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  1. Hawrylycz, Michael (Ed.)
    Studies comparing single cell RNA-Seq (scRNA-Seq) data between conditions mainly focus on differences in the proportion of cell types or on differentially expressed genes. In many cases these differences are driven by changes in cell interactions which are challenging to infer without spatial information. To determine cell-cell interactions that differ between conditions we developed the Cell Interaction Network Inference (CINS) pipeline. CINS combines Bayesian network analysis with regression-based modeling to identify differential cell type interactions and the proteins that underlie them. We tested CINS on a disease case control and on an aging mouse dataset. In both cases CINS correctly identifies cell type interactions and the ligands involved in these interactions improving on prior methods suggested for cell interaction predictions. We performed additional mouse aging scRNA-Seq experiments which further support the interactions identified by CINS.
    Free, publicly-accessible full text available September 12, 2023
  2. Prior research has highlighted opportunities for technology to better support the tabletop game experience in offline and online settings, but little work has focused on the social aspect of tabletop gaming. We investigated the social and collaborative aspects of tabletop gaming in the unique context of “social distancing” during the 2020 COVID-19 pandemic to shed light on the experience of remote tabletop gaming. With a multi-method qualitative approach (including digital ethnography and in-depth interviews), we empirically studied how people appropriate existing technologies and adapt their offline practices to play tabletop games remotely. We identify three themes that describe people’s game and social experience during remote play: creating a shared tabletop environment (shared space), enabling a collective understanding (shared information and awareness), and facilitating a communal temporal experience (shared time). We reflect on challenges and design opportunities for a better experience in the age of remote collaboration.
  3. Swing oscillation is widely observed among indoor miniature autonomous blimps (MABs) due to their underactuated design and unique aerodynamic shape. This paper presents the modeling, identification and control system design that reduce the swing oscillation of an MAB during hovering flight. We establish a dynamic model to describe the swing motion of the MAB. The model parameters are identified from both physical measurements, computer modeling and experimental data captured during flight. A control system is designed to stabilize the swing motion with features including low latency and center-of-mass (CM) position estimation. The modeling and control methods are verified with the Georgia-Tech Miniature Autonomous Blimp (GT-MAB) during hovering flight. The experimental results show that the proposed methods can effectively reduce the swing oscillation of GT-MAB.
  4. We investigate the mechanical response of packings of purely repulsive, frictionless disks to quasistatic deformations. The deformations include simple shear strain at constant packing fraction and at constant pressure, “polydispersity” strain (in which we change the particle size distribution) at constant packing fraction and at constant pressure, and isotropic compression. For each deformation, we show that there are two classes of changes in the interparticle contact networks: jump changes and point changes. Jump changes occur when a contact network becomes mechanically unstable, particles “rearrange”, and the potential energy (when the strain is applied at constant packing fraction) or enthalpy (when the strain is applied at constant pressure) and all derivatives are discontinuous. During point changes, a single contact is either added to or removed from the contact network. For repulsive linear spring interactions, second- and higher-order derivatives of the potential energy/enthalpy are discontinuous at a point change, while for Hertzian interactions, third- and higher-order derivatives of the potential energy/enthalpy are discontinuous. We illustrate the importance of point changes by studying the transition from a hexagonal crystal to a disordered crystal induced by applying polydispersity strain. During this transition, the system only undergoes point changes, with no jump changes. We emphasizemore »that one must understand point changes, as well as jump changes, to predict the mechanical properties of jammed packings.« less
  5. Artificial intelligence algorithms have been used to enhance a wide variety of products and services, including assisting human decision making in high-stake contexts. However, these algorithms are complex and have trade-offs, notably between prediction accuracy and fairness to population subgroups. This makes it hard for designers to understand algorithms and design products or services in a way that respects users' goals, values, and needs. We proposed a method to help designers and users explore algorithms, visualize their trade-offs, and select algorithms with trade-offs consistent with their goals and needs. We evaluated our method on the problem of predicting criminal defendants' likelihood to re-offend through (i) a large-scale Amazon Mechanical Turk experiment, and (ii) in-depth interviews with domain experts. Our evaluations show that our method can help designers and users of these systems better understand and navigate algorithmic trade-offs. This paper contributes a new way of providing designers the ability to understand and control the outcomes of algorithmic systems they are creating.
  6. Several methods were developed to mine gene–gene relationships from expression data. Examples include correlation and mutual information methods for coexpression analysis, clustering and undirected graphical models for functional assignments, and directed graphical models for pathway reconstruction. Using an encoding for gene expression data, followed by deep neural networks analysis, we present a framework that can successfully address all of these diverse tasks. We show that our method, convolutional neural network for coexpression (CNNC), improves upon prior methods in tasks ranging from predicting transcription factor targets to identifying disease-related genes to causality inference. CNNC’s encoding provides insights about some of the decisions it makes and their biological basis. CNNC is flexible and can easily be extended to integrate additional types of genomics data, leading to further improvements in its performance.

  7. Background The novel coronavirus SARS-CoV-2 and its associated disease, COVID-19, have caused worldwide disruption, leading countries to take drastic measures to address the progression of the disease. As SARS-CoV-2 continues to spread, hospitals are struggling to allocate resources to patients who are most at risk. In this context, it has become important to develop models that can accurately predict the severity of infection of hospitalized patients to help guide triage, planning, and resource allocation. Objective The aim of this study was to develop accurate models to predict the mortality of hospitalized patients with COVID-19 using basic demographics and easily obtainable laboratory data. Methods We performed a retrospective study of 375 hospitalized patients with COVID-19 in Wuhan, China. The patients were randomly split into derivation and validation cohorts. Regularized logistic regression and support vector machine classifiers were trained on the derivation cohort, and accuracy metrics (F1 scores) were computed on the validation cohort. Two types of models were developed: the first type used laboratory findings from the entire length of the patient’s hospital stay, and the second type used laboratory findings that were obtained no later than 12 hours after admission. The models were further validated on a multicenter external cohortmore »of 542 patients. Results Of the 375 patients with COVID-19, 174 (46.4%) died of the infection. The study cohort was composed of 224/375 men (59.7%) and 151/375 women (40.3%), with a mean age of 58.83 years (SD 16.46). The models developed using data from throughout the patients’ length of stay demonstrated accuracies as high as 97%, whereas the models with admission laboratory variables possessed accuracies of up to 93%. The latter models predicted patient outcomes an average of 11.5 days in advance. Key variables such as lactate dehydrogenase, high-sensitivity C-reactive protein, and percentage of lymphocytes in the blood were indicated by the models. In line with previous studies, age was also found to be an important variable in predicting mortality. In particular, the mean age of patients who survived COVID-19 infection (50.23 years, SD 15.02) was significantly lower than the mean age of patients who died of the infection (68.75 years, SD 11.83; P<.001). Conclusions Machine learning models can be successfully employed to accurately predict outcomes of patients with COVID-19. Our models achieved high accuracies and could predict outcomes more than one week in advance; this promising result suggests that these models can be highly useful for resource allocation in hospitals.« less
  8. Recently, significant efforts are made to explore device-free human activity recognition techniques that utilize the information collected by existing indoor wireless infrastructures without the need for the monitored subject to carry a dedicated device. Most of the existing work, however, focuses their attention on the analysis of the signal received by a single device. In practice, there are usually multiple devices "observing" the same subject. Each of these devices can be regarded as an information source and provides us an unique "view" of the observed subject. Intuitively, if we can combine the complementary information carried by the multiple views, we will be able to improve the activity recognition accuracy. Towards this end, we propose DeepMV, a unified multi-view deep learning framework, to learn informative representations of heterogeneous device-free data. DeepMV can combine different views' information weighted by the quality of their data and extract commonness shared across different environments to improve the recognition performance. To evaluate the proposed DeepMV model, we set up a testbed using commercialized WiFi and acoustic devices. Experiment results show that DeepMV can effectively recognize activities and outperform the state-of-the-art human activity recognition methods.