A Comprehensive Pytorch Framework to Benchmark CNN and ViT Models

Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) have shown remarkable performance in computer vision tasks, including object detection and image recognition. These models have evolved significantly in architecture, efficiency, and versatility. Concurrently, deep learning frameworks have diversified, with versions that often complicate reproducibility and unified benchmarking. We propose ConVision Benchmark, a comprehensive framework in PyTorch, to standardize the implementation and evaluation of state-of-the-art CNN and ViT models. This framework addresses common challenges such as version mismatches and inconsistent validation metrics. As a proof of concept, we perform an extensive benchmark analysis on a COVID-19 dataset, encompassing nearly 200 CNN and ViT models in which DenseNet-161 and MaxViT-Tiny achieve exceptional accuracy with a peak performance of around 95%. Although we primarily used the COVID-19 dataset for image classification, the framework is adaptable to a variety of datasets, enhancing its applicability across different domains. Our methodology includes rigorous performance evaluations, highlighting metrics such as accuracy, precision, recall, F1 score, and computational efficiency (FLOPs, MACs, CPU, and GPU latency). The ConVision Benchmark facilitates a comprehensive understanding of model efficacy, aiding researchers in deploying high-performance models for diverse applications

Art, Object, Religion, & Relationality / Religion, Art, Objects (of Study)

Art and Object Central to this journal’s focus are things—things of many sorts, from household objects to high art. Today, more so than when Material Religion published its first issue in 2005, scholars are accustomed to considering the “stuff” of religion. As David Morgan, one of the journal’s founding editors, has argued, an unspecific thing becomes a particular object as humans assign it value and meaning—but things may still retain meaningful potentiality beyond and outside of the meanings humans place on them.1 Scholars now recognize that things are central to religious traditions, and that the processes of meaning-making with and about things are important subjects in the study of religion. There is collective agreement that objects hold value for individuals and communities as receptacles of history, memory, and tradition. Over the past few decades, understandings of religion as a category that, for so long, privileged belief over other facets of human religious experience—to the detriment of (our understandings of) non-Protestant religions—have given way to more expansive definitions of religion encompassing practices, bodies, and material culture.This accepted article is published as Dees, S., Art, Object, Religion, & Relationality / Religion, Art, Objects (of Study). Material Religion: The Journal of Objects, Art and Belief., March 2024, Latest Articles; https://doi.org/10.1080/17432200.2024.2320595. Posted with permission

Improvement of Surimi Gel from Frozen-Stored Silver Carp

Silver Carp (SC) is an under-utilized, invasive species in North American river systems. In this study, the synergistic effects of manufactured Microfiber (MMF), Transglutaminase (TG), and chicken skin collagen (CLG)) to enhance surimi gel quality from frozen SC were studied. The gel strength, textural properties, rheological properties, water-holding capacity (WHC), water mobility, microstructure, and protein composition of the gel samples were determined to assess the impact of the additives individually and synergistically. The results suggested that TG had the most pronounced effect on the surimi gel properties by promoting protein cross-linking. Synergistic effects between TG, MMF, and CLG can bring effective gel property enhancement larger than the individual effect of each additive alone. With the established response-surface models, the combination of CLG and MMF can be optimized to produce surimi gels with less TG but comparable in properties to that of the optimal result with high TG usage. The findings of this study provided a technical foundation for making high-quality surimi gel products out of frozen-stored SC with synergistic utilization of additives, which could serve as guidelines for the industrial development of new surimi products.This article is published as Yang, Jingyi, Xiliang Yu, Xiuping Dong, and Chenxu Yu. "Improvement of Surimi Gel from Frozen-Stored Silver Carp." Gels 10, no. 6 (2024): 374. doi: https://doi.org/10.3390/gels10060374. © 2024 by the authors. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/)

Beyond This Door: Photographic Vision and Carceral Experience

This chapter details the experience of teaching photography at Westville Correctional Facility in Westville, Indiana as part of the Moreau College Initiative, an academic collaboration between Holy Cross College and the University of Notre Dame in partnership with the Indiana Department of Correction. The limitations of using cameras in prison provided teaching challenges for logistics and photographic content. However, students worked within constraints to make creative photography that was deeply personal, reflecting their experiences and aspirations.This accepted book chapter is published as Hume, E. Beyond This Door: Photographic Vision and Carceral Experience,” In Higher Education and the Carceral State: Transforming Together, ed. Annie Buckley, Routledge. 2024, Chapter 13;11. https://doi.org/10.4324/9781003394426-16

Formal specifications for cyber-physical systems

Formal methods are used extensively in software and hardware verification, quantum system verification, ensuring autonomous vehicle safety, and protecting security-critical software from threats. However, the validity of formal methods critically depends on the correctness of specifications. This thesis contributes to (a) developing a new specification language, Mission-time Linear Temporal Logic Multi-type (MLTLM), to ease writing and verifying specifications that involve multiple types, e.g., different time scales, (b) solving for the satisfiability and maximum satisfiability of two popular specification languages, MLTL and LTL to aid specification debugging and optimally design systems that are safe by construction. Chapter 2 introduces MLTLM as a specification language and provides many examples of system specifications that involve different types. We prove the succinctness of MLTLM and develop translations to MLTL that are minimally succinct and equivalent to MLTL. Lastly, we integrate an MLTLM runtime verification (RV) monitor into the popular R2U2 MLTL RV monitor. Comparisons between the optimal MLTL translations and MLTLM specifications on the native MLTL and MLTLM RV monitors suggest that the latter results in substantially lower hardware resource usage and verification times. Chapter 3 explores solving for the maximum satisfiability (MaxSAT) of MLTL specifications. Given a set of specifications, MaxSAT solves for the subset of the largest cardinality that is simultaneously satisfiable. MaxSAT is important for feature prioritization and cost analysis while designing systems that are safe by construction. We develop a new algorithm that does fast translations to Boolean logic, and use off-the-shelf Boolean MaxSAT solvers to solve the MLTL MaxSAT problem. Results show that MLTL satisfiability checking is faster using the Boolean translations of this work compared to other recent approaches. Chapter 4 provides a solution to the MaxSAT of LTL specifications. Whereas MLTL specifications have equivalent Boolean logic formulas, such translations are unavailable for LTL. Hence, we approach the problem using core-based techniques. We modify an existing algorithm to extract the unsatisfiable core from a set of LTL formulas and then we use the unsatisfiable core with a Boolean MaxSAT algorithm to solve for LTL MaxSAT. Compared to the original algorithm, the core-extraction feature has minimal overhead ($\mathcal O(1)$). The LTL MaxSAT solver is applied to two real design instances: robot navigation and power load distribution, and on randomly generated instances

Training to increase student perceptions of fairness in peer assessment

Peer assessment training was motivated, developed and evaluated to address fairness in higher education group learning. Team-centric pedagogies, such as team-based learning have been shown to improve engagement and learning outcomes. For many instructors using teams, peer assessments are integral for monitoring team performance and ensuring accountability. However, students often view the peer assessment process as unfair due to the potential for biased ratings or perceived lack of peer qualification. Peer assessment fairness training was developed by combining lessons learned from focus groups with instructors, students and learning experts with bias-reducing techniques found to be effective in other settings. The resulting training underwent a summative evaluation across multiple classrooms. Results indicated that students had higher perceptions of fairness in their peer assessments after training. Students were also more confident in their and their peers’ fair rating skills. These results indicate that classroom training could be used to increase peer assessment fairness. Fairer peer assessment provides enhanced access to active and team learning benefits to a broader range of students, potentially impacting the retention of a more diverse population of practitioners in the field.This is a manuscript of the article Published as H. Stonewall, Jacklin, Michael C. Dorneich, and Jane Rongerude. "Training to increase student perceptions of fairness in peer assessment." Assessment & Evaluation in Higher Education (2024): 1-17. doi: https://doi.org/10.1080/02602938.2024.2327858. Posted with Permission. Copyright 2024 The Authors. CC BY-NC

Guiding principles and processes of scholarship of teaching and learning and scholarship of practice

The concepts of scholarship of teaching and learning and the scholarship of practice are relatively new; therefore, their value within student affairs and institutions of higher education may be questioned. Unfamiliarity with these activities may also impede student affairs graduate faculty and scholar-practitioners from engaging in this work. In this article, we outline why these activities should be viewed as scholarship and demonstrate how student affairs faculty and practitioners may already possess the skills needed to engage in this work.This article is published as Gansemer-Topf, A. M., Mendee, A., & Braxton, J. M. (2024). Guiding principles and processes of scholarship of teaching and learning and scholarship of practice. New Directions for Student Services, 1–9. https://doi.org/10.1002/ss.20506. Posted with permission. © 2024 The Authors. New Directions for Student Services published by Wiley Periodicals LLC.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

Is income inequality linked to infectious disease prevalence? A hypothesis-generating study using tuberculosis

Background This paper studies the association between infectious disease prevalence and ambient income inequality. We hypothesize that random social mixing in an income-unequal society brings into contact a) the abundant poor, both susceptible and infected, and b) the infected-poor and the susceptible-rich, raising infectious disease prevalence. If true, this would suggest that two countries with similar incomes per capita but varying income inequality levels would exhibit significantly different levels of infectious disease prevalence. We investigate this association by examining whether countries with elevated levels of income inequality have higher rates of pulmonary Tuberculosis (TB) incidence per capita. Our choice of TB is appropriate because it is airborne and transmitted via community mixing. Moreover, it is well known that the four stages of TB pathogenesis (exposure to infection, progression to disease, late or inappropriate diagnosis and treatment, and treatment adherence) vary across rich and poor individuals. Methods We used publicly available panel data for a large cross-section of countries between 1995 and 2013. The data include TB incidence and prevalence per 100,000 people. It also contains data on income inequality (Gini coefficient) across countries and time within countries. Our multivariate regression model controlled, among other variables, economic output per capita, HIV prevalence, public health expenditures, population density, age composition, and poverty, incorporating country-level and time-fixed effects. We also included external instruments (foreign direct investment and trade) known to be exogenous shifters of inequality. A “negative control” using anemia (a non-communicable disease, and hence impervious to the hypothesized mechanism) is also applied. Findings Overall, elevated levels of income inequality were positively associated with tuberculosis prevalence. All else the same, countries with income-Gini coefficients a mere 10% apart see a statistically significant 4% difference in tuberculosis incidence. GDP per capita was negatively and significantly associated, and HIV prevalence was positively and significantly associated with TB incidence. Income inequality had a null effect on anemia, the negative control. Interpretation We view our work more as hypothesis-generating rather than hypothesis-testing. Our “mixing hypothesis” outlines an underlying causal mechanism that cannot be tested using cross-country data. To confirm our hypothesis, one would need social contact (“shared air”) data disaggregated by income -- which does not exist. Aside from generating a hypothesis, the cross-country regression results suggest TB may be a negative externality whose reach is amplified by income inequality. Around the world, the emergence of COVID-19 has renewed focus on the importance of reducing income differences. We join that chorus by arguing that policy action to reduce income inequities could directly contribute to a reduced TB burden.This is a manuscript of an article published as Kim, Min Kyong, Jayanta Bhattacharya, and Joydeep Bhattacharya. "Is income inequality linked to infectious disease prevalence? A hypothesis-generating study using tuberculosis." Social Science & Medicine 345 (2024): 116639. doi:10.1016/j.socscimed.2024.116639. This manuscript is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License

Effects of plant diversity on productivity strengthen over time due to trait-dependent shifts in species overyielding

Plant diversity effects on community productivity often increase over time. Whether the strengthening of diversity effects is caused by temporal shifts in species-level overyielding (i.e., higher species-level productivity in diverse communities compared with monocultures) remains unclear. Here, using data from 65 grassland and forest biodiversity experiments, we show that the temporal strength of diversity effects at the community scale is underpinned by temporal changes in the species that yield. These temporal trends of species-level overyielding are shaped by plant ecological strategies, which can be quantitatively delimited by functional traits. In grasslands, the temporal strengthening of biodiversity effects on community productivity was associated with increasing biomass overyielding of resource-conservative species increasing over time, and with overyielding of species characterized by fast resource acquisition either decreasing or increasing. In forests, temporal trends in species overyielding differ when considering above- versus belowground resource acquisition strategies. Overyielding in stem growth decreased for species with high light capture capacity but increased for those with high soil resource acquisition capacity. Our results imply that a diversity of species with different, and potentially complementary, ecological strategies is beneficial for maintaining community productivity over time in both grassland and forest ecosystems.This article is published as Zheng, L., Barry, K.E., Guerrero-Ramírez, N.R. et al. Effects of plant diversity on productivity strengthen over time due to trait-dependent shifts in species overyielding. Nat Commun 15, 2078 (2024). https://doi.org/10.1038/s41467-024-46355-z. Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted

Above-ground biomass and surface residue traits in soybean

The drive to increase seed yield in soybean [Glycine max (L.) Merr.] has traditionally overshadowed the exploration of biomass partitioning and the compositional characteristics of plant residue traits such as leaves, petioles, stems, and pods. Recognizing this gap, our study aimed to investigate the variability in these traits across 32 genetically diverse soybean genotypes cultivated over two years in central Iowa. Through detailed collection and analysis of vegetative parts at critical growth stages (R1, R4, and R8), we assessed both biomass traits and their compositional characteristics, focusing on soybean residue traits to enhance soil health and their importance in soybean cropping systems. We present heritability estimates for biomass and residue composition traits in soybean. The large variation and high heritability estimates suggest avenues for breeding strategies to optimize variety development through improved biomass partitioning and residue traits. Utilizing the Agriculture Production Systems Simulator (APSIM), we conducted a sensitivity analysis to evaluate the impact of soybean residue quality on soil nutrient cycling and its effects on the subsequent maize [Zea mays L.] crop. The study underscores the importance of soybean residue management, emphasizing the need for integrated approaches in breeding and agricultural practices that utilize the genetic diversity of these traits