-order similarities, i.e., common overlap with a third set of trajectories. This work clusters trajectories across two types of layers: (a) temporal, and (b) ranges of independent outcome variable (representative of disease severity), both of which yield four distinct subtypes. The former subtypes exhibit differences in progression of disease domains (Cognitive, Mental Health etc.), whereas the latter subtypes exhibit different degrees of progression, i.e., some remain mild, whereas others show significant deterioration after 5 years. The TC approach is validated through statistical analyses and consistency of the identified subtypes with medical literature. This generalizable and robust method can easily be extended to other progressive multi-variate disease datasets, and can effectively assist in targeted subtype-specific treatment in the field of personalized medicine.
Reducing Magnetic Resonance Image Spacing by Learning Without Ground-Truth
Authors: Kai Xuan, Liping Si, Lichi Zhang, Zhong Xue, Yining Jiao, Weiwu Yao, Dinggang Shen, Dijia Wu, Qian Wang
Date: 2020-03-27 00:00:00
Tasks: Medical Image Analysis, Super-Resolution

High-quality magnetic resonance (MR) image, i.e., with near isotropic voxel spacing, is desirable in various scenarios of medical image analysis. However, many MR acquisitions use large inter-slice spacing in clinical practice. In this work, we propose a novel deep-learning-based super-resolution algorithm to generate high-resolution (HR) MR images with small slice spacing from low-resolution (LR) inputs of large slice spacing. Notice that most existing deep-learning-based methods need paired LR and HR images to supervise the training, but in clinical scenarios, usually no HR images will be acquired. Therefore, our unique goal herein is to design and train the super-resolution network with no real HR ground-truth. Specifically, two training stages are used in our method. First, HR images of reduced slice spacing are synthesized from real LR images using variational auto-encoder (VAE). Although these synthesized HR images are as realistic as possible, they may still suffer from unexpected morphing induced by VAE, implying that the synthesized HR images cannot be paired with the real LR images in terms of anatomical structure details. In the second stage, we degrade the synthesized HR images to generate corresponding LR images and train a super-resolution network based on these synthesized HR and degraded LR pairs. The underlying mechanism is that such a super-resolution network is less vulnerable to anatomical variability. Experiments on knee MR images successfully demonstrate the effectiveness of our proposed solution to reduce the slice spacing for better rendering.
Nonlinear Dynamic Systems Parameterization Using Interval-Based Global Optimization: Computing Lipschitz Constants and Beyond
Authors: Sebastian A. Nugroho, Ahmad F. Taha, and Vu Hoang
Date: 2020-04-25 00:00:00
Tasks: global-optimization

Numerous state-feedback and observer designs for nonlinear dynamic systems (NDS) have been developed in the past three decades. These designs assume that NDS nonlinearities satisfy one of the following function set classifications: bounded Jacobian, Lipschitz continuity, one-sided Lipschitz, quadratic inner-boundedness, and quadratic boundedness. These function sets are characterized by constant scalars or matrices bounding the NDS' nonlinearities. These constants (i) depend on the NDS' operating region, topology, and parameters, and (ii) are utilized to synthesize observer/controller gains. Unfortunately, there is a near-complete absence of algorithms to compute such bounding constants. In this paper, we develop analytical then computational methods to compute such constants. First, for every function set classification, we derive analytical expressions for these bounding constants through global maximization formulations. Second, we utilize a derivative-free, interval-based global maximization algorithm based on branch-and-bound framework to numerically obtain the bounding constants. Third, we showcase the effectiveness of our approaches to compute the corresponding parameters on some NDS such as highway traffic networks and synchronous generator models.
A Flexible Storage Model for Power Network Optimization
Authors: Frederik Geth, Carleton Coffrin, David M Fobes
Date: 2020-04-29 00:00:00
Tasks: model, Scheduling

This paper proposes a simple and flexible storage model for use in a variety of multi-period optimal power flow problems. The proposed model is designed for research use in a broad assortment of contexts enabled by the following key features: (i) the model can represent the dynamics of an energy buffer at a wide range of scales, from residential battery storage to grid-scale pumped hydro; (ii) it is compatible with both balanced and unbalanced formulations of the power flow equations; (iii) convex relaxations and linear approximations to allow seamless integration of the proposed model into applications where convexity or linearity is required are developed; (iv) a minimalist and standardized data model is presented, to facilitate easy of use by the research community. The proposed model is validated using a proof-of-concept twenty-four hour storage scheduling task that demonstrates the value of the model's key features. An open-source implementation of the model is provided as part of the PowerModels and PowerModelsDistribution optimization toolboxes.
If your P value looks too good to be true, it probably is: Communicating reproducibility and variability in cell biology
Authors: Samuel J. Lord, Katrina B. Velle, R. Dyche Mullins, Lillian K. Fritz-Laylin
Date: 2019-11-08 00:00:00

The cell biology literature is littered with erroneously tiny P values, often the result of evaluating individual cells as independent samples. Because readers use P values and error bars to infer whether a reported difference would likely recur if the experiment were repeated, the sample size N used for statistical tests should actually be the number of times an experiment is performed, not the number of cells (or subcellular structures) analyzed across all experiments. P values calculated using the number of cells do not reflect the reproducibility of the result and are thus highly misleading. To help authors avoid this mistake, we provide examples and practical tutorials for creating figures that communicate both the cell-level variability and the experimental reproducibility.
Detecting, identifying, and localizing radiological material in urban environments using scan statistics
Authors: Michael D. Porter, Alphonse Akakpo
Date: 2020-02-08 00:00:00

A method is proposed, based on scan statistics, to detect, identify, and localize illicit radiological material using mobile sensors in an urban environment. Our method handles varying levels of background radiation that change according to an (unknown) environment. Our method can accurately determine if a source is present along a street segment as well as identify which of six possible sources generated the radiation. Our method can also localize the source, when detected, to within a few seconds. We have presented our results across a range of decision thresholds allowing stakeholders to evaluate the performance at different false alarm rates. Due to the simplicity of our approach, our models can be trained in a few minutes with very little training data and holds the potential to score a run in real-time. Our method was one of the top performing submissions in the 'Detecting Radiological Threats in Urban Areas' competition.
Quantifying socioeconomic activities and weather effects on the global spread of COVID-19 epidemic
Authors: Xinyi Shen, Chenkai Cai, Hui Li
Date: 2020-05-20 00:00:00

The COVID-19 has caused more than three million infections and over two hundred thousand deaths by April 20201. Limiting socioeconomic activities (SA) is among the most adopted governmental mitigating efforts to combat the transmission of the virus, though the degree varies dramatically among different regimes2. This study aims to quantify the contribution from the SA and weather conditions to the transmission of COVID-19 at global scale. Ruling out the unobservable factors including medical facilities and other control policies (MOC) through region-by-time fixed effects3,4, we show that the limiting SA has a leading contribution to lower the reproductive number by 18.3%, while weather conditions, including ultraviolet, relative humidity, and wind explain a smaller amount of variation. Temperature might have a non-monotonic impact on the transmission. We further show that in developed countries5 and China, the SA effect is more pronounced whereas the weather effect is significantly downplayed possibly because people tend to stay indoors most of the time with a controlled climate. We finally estimate the reduced reproductive number and the population spared from infections due to restricting SA at 40,964, 180,336, 174,494, in China, United States, and Europe respectively. From late January to mid-April, all regions, except for China, Australia, and south Korea show a steep upward trend of spared infections due to restricting SA. US and Europe, in particular, show far steeper upward trends of spared infections in the analyzed timeframe, signaling a greater risk of reopening the economy too soon.
Low-rank representation of head impact kinematics: A data-driven emulator
Authors: Patricio Arrue, Nima Toosizadeh, Hessam Babaee, Kaveh Laksari
Date: 2020-04-27 00:00:00
Tasks: Data Augmentation, Injury Prediction, Specificity

Head motion induced by impacts has been deemed as one of the most important measures in brain injury prediction, given that the majority of brain injury metrics use head kinematics as input. Recently, researchers have focused on using fast approaches, such as machine learning, to approximate brain deformation in real-time for early brain injury diagnosis. However, those requires large number of kinematic measurements, and therefore data augmentation is required given the limited on-field measured data available. In this study we present a principal component analysis-based method that emulates an empirical low-rank substitution for head impact kinematics, while requiring low computational cost. In characterizing our existing data set of 537 head impacts, consisting of 6 degrees of freedom measurements, we found that only a few modes, e.g. 15 in the case of angular velocity, is sufficient for accurate reconstruction of the entire data set. Furthermore, these modes are predominantly low frequency since over 70% to 90% of the angular velocity response can be captured by modes that have frequencies under 40Hz. We compared our proposed method against existing impact parametrization methods and showed significantly better performance in injury prediction using a range of kinematic-based metrics -- such as head injury criterion and rotational injury criterion (RIC) -- and brain tissue deformation-metrics -- such as brain angle metric, maximum principal strain (MPS) and axonal fiber strains (FS). In all cases, our approach reproduced injury metrics similar to the ground truth measurements with no significant difference, whereas the existing methods obtained significantly different (p<0.01) values as well as poor injury classification sensitivity and specificity. This emulator will enable us to provide the necessary data augmentation to build a head impact kinematic data set of any size.
Science Concierge: A fast content-based recommendation system for scientific publications
Authors: Titipat Achakulvisut, Daniel E. Acuna, Tulakan Ruangrong, Konrad Kording
Date: 2016-04-04 00:00:00
Tasks: Articles, Recommendation Systems

Finding relevant publications is important for scientists who have to cope with exponentially increasing numbers of scholarly material. Algorithms can help with this task as they help for music, movie, and product recommendations. However, we know little about the performance of these algorithms with scholarly material. Here, we develop an algorithm, and an accompanying Python library, that implements a recommendation system based on the content of articles. Design principles are to adapt to new content, provide near-real time suggestions, and be open source. We tested the library on 15K posters from the Society of Neuroscience Conference 2015. Human curated topics are used to cross validate parameters in the algorithm and produce a similarity metric that maximally correlates with human judgments. We show that our algorithm significantly outperformed suggestions based on keywords. The work presented here promises to make the exploration of scholarly material faster and more accurate.
Automation and occupational mobility: A data-driven network model
Authors: R. Maria del Rio-Chanona, Penny Mealy, Mariano Beguerisse-Díaz, Francois Lafond, J. Doyne Farmer
Date: 2019-06-10 00:00:00

The potential impact of automation on the labor market is a topic that has generated significant interest and concern amongst scholars, policymakers, and the broader public. A number of studies have estimated occupation-specific risk profiles by examining the automatability of associated skills and tasks. However, relatively little work has sought to take a more holistic view on the process of labor reallocation and how employment prospects are impacted as displaced workers transition into new jobs. In this paper, we develop a new data-driven model to analyze how workers move through an empirically derived occupational mobility network in response to automation scenarios which increase labor demand for some occupations and decrease it for others. At the macro level, our model reproduces a key stylized fact in the labor market known as the Beveridge curve and provides new insights for explaining the curve's counter-clockwise cyclicality. At the micro level, our model provides occupation-specific estimates of changes in short and long-term unemployment corresponding to a given automation shock. We find that the network structure plays an important role in determining unemployment levels, with occupations in particular areas of the network having very few job transition opportunities. Such insights could be fruitfully applied to help design more efficient and effective policies aimed at helping workers adapt to the changing nature of the labor market.
BiRank: Towards Ranking on Bipartite Graphs
Authors: Xiangnan He, Ming Gao, Min-Yen Kan, Dingxian Wang
Date: 2017-08-15 00:00:00

The bipartite graph is a ubiquitous data structure that can model the relationship between two entity types: for instance, users and items, queries and webpages. In this paper, we study the problem of ranking vertices of a bipartite graph, based on the graph's link structure as well as prior information about vertices (which we term a query vector). We present a new solution, BiRank, which iteratively assigns scores to vertices and finally converges to a unique stationary ranking. In contrast to the traditional random walk-based methods, BiRank iterates towards optimizing a regularization function, which smooths the graph under the guidance of the query vector. Importantly, we establish how BiRank relates to the Bayesian methodology, enabling the future extension in a probabilistic way. To show the rationale and extendability of the ranking methodology, we further extend it to rank for the more generic n-partite graphs. BiRank's generic modeling of both the graph structure and vertex features enables it to model various ranking hypotheses flexibly. To illustrate its functionality, we apply the BiRank and TriRank (ranking for tripartite graphs) algorithms to two real-world applications: a general ranking scenario that predicts the future popularity of items, and a personalized ranking scenario that recommends items of interest to users. Extensive experiments on both synthetic and real-world datasets demonstrate BiRank's soundness (fast convergence), efficiency (linear in the number of graph edges) and effectiveness (achieving state-of-the-art in the two real-world tasks).
Speech Pseudonymisation Assessment Using Voice Similarity Matrices
Authors: Paul-Gauthier Noé, Jean-François Bonastre, Driss Matrouf, Natalia Tomashenko, Andreas Nautsch, Nicholas Evans
Date: 2020-08-30 00:00:00
Tasks: De-identification, Voice Similarity

The proliferation of speech technologies and rising privacy legislation calls for the development of privacy preservation solutions for speech applications. These are essential since speech signals convey a wealth of rich, personal and potentially sensitive information. Anonymisation, the focus of the recent VoicePrivacy initiative, is one strategy to protect speaker identity information. Pseudonymisation solutions aim not only to mask the speaker identity and preserve the linguistic content, quality and naturalness, as is the goal of anonymisation, but also to preserve voice distinctiveness. Existing metrics for the assessment of anonymisation are ill-suited and those for the assessment of pseudonymisation are completely lacking. Based upon voice similarity matrices, this paper proposes the first intuitive visualisation of pseudonymisation performance for speech signals and two novel metrics for objective assessment. They reflect the two, key pseudonymisation requirements of de-identification and voice distinctiveness.
Slope One Predictors for Online Rating-Based Collaborative Filtering
Authors: Daniel Lemire, Anna Maclachlan
Date: 2007-02-24 00:00:00
Tasks: Collaborative Filtering

Rating-based collaborative filtering is the process of predicting how a user would rate a given item from other user ratings. We propose three related slope one schemes with predictors of the form f(x) = x + b, which precompute the average difference between the ratings of one item and another for users who rated both. Slope one algorithms are easy to implement, efficient to query, reasonably accurate, and they support both online queries and dynamic updates, which makes them good candidates for real-world systems. The basic slope one scheme is suggested as a new reference scheme for collaborative filtering. By factoring in items that a user liked separately from items that a user disliked, we achieve results competitive with slower memory-based schemes over the standard benchmark EachMovie and Movielens data sets while better fulfilling the desiderata of CF applications.
Spatio-temporal Dynamics of Foot-and-Mouth Disease Virus in South America
Authors: Luiz Max Carvalho, Nuno Rodrigues Faria, Andres M. Perez, Marc A. Suchard, Philippe Lemey, Waldemir de Castro Silveira, Andrew Rambaut, Guy Baele
Date: 2015-05-05 00:00:00

Although foot-and-mouth disease virus (FMDV) incidence has decreased in South America over the last years, the pathogen still circulates in the region and the risk of re-emergence in previously FMDV-free areas is a veterinary public health concern. In this paper we merge environmental, epidemiological and genetic data to reconstruct spatiotemporal patterns and determinants of FMDV serotypes A and O dispersal in South America. Our dating analysis suggests that serotype A emerged in South America around 1930, while serotype O emerged around 1990. The rate of evolution for serotype A was significantly higher compared to serotype O. Phylogeographic inference identified two well-connected sub networks of viral flow, one including Venezuela, Colombia and Ecuador; another including Brazil, Uruguay and Argentina. The spread of serotype A was best described by geographic distances, while trade of live cattle was the predictor that best explained serotype O spread. Our findings show that the two serotypes have different underlying evolutionary and spatial dynamics and may pose different threats to control programmes. Key-words: Phylogeography, foot-and-mouth disease virus, South America, animal trade.
Mass-Radius Relationships for Solid Exoplanets
Authors: S. Seager, M. Kuchner, C. Hier-Majumder, B. Militzer
Date: 2007-07-19 00:00:00

We use new interior models of cold planets to investigate the mass-radius relationships of solid exoplanets, considering planets made primarily of iron, silicates, water, and carbon compounds. We find that the mass-radius relationships for cold terrestrial-mass planets of all compositions we considered follow a generic functional form that is not a simple power law: $\log_{10} R_s = k_1 + 1/3 \log_{10}(M_s) - k_2 M_s^{k_3}$ for up to $M_p \approx 20 M_{\oplus}$, where $M_s$ and $R_s$ are scaled mass and radius values. This functional form arises because the common building blocks of solid planets all have equations of state that are well approximated by a modified polytrope of the form $\rho = \rho_0 + c P^n$. We find that highly detailed planet interior models, including temperature structure and phase changes, are not necessary to derive solid exoplanet bulk composition from mass and radius measurements. For solid exoplanets with no substantial atmosphere we have also found that: with 5% fractional uncertainty in planet mass and radius it is possible to distinguish among planets composed predominantly of iron or silicates or water ice but not more detailed compositions; with $\sim$~5% uncertainty water ice planets with $\gtrsim 25%$ water by mass may be identified; the minimum plausible planet size for a given mass is that of a pure iron planet; and carbon planet mass-radius relationships overlap with those of silicate and water planets due to similar zero-pressure densities and equations of state. We propose a definition of "super Earths'' based on the clear distinction in radii between planets with significant gas envelopes and those without.
Algorithmic Theories of Everything
Authors: Juergen Schmidhuber
Date: 2000-11-30 00:00:00
Tasks: Inductive Bias, Philosophy

The probability distribution P from which the history of our universe is sampled represents a theory of everything or TOE. We assume P is formally describable. Since most (uncountably many) distributions are not, this imposes a strong inductive bias. We show that P(x) is small for any universe x lacking a short description, and study the spectrum of TOEs spanned by two Ps, one reflecting the most compact constructive descriptions, the other the fastest way of computing everything. The former derives from generalizations of traditional computability, Solomonoff's algorithmic probability, Kolmogorov complexity, and objects more random than Chaitin's Omega, the latter from Levin's universal search and a natural resource-oriented postulate: the cumulative prior probability of all x incomputable within time t by this optimal algorithm should be 1/t. Between both Ps we find a universal cumulatively enumerable measure that dominates traditional enumerable measures; any such CEM must assign low probability to any universe lacking a short enumerating program. We derive P-specific consequences for evolving observers, inductive reasoning, quantum physics, philosophy, and the expected duration of our universe.