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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Rujun Gao; Hillary E. Merzdorf; Saira Anwar; M. Cynthia Hipwell; +1 Authors

    Text-based open-ended questions in academic formative and summative assessments help students become deep learners and prepare them to understand concepts for a subsequent conceptual assessment. However, grading text-based questions, especially in large courses, is tedious and time-consuming for instructors. Text processing models continue progressing with the rapid development of Artificial Intelligence (AI) tools and Natural Language Processing (NLP) algorithms. Especially after breakthroughs in Large Language Models (LLM), there is immense potential to automate rapid assessment and feedback of text-based responses in education. This systematic review adopts a scientific and reproducible literature search strategy based on the PRISMA process using explicit inclusion and exclusion criteria to study text-based automatic assessment systems in post-secondary education, screening 838 papers and synthesizing 93 studies. To understand how text-based automatic assessment systems have been developed and applied in education in recent years, three research questions are considered. All included studies are summarized and categorized according to a proposed comprehensive framework, including the input and output of the system, research motivation, and research outcomes, aiming to answer the research questions accordingly. Additionally, the typical studies of automated assessment systems, research methods, and application domains in these studies are investigated and summarized. This systematic review provides an overview of recent educational applications of text-based assessment systems for understanding the latest AI/NLP developments assisting in text-based assessments in higher education. Findings will particularly benefit researchers and educators incorporating LLMs such as ChatGPT into their educational activities. Comment: 27 pages, 4 figures, 6 tables

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    Computers and Education: Artificial Intelligence
    Article . 2024 . Peer-reviewed
    License: CC BY NC ND
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    arXiv.org e-Print Archive
    Other literature type . Preprint . 2023
    https://doi.org/10.48550/arxiv...
    Article . 2023
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Computers and Educat...arrow_drop_down
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      Computers and Education: Artificial Intelligence
      Article . 2024 . Peer-reviewed
      License: CC BY NC ND
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      arXiv.org e-Print Archive
      Other literature type . Preprint . 2023
      https://doi.org/10.48550/arxiv...
      Article . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Moon Duchin; Bridget Eileen Tenner;

    "Compactness," or the use of shape as a proxy for fairness, has been a long-running theme in the scrutiny of electoral districts; badly-shaped districts are often flagged as examples of the abuse of power known as gerrymandering. The most popular compactness metrics in the redistricting literature belong to a class of scores that we call contour-based, making heavy use of area and perimeter. This entire class of district scores has some common drawbacks, outlined here. We make the case for discrete shape scores and offer two promising ideas: a cut score and a spanning tree score. We use recent United States redistricting history as a source of examples. No shape metric can work alone as a seal of fairness, but we argue that discrete metrics are better aligned both with the grounding of the redistricting problem in geography and with the computational tools that have recently gained significant traction in the courtroom. Comment: 32 pages, 15 figures; substantially revised

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Political Geographyarrow_drop_down
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    Political Geography
    Article . 2024 . Peer-reviewed
    License: CC BY NC ND
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    arXiv.org e-Print Archive
    Other literature type . Preprint . 2018
    https://doi.org/10.48550/arxiv...
    Article . 2018
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      Political Geography
      Article . 2024 . Peer-reviewed
      License: CC BY NC ND
      Data sources: Crossref
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      arXiv.org e-Print Archive
      Other literature type . Preprint . 2018
      https://doi.org/10.48550/arxiv...
      Article . 2018
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Lejeune, Miguel; Ma, Wenbo;

    We propose a new stochastic emergency network design model that uses a fleet of drones to quickly deliver naxolone in response to opioid overdoses. The network is represented as a collection of M/G/K queuing systems in which the capacity K of each system is a decision variable and the service time is modelled as a decision-dependent random variable. The model is an optimization-based queuing problem which locates fixed (drone bases) and mobile (drones) servers and determines the drone dispatching decisions, and takes the form of a nonlinear integer problem, which is intractable in its original form. We develop an efficient reformulation and algorithmic framework. Our approach reformulates the multiple nonlinearities (fractional, polynomial, exponential, factorial terms) to give a mixed-integer linear programming (MILP) formulation. We demonstrate its generalizablity and show that the problem of minimizing the average response time of a network of M/G/K queuing systems with unknown capacity K is always MILP-representable. We design two algorithms and demonstrate that the outer approximation branch-and-cut method is the most efficient and scales well. The analysis based on real-life overdose data reveals that drones can in Virginia Beach: 1) decrease the response time by 78%, 2) increase the survival chance by 432%, 3) save up to 34 additional lives per year, and 4) provide annually up to 287 additional quality-adjusted life years.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
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    arXiv.org e-Print Archive
    Other literature type . Preprint . 2022
    https://doi.org/10.48550/arxiv...
    Article . 2022
    License: CC BY
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    SSRN Electronic Journal
    Article . 2024 . Peer-reviewed
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      arXiv.org e-Print Archive
      Other literature type . Preprint . 2022
      https://doi.org/10.48550/arxiv...
      Article . 2022
      License: CC BY
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      SSRN Electronic Journal
      Article . 2024 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Papanicolaou, N C; Christov, I C;

    Sixth-order boundary value problems (BVPs) arise in thin-film flows with a surface that has elastic bending resistance. To solve such problems, we first derive a complete set of odd and even orthonormal eigenfunctions -- resembling trigonometric sines and cosines, as well as the so-called ``beam'' functions. These functions intrinsically satisfy boundary conditions (BCs) of relevance to thin-film flows, since they are the solutions of a self-adjoint sixth-order Sturm--Liouville BVP with the same BCs. Next, we propose a Galerkin spectral approach for sixth-order problems; namely the sought function as well as all its derivatives and terms appearing in the differential equation are expanded into an infinite series with respect to the derived complete orthonormal (CON) set of eigenfunctions. The unknown coefficients in the series expansion are determined by solving the algebraic system derived by taking successive inner products with each member of the CON set of eigenfunctions. The proposed method and its convergence are demonstrated by solving two model sixth-order BVPs. Comment: 18 pages, 5 figures, IoP jpconf style; v2: correct minor typos, to appear in the proceedings of the Fifteenth Conference of the Euro-American Consortium for Promoting the Application of Mathematics in Technical and Natural Sciences (AMiTaNS'23)

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Journal of Physics :...arrow_drop_down
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    Journal of Physics : Conference Series
    Article . 2023 . Peer-reviewed
    License: CC BY
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    arXiv.org e-Print Archive
    Other literature type . Preprint . 2023
    https://doi.org/10.48550/arxiv...
    Article . 2023
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Journal of Physics :...arrow_drop_down
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      Journal of Physics : Conference Series
      Article . 2023 . Peer-reviewed
      License: CC BY
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      arXiv.org e-Print Archive
      Other literature type . Preprint . 2023
      https://doi.org/10.48550/arxiv...
      Article . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Barrett, Jeffrey; Goldbring, Isaac;

    Using the tools of nonstandard analysis, we develop and present an alternative formulation of Bohmian mechanics. This approach allows one to describe a broader assortment of physical systems than the standard formulation of the theory. It also allows one to make predictions in more situations. We motivate the nonstandard formulation with a Bohmian example system that exhibits behavior akin to Earman's (1986) classical space invaders and reverse space invaders. We then use the example to illustrate how the alternative formulation of Bohmian mechanics works. Comment: 16 pages; first draft; comments welcome!

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    arXiv.org e-Print Archive
    Other literature type . Preprint . 2023
    The British Journal for the Philosophy of Science
    Article . 2023 . Peer-reviewed
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      arXiv.org e-Print Archive
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    Authors: Zhaoyi Sun; Mingquan Lin; Qingqing Zhu; Qianqian Xie; +3 Authors

    Computer-assisted diagnostic and prognostic systems of the future should be capable of simultaneously processing multimodal data. Multimodal deep learning (MDL), which involves the integration of multiple sources of data, such as images and text, has the potential to revolutionize the analysis and interpretation of biomedical data. However, it only caught researchers' attention recently. To this end, there is a critical need to conduct a systematic review on this topic, identify the limitations of current work, and explore future directions. In this scoping review, we aim to provide a comprehensive overview of the current state of the field and identify key concepts, types of studies, and research gaps with a focus on biomedical images and texts joint learning, mainly because these two were the most commonly available data types in MDL research. This study reviewed the current uses of multimodal deep learning on five tasks: (1) Report generation, (2) Visual question answering, (3) Cross-modal retrieval, (4) Computer-aided diagnosis, and (5) Semantic segmentation. Our results highlight the diverse applications and potential of MDL and suggest directions for future research in the field. We hope our review will facilitate the collaboration of natural language processing (NLP) and medical imaging communities and support the next generation of decision-making and computer-assisted diagnostic system development. Comment: This paper has been accepted by the Journal of Biomedical Informatics

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    Europe PubMed Central
    Other literature type . 2023
    Data sources: PubMed Central
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    arXiv.org e-Print Archive
    Other literature type . Preprint . 2023
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Journal of Biomedical Informatics
    Article . 2023 . Peer-reviewed
    License: Elsevier TDM
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    https://doi.org/10.48550/arxiv...
    Article . 2023
    License: arXiv Non-Exclusive Distribution
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      Journal of Biomedical Informatics
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    Authors: Maciej J. Capiński; Shane Kepley; J.D. Mireles James;

    This paper considers two point boundary value problems for conservative systems defined in multiple coordinate systems, and develops a flexible a-posteriori framework for computer assisted existence proofs. Our framework is applied to the study collision and near collision orbits in the circular restricted three body problem. In this case the coordinate systems are the standard rotating coordinates, and the two Levi-Civita coordinate systems regularizing collisions with each of the massive primaries. The proposed framework is used to prove the existence of a number of orbits which have long been studied numerically in the celestial mechanics literature, but for which there are no existing analytical proofs at the mass and energy values considered here. These include transverse ejection/collisions from one primary body to the other, Str\"{o}mgren's assymptotic periodic orbits (transverse homoclinics for $L_{4,5}$), families of periodic orbits passing through collision, and orbits connecting $L_4$ to ejection or collision. Comment: 58 pages, 9 figures

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    AbstractProtein engineering is an emerging field in biotechnology that has the potential to revolutionize various areas, such as antibody design, drug discovery, food security, ecology, and more. However, the mutational space involved is too vast to be handled through experimental means alone. Leveraging accumulative protein databases, machine learning (ML) models, particularly those based on natural language processing (NLP), have considerably expedited protein engineering. Moreover, advances in topological data analysis (TDA) and artificial intelligence-based protein structure prediction, such as AlphaFold2, have made more powerful structure-based ML-assisted protein engineering strategies possible. This review aims to offer a comprehensive, systematic, and indispensable set of methodological components, including TDA and NLP, for protein engineering and to facilitate their future development.

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    Briefings in Bioinformatics
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    Authors: Randall Pruim; Maria-Cristiana Gîrjău; Nicholas J. Horton;

    Many data science students and practitioners don't see the value in making time to learn and adopt good coding practices as long as the code "works". However, code standards are an important part of modern data science practice, and they play an essential role in the development of data acumen. Good coding practices lead to more reliable code and save more time than they cost, making them important even for beginners. We believe that principled coding is vital for quality data science practice. To effectively instill these practices within academic programs, instructors and programs need to begin establishing these practices early, to reinforce them often, and to hold themselves to a higher standard while guiding students. We describe key aspects of good coding practices for data science, illustrating with examples in R and in Python, though similar standards are applicable to other software environments. Practical coding guidelines are organized into a top ten list.

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    Authors: Ramteja Sajja; Yusuf Sermet; David Cwiertny; Ibrahim Demir;

    Miscommunication and communication challenges between instructors and students represents one of the primary barriers to post-secondary learning. Students often avoid or miss opportunities to ask questions during office hours due to insecurities or scheduling conflicts. Moreover, students need to work at their own pace to have the freedom and time for the self-contemplation needed to build conceptual understanding and develop creative thinking skills. To eliminate barriers to student engagement, academic institutions need to redefine their fundamental approach to education by proposing flexible educational pathways that recognize continuous learning. To this end, we developed an AI-augmented intelligent educational assistance framework based on a power language model (i.e., GPT-3) that automatically generates course-specific intelligent assistants regardless of discipline or academic level. The virtual intelligent teaching assistant (TA) system will serve as a voice-enabled helper capable of answering course-specific questions concerning curriculum, logistics and course policies. It is envisioned to improve access to course-related information for the students and reduce logistical workload for the instructors and TAs. Its GPT-3-based knowledge discovery component as well as the generalized system architecture is presented accompanied by a methodical evaluation of the system accuracy and performance. Comment: 26 pages, 7 figures, 5 tables

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    International Journal of Educational Technology in Higher Education
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      International Journal of Educational Technology in Higher Education
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Rujun Gao; Hillary E. Merzdorf; Saira Anwar; M. Cynthia Hipwell; +1 Authors

    Text-based open-ended questions in academic formative and summative assessments help students become deep learners and prepare them to understand concepts for a subsequent conceptual assessment. However, grading text-based questions, especially in large courses, is tedious and time-consuming for instructors. Text processing models continue progressing with the rapid development of Artificial Intelligence (AI) tools and Natural Language Processing (NLP) algorithms. Especially after breakthroughs in Large Language Models (LLM), there is immense potential to automate rapid assessment and feedback of text-based responses in education. This systematic review adopts a scientific and reproducible literature search strategy based on the PRISMA process using explicit inclusion and exclusion criteria to study text-based automatic assessment systems in post-secondary education, screening 838 papers and synthesizing 93 studies. To understand how text-based automatic assessment systems have been developed and applied in education in recent years, three research questions are considered. All included studies are summarized and categorized according to a proposed comprehensive framework, including the input and output of the system, research motivation, and research outcomes, aiming to answer the research questions accordingly. Additionally, the typical studies of automated assessment systems, research methods, and application domains in these studies are investigated and summarized. This systematic review provides an overview of recent educational applications of text-based assessment systems for understanding the latest AI/NLP developments assisting in text-based assessments in higher education. Findings will particularly benefit researchers and educators incorporating LLMs such as ChatGPT into their educational activities. Comment: 27 pages, 4 figures, 6 tables

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    Computers and Education: Artificial Intelligence
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    Authors: Moon Duchin; Bridget Eileen Tenner;

    "Compactness," or the use of shape as a proxy for fairness, has been a long-running theme in the scrutiny of electoral districts; badly-shaped districts are often flagged as examples of the abuse of power known as gerrymandering. The most popular compactness metrics in the redistricting literature belong to a class of scores that we call contour-based, making heavy use of area and perimeter. This entire class of district scores has some common drawbacks, outlined here. We make the case for discrete shape scores and offer two promising ideas: a cut score and a spanning tree score. We use recent United States redistricting history as a source of examples. No shape metric can work alone as a seal of fairness, but we argue that discrete metrics are better aligned both with the grounding of the redistricting problem in geography and with the computational tools that have recently gained significant traction in the courtroom. Comment: 32 pages, 15 figures; substantially revised

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    Political Geography
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    Authors: Lejeune, Miguel; Ma, Wenbo;

    We propose a new stochastic emergency network design model that uses a fleet of drones to quickly deliver naxolone in response to opioid overdoses. The network is represented as a collection of M/G/K queuing systems in which the capacity K of each system is a decision variable and the service time is modelled as a decision-dependent random variable. The model is an optimization-based queuing problem which locates fixed (drone bases) and mobile (drones) servers and determines the drone dispatching decisions, and takes the form of a nonlinear integer problem, which is intractable in its original form. We develop an efficient reformulation and algorithmic framework. Our approach reformulates the multiple nonlinearities (fractional, polynomial, exponential, factorial terms) to give a mixed-integer linear programming (MILP) formulation. We demonstrate its generalizablity and show that the problem of minimizing the average response time of a network of M/G/K queuing systems with unknown capacity K is always MILP-representable. We design two algorithms and demonstrate that the outer approximation branch-and-cut method is the most efficient and scales well. The analysis based on real-life overdose data reveals that drones can in Virginia Beach: 1) decrease the response time by 78%, 2) increase the survival chance by 432%, 3) save up to 34 additional lives per year, and 4) provide annually up to 287 additional quality-adjusted life years.

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    Authors: Papanicolaou, N C; Christov, I C;

    Sixth-order boundary value problems (BVPs) arise in thin-film flows with a surface that has elastic bending resistance. To solve such problems, we first derive a complete set of odd and even orthonormal eigenfunctions -- resembling trigonometric sines and cosines, as well as the so-called ``beam'' functions. These functions intrinsically satisfy boundary conditions (BCs) of relevance to thin-film flows, since they are the solutions of a self-adjoint sixth-order Sturm--Liouville BVP with the same BCs. Next, we propose a Galerkin spectral approach for sixth-order problems; namely the sought function as well as all its derivatives and terms appearing in the differential equation are expanded into an infinite series with respect to the derived complete orthonormal (CON) set of eigenfunctions. The unknown coefficients in the series expansion are determined by solving the algebraic system derived by taking successive inner products with each member of the CON set of eigenfunctions. The proposed method and its convergence are demonstrated by solving two model sixth-order BVPs. Comment: 18 pages, 5 figures, IoP jpconf style; v2: correct minor typos, to appear in the proceedings of the Fifteenth Conference of the Euro-American Consortium for Promoting the Application of Mathematics in Technical and Natural Sciences (AMiTaNS'23)

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    Authors: Barrett, Jeffrey; Goldbring, Isaac;

    Using the tools of nonstandard analysis, we develop and present an alternative formulation of Bohmian mechanics. This approach allows one to describe a broader assortment of physical systems than the standard formulation of the theory. It also allows one to make predictions in more situations. We motivate the nonstandard formulation with a Bohmian example system that exhibits behavior akin to Earman's (1986) classical space invaders and reverse space invaders. We then use the example to illustrate how the alternative formulation of Bohmian mechanics works. Comment: 16 pages; first draft; comments welcome!

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    Authors: Zhaoyi Sun; Mingquan Lin; Qingqing Zhu; Qianqian Xie; +3 Authors

    Computer-assisted diagnostic and prognostic systems of the future should be capable of simultaneously processing multimodal data. Multimodal deep learning (MDL), which involves the integration of multiple sources of data, such as images and text, has the potential to revolutionize the analysis and interpretation of biomedical data. However, it only caught researchers' attention recently. To this end, there is a critical need to conduct a systematic review on this topic, identify the limitations of current work, and explore future directions. In this scoping review, we aim to provide a comprehensive overview of the current state of the field and identify key concepts, types of studies, and research gaps with a focus on biomedical images and texts joint learning, mainly because these two were the most commonly available data types in MDL research. This study reviewed the current uses of multimodal deep learning on five tasks: (1) Report generation, (2) Visual question answering, (3) Cross-modal retrieval, (4) Computer-aided diagnosis, and (5) Semantic segmentation. Our results highlight the diverse applications and potential of MDL and suggest directions for future research in the field. We hope our review will facilitate the collaboration of natural language processing (NLP) and medical imaging communities and support the next generation of decision-making and computer-assisted diagnostic system development. Comment: This paper has been accepted by the Journal of Biomedical Informatics

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    Authors: Maciej J. Capiński; Shane Kepley; J.D. Mireles James;

    This paper considers two point boundary value problems for conservative systems defined in multiple coordinate systems, and develops a flexible a-posteriori framework for computer assisted existence proofs. Our framework is applied to the study collision and near collision orbits in the circular restricted three body problem. In this case the coordinate systems are the standard rotating coordinates, and the two Levi-Civita coordinate systems regularizing collisions with each of the massive primaries. The proposed framework is used to prove the existence of a number of orbits which have long been studied numerically in the celestial mechanics literature, but for which there are no existing analytical proofs at the mass and energy values considered here. These include transverse ejection/collisions from one primary body to the other, Str\"{o}mgren's assymptotic periodic orbits (transverse homoclinics for $L_{4,5}$), families of periodic orbits passing through collision, and orbits connecting $L_4$ to ejection or collision. Comment: 58 pages, 9 figures

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    AbstractProtein engineering is an emerging field in biotechnology that has the potential to revolutionize various areas, such as antibody design, drug discovery, food security, ecology, and more. However, the mutational space involved is too vast to be handled through experimental means alone. Leveraging accumulative protein databases, machine learning (ML) models, particularly those based on natural language processing (NLP), have considerably expedited protein engineering. Moreover, advances in topological data analysis (TDA) and artificial intelligence-based protein structure prediction, such as AlphaFold2, have made more powerful structure-based ML-assisted protein engineering strategies possible. This review aims to offer a comprehensive, systematic, and indispensable set of methodological components, including TDA and NLP, for protein engineering and to facilitate their future development.

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    Briefings in Bioinformatics
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      Briefings in Bioinformatics
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    Authors: Randall Pruim; Maria-Cristiana Gîrjău; Nicholas J. Horton;

    Many data science students and practitioners don't see the value in making time to learn and adopt good coding practices as long as the code "works". However, code standards are an important part of modern data science practice, and they play an essential role in the development of data acumen. Good coding practices lead to more reliable code and save more time than they cost, making them important even for beginners. We believe that principled coding is vital for quality data science practice. To effectively instill these practices within academic programs, instructors and programs need to begin establishing these practices early, to reinforce them often, and to hold themselves to a higher standard while guiding students. We describe key aspects of good coding practices for data science, illustrating with examples in R and in Python, though similar standards are applicable to other software environments. Practical coding guidelines are organized into a top ten list.

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    Authors: Ramteja Sajja; Yusuf Sermet; David Cwiertny; Ibrahim Demir;

    Miscommunication and communication challenges between instructors and students represents one of the primary barriers to post-secondary learning. Students often avoid or miss opportunities to ask questions during office hours due to insecurities or scheduling conflicts. Moreover, students need to work at their own pace to have the freedom and time for the self-contemplation needed to build conceptual understanding and develop creative thinking skills. To eliminate barriers to student engagement, academic institutions need to redefine their fundamental approach to education by proposing flexible educational pathways that recognize continuous learning. To this end, we developed an AI-augmented intelligent educational assistance framework based on a power language model (i.e., GPT-3) that automatically generates course-specific intelligent assistants regardless of discipline or academic level. The virtual intelligent teaching assistant (TA) system will serve as a voice-enabled helper capable of answering course-specific questions concerning curriculum, logistics and course policies. It is envisioned to improve access to course-related information for the students and reduce logistical workload for the instructors and TAs. Its GPT-3-based knowledge discovery component as well as the generalized system architecture is presented accompanied by a methodical evaluation of the system accuracy and performance. Comment: 26 pages, 7 figures, 5 tables

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    International Journal of Educational Technology in Higher Education
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