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1. Mimicking Complexity of Structured Data Matrix’s Information Content: Categorical Exploratory Data Analysis

   https://doi.org/10.3390/e23050594  

   Hsieh, Fushing; Chou, Elizabeth P.; Chen, Ting-Li (May 2021, Entropy)

   null (Ed.)

   We develop Categorical Exploratory Data Analysis (CEDA) with mimicking to explore and exhibit the complexity of information content that is contained within any data matrix: categorical, discrete, or continuous. Such complexity is shown through visible and explainable serial multiscale structural dependency with heterogeneity. CEDA is developed upon all features’ categorical nature via histogram and it is guided by all features’ associative patterns (order-2 dependence) in a mutual conditional entropy matrix. Higher-order structural dependency of k(≥3) features is exhibited through block patterns within heatmaps that are constructed by permuting contingency-kD-lattices of counts. By growing k, the resultant heatmap series contains global and large scales of structural dependency that constitute the data matrix’s information content. When involving continuous features, the principal component analysis (PCA) extracts fine-scale information content from each block in the final heatmap. Our mimicking protocol coherently simulates this heatmap series by preserving global-to-fine scales structural dependency. Upon every step of mimicking process, each accepted simulated heatmap is subject to constraints with respect to all of the reliable observed categorical patterns. For reliability and robustness in sciences, CEDA with mimicking enhances data visualization by revealing deterministic and stochastic structures within each scale-specific structural dependency. For inferences in Machine Learning (ML) and Statistics, it clarifies, upon which scales, which covariate feature-groups have major-vs.-minor predictive powers on response features. For the social justice of Artificial Intelligence (AI) products, it checks whether a data matrix incompletely prescribes the targeted system. 

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2. Categorical Nature of Major Factor Selection via Information Theoretic Measurements

   https://doi.org/10.3390/e23121684  

   Chen, Ting-Li; Chou, Elizabeth P.; Fushing, Hsieh (December 2021, Entropy)

   Without assuming any functional or distributional structure, we select collections of major factors embedded within response-versus-covariate (Re-Co) dynamics via selection criteria [C1: confirmable] and [C2: irrepaceable], which are based on information theoretic measurements. The two criteria are constructed based on the computing paradigm called Categorical Exploratory Data Analysis (CEDA) and linked to Wiener–Granger causality. All the information theoretical measurements, including conditional mutual information and entropy, are evaluated through the contingency table platform, which primarily rests on the categorical nature within all involved features of any data types: quantitative or qualitative. Our selection task identifies one chief collection, together with several secondary collections of major factors of various orders underlying the targeted Re-Co dynamics. Each selected collection is checked with algorithmically computed reliability against the finite sample phenomenon, and so is each member’s major factor individually. The developments of our selection protocol are illustrated in detail through two experimental examples: a simple one and a complex one. We then apply this protocol on two data sets pertaining to two somewhat related but distinct pitching dynamics of two pitch types: slider and fastball. In particular, we refer to a specific Major League Baseball (MLB) pitcher and we consider data of multiple seasons. 

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3. Unraveling Hidden Major Factors by Breaking Heterogeneity into Homogeneous Parts within Many-System Problems

   https://doi.org/10.3390/e24020170  

   Chou, Elizabeth P.; Chen, Ting-Li; Fushing, Hsieh (February 2022, Entropy)

   For a large ensemble of complex systems, a Many-System Problem (MSP) studies how heterogeneity constrains and hides structural mechanisms, and how to uncover and reveal hidden major factors from homogeneous parts. All member systems in an MSP share common governing principles of dynamics, but differ in idiosyncratic characteristics. A typical dynamic is found underlying response features with respect to covariate features of quantitative or qualitative data types. Neither all-system-as-one-whole nor individual system-specific functional structures are assumed in such response-vs-covariate (Re–Co) dynamics. We developed a computational protocol for identifying various collections of major factors of various orders underlying Re–Co dynamics. We first demonstrate the immanent effects of heterogeneity among member systems, which constrain compositions of major factors and even hide essential ones. Secondly, we show that fuller collections of major factors are discovered by breaking heterogeneity into many homogeneous parts. This process further realizes Anderson’s “More is Different” phenomenon. We employ the categorical nature of all features and develop a Categorical Exploratory Data Analysis (CEDA)-based major factor selection protocol. Information theoretical measurements—conditional mutual information and entropy—are heavily used in two selection criteria: C1—confirmable and C2—irreplaceable. All conditional entropies are evaluated through contingency tables with algorithmically computed reliability against the finite sample phenomenon. We study one artificially designed MSP and then two real collectives of Major League Baseball (MLB) pitching dynamics with 62 slider pitchers and 199 fastball pitchers, respectively. Finally, our MSP data analyzing techniques are applied to resolve a scientific issue related to the Rosenberg Self-Esteem Scale. 

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4. Multi-organ spatial stratification of 3-D dose distributions improves risk prediction of long-term self-reported severe symptoms in oropharyngeal cancer patients receiving radiotherapy: development of a pre-treatment decision support tool

   https://doi.org/10.3389/fonc.2023.1210087  

   Wentzel, Andrew; Mohamed, Abdallah_S R; Naser, Mohamed A; van_Dijk, Lisanne V; Hutcheson, Katherine; Moreno, Amy M; Fuller, Clifton D; Canahuate, Guadalupe; Marai, G Elisabeta (August 2023, Frontiers in Oncology)

   PURPOSE: Identify Oropharyngeal cancer (OPC) patients at high-risk of developing long-term severe radiation-associated symptoms using dose volume histograms for organs-at-risk, via unsupervised clustering. MATERIAL AND METHODS: All patients were treated using radiation therapy for OPC. Dose-volume histograms of organs-at-risk were extracted from patients’ treatment plans. Symptom ratings were collected via the MD Anderson Symptom Inventory (MDASI) given weekly during, and 6 months post-treatment. Drymouth, trouble swallowing, mucus, and vocal dysfunction were selected for analysis in this study. Patient stratifications were obtained by applying Bayesian Mixture Models with three components to patient’s dose histograms for relevant organs. The clusters with the highest total mean doses were translated into dose thresholds using rule mining. Patient stratifications were compared against Tumor staging information using multivariate likelihood ratio tests. Model performance for prediction of moderate/severe symptoms at 6 months was compared against normal tissue complication probability (NTCP) models using cross-validation. RESULTS: A total of 349 patients were included for long-term symptom prediction. High-risk clusters were significantly correlated with outcomes for severe late drymouth (p <.0001, OR = 2.94), swallow (p = .002, OR = 5.13), mucus (p = .001, OR = 3.18), and voice (p = .009, OR = 8.99). Simplified clusters were also correlated with late severe symptoms for drymouth (p <.001, OR = 2.77), swallow (p = .01, OR = 3.63), mucus (p = .01, OR = 2.37), and voice (p <.001, OR = 19.75). Proposed cluster stratifications show better performance than NTCP models for severe drymouth (AUC.598 vs.559, MCC.143 vs.062), swallow (AUC.631 vs.561, MCC.20 vs -.030), mucus (AUC.596 vs.492, MCC.164 vs -.041), and voice (AUC.681 vs.555, MCC.181 vs -.019). Simplified dose thresholds also show better performance than baseline models for predicting late severe ratings for all symptoms. CONCLUSION: Our results show that leveraging the 3-D dose histograms from radiation therapy plan improves stratification of patients according to their risk of experiencing long-term severe radiation associated symptoms, beyond existing NTPC models. Our rule-based method can approximate our stratifications with minimal loss of accuracy and can proactively identify risk factors for radiation-associated toxicity. 

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5. Modeling naturalistic face processing in humans with deep convolutional neural networks

   https://doi.org/10.1073/pnas.2304085120  

   Jiahui, Guo; Feilong, Ma; Visconti di Oleggio Castello, Matteo; Nastase, Samuel A.; Haxby, James V.; Gobbini, M. Ida (October 2023, Proceedings of the National Academy of Sciences)

   Deep convolutional neural networks (DCNNs) trained for face identification can rival and even exceed human-level performance. The ways in which the internal face representations in DCNNs relate to human cognitive representations and brain activity are not well understood. Nearly all previous studies focused on static face image processing with rapid display times and ignored the processing of naturalistic, dynamic information. To address this gap, we developed the largest naturalistic dynamic face stimulus set in human neuroimaging research (700+ naturalistic video clips of unfamiliar faces). We used this naturalistic dataset to compare representational geometries estimated from DCNNs, behavioral responses, and brain responses. We found that DCNN representational geometries were consistent across architectures, cognitive representational geometries were consistent across raters in a behavioral arrangement task, and neural representational geometries in face areas were consistent across brains. Representational geometries in late, fully connected DCNN layers, which are optimized for individuation, were much more weakly correlated with cognitive and neural geometries than were geometries in late-intermediate layers. The late-intermediate face-DCNN layers successfully matched cognitive representational geometries, as measured with a behavioral arrangement task that primarily reflected categorical attributes, and correlated with neural representational geometries in known face-selective topographies. Our study suggests that current DCNNs successfully capture neural cognitive processes for categorical attributes of faces but less accurately capture individuation and dynamic features. 

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