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1. Data mining a design repository to generate linear functional chains: a step toward automating functional modeling

   Edmonds, Katherine ; Mikes, Alex ; DuPont, Bryony ; Stone, Robert B. ( December 2020 , Design Computing and Cognition 2020)

   null (Ed.)

   Populating the different types of data for a design repository is a difficult and time-consuming task. In this work, we report on techniques to automate the population of data related to product function. We explore a preliminary method to automate the generation of the functional chains of components from new products based on hierarchical data from an existing design repos- itory. We use datasets of various scale and specificity to find correlations between functions and flows for components of products in the Design Repos- itory. We use the results to predict the most likely functions and flows for a component, and then verify the accuracy of our algorithm by cross-validating a subsection of the data against the automation results. We apply existing grammar rules to order the functions and flows in a linear functional chain. Ultimately, these findings suggest methods for further automating the process of generating functional models. 

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2. Classifying Component Function in Product Assemblies With Graph Neural Networks

   https://doi.org/10.1115/1.4052720  

   Ferrero, Vincenzo ; DuPont, Bryony ; Hassani, Kaveh ; Grandi, Daniele ( February 2022 , Journal of Mechanical Design)

   Abstract Function is defined as the ensemble of tasks that enable the product to complete the designed purpose. Functional tools, such as functional modeling, offer decision guidance in the early phase of product design, where explicit design decisions are yet to be made. Function-based design data is often sparse and grounded in individual interpretation. As such, function-based design tools can benefit from automatic function classification to increase data fidelity and provide function representation models that enable function-based intelligent design agents. Function-based design data is commonly stored in manually generated design repositories. These design repositories are a collection of expert knowledge and interpretations of function in product design bounded by function-flow and component taxonomies. In this work, we represent a structured taxonomy-based design repository as assembly-flow graphs, then leverage a graph neural network (GNN) model to perform automatic function classification. We support automated function classification by learning from repository data to establish the ground truth of component function assignment. Experimental results show that our GNN model achieves a micro-average F1-score of 0.617 for tier 1 (broad), 0.624 for tier 2, and 0.415 for tier 3 (specific) functions. Given the imbalance of data features and the subjectivity in the definition of product function, the results are encouraging. Our efforts in this paper can be a starting point for more sophisticated applications in knowledge-based CAD systems and Design-for-X consideration in function-based design. 

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3. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

   https://doi.org/10.1126/science.abk3112  

   Hoyt, Savannah J. ; Storer, Jessica M. ; Hartley, Gabrielle A. ; Grady, Patrick G. ; Gershman, Ariel ; de Lima, Leonardo G. ; Limouse, Charles ; Halabian, Reza ; Wojenski, Luke ; Rodriguez, Matias ; et al ( April 2022 , Science)

   INTRODUCTION Transposable elements (TEs), repeat expansions, and repeat-mediated structural rearrangements play key roles in chromosome structure and species evolution, contribute to human genetic variation, and substantially influence human health through copy number variants, structural variants, insertions, deletions, and alterations to gene transcription and splicing. Despite their formative role in genome stability, repetitive regions have been relegated to gaps and collapsed regions in human genome reference GRCh38 owing to the technological limitations during its development. The lack of linear sequence in these regions, particularly in centromeres, resulted in the inability to fully explore the repeat content of the human genome in the context of both local and regional chromosomal environments. RATIONALE Long-read sequencing supported the complete, telomere-to-telomere (T2T) assembly of the pseudo-haploid human cell line CHM13. This resource affords a genome-scale assessment of all human repetitive sequences, including TEs and previously unknown repeats and satellites, both within and outside of gaps and collapsed regions. Additionally, a complete genome enables the opportunity to explore the epigenetic and transcriptional profiles of these elements that are fundamental to our understanding of chromosome structure, function, and evolution. Comparative analyses reveal modes of repeat divergence, evolution, and expansion or contraction with locus-level resolution. RESULTS We implemented a comprehensive repeat annotation workflow using previously known human repeats and de novo repeat modeling followed by manual curation, including assessing overlaps with gene annotations, segmental duplications, tandem repeats, and annotated repeats. Using this method, we developed an updated catalog of human repetitive sequences and refined previous repeat annotations. We discovered 43 previously unknown repeats and repeat variants and characterized 19 complex, composite repetitive structures, which often carry genes, across T2T-CHM13. Using precision nuclear run-on sequencing (PRO-seq) and CpG methylated sites generated from Oxford Nanopore Technologies long-read sequencing data, we assessed RNA polymerase engagement across retroelements genome-wide, revealing correlations between nascent transcription, sequence divergence, CpG density, and methylation. These analyses were extended to evaluate RNA polymerase occupancy for all repeats, including high-density satellite repeats that reside in previously inaccessible centromeric regions of all human chromosomes. Moreover, using both mapping-dependent and mapping-independent approaches across early developmental stages and a complete cell cycle time series, we found that engaged RNA polymerase across satellites is low; in contrast, TE transcription is abundant and serves as a boundary for changes in CpG methylation and centromere substructure. Together, these data reveal the dynamic relationship between transcriptionally active retroelement subclasses and DNA methylation, as well as potential mechanisms for the derivation and evolution of new repeat families and composite elements. Focusing on the emerging T2T-level assembly of the HG002 X chromosome, we reveal that a high level of repeat variation likely exists across the human population, including composite element copy numbers that affect gene copy number. Additionally, we highlight the impact of repeats on the structural diversity of the genome, revealing repeat expansions with extreme copy number differences between humans and primates while also providing high-confidence annotations of retroelement transduction events. CONCLUSION The comprehensive repeat annotations and updated repeat models described herein serve as a resource for expanding the compendium of human genome sequences and reveal the impact of specific repeats on the human genome. In developing this resource, we provide a methodological framework for assessing repeat variation within and between human genomes. The exhaustive assessment of the transcriptional landscape of repeats, at both the genome scale and locally, such as within centromeres, sets the stage for functional studies to disentangle the role transcription plays in the mechanisms essential for genome stability and chromosome segregation. Finally, our work demonstrates the need to increase efforts toward achieving T2T-level assemblies for nonhuman primates and other species to fully understand the complexity and impact of repeat-derived genomic innovations that define primate lineages, including humans. Telomere-to-telomere assembly of CHM13 supports repeat annotations and discoveries. The human reference T2T-CHM13 filled gaps and corrected collapsed regions (triangles) in GRCh38. Combining long read–based methylation calls, PRO-seq, and multilevel computational methods, we provide a compendium of human repeats, define retroelement expression and methylation profiles, and delineate locus-specific sites of nascent transcription genome-wide, including previously inaccessible centromeres. SINE, short interspersed element; SVA, SINE–variable number tandem repeat– Alu ; LINE, long interspersed element; LTR, long terminal repeat; TSS, transcription start site; pA, xxxxxxxxxxxxxxxx. 

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4. Using Decision Trees Supported by Data Mining to Improve Function-Based Design

   https://doi.org/10.1115/DETC2020-22498  

   Ferrero, Vincenzo J. ; Alqseer, Naser ; Tensa, Melissa ; DuPont, Bryony ( August 2020 , ASME IDETC/CIE 2020)

   null (Ed.)

   Engineering designers currently use downstream information about product and component functions to facilitate ideation and concept generation of analogous products. These processes, often called Function-Based Design, can be reliant on designer definitions of product function, which are inconsistent from designer to designer. In this paper, we employ supervised learning algorithms to reduce the variety of component functions that are available to designers in a design repository, thus enabling designers to focus their function-based design efforts on more accurate, reduced sets of potential functions. To do this, we generate decisions trees and rules that define the functions of components based on the identity of neighboring components. The resultant decision trees and rulesets reduce the number of feasible functions for components within a product, which is of particular interest for use by novice designers, as reducing the feasible functional space can help focus the design activities of the designer. This reduction was evident in both case studies: one exploring a component that is known to the designer, and the other looking at defining function of an unrecognizable component. The work presented here contributes to the recent popularity of using product data in data-driven design methodologies, especially those focused on supplementing designer cognition. Importantly, we found that this methodology is reliant on repository data quality, and the results indicate a need to continue the development of design repository data schemas with improved data consistency and fidelity. This research is a necessary precursor for the development of function-based design tools, including automated functional modeling. 

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5. An Association Rule Approach for Identifying Physical System-User Interactions and Potential Human Errors Using a Design Repository

   https://doi.org/10.1115/DETC2019-98424  

   Soria Zurita, Nicolás F. ; Tensa, Melissa Anne ; Ferrero, Vincenzo ; Stone, Robert B. ; DuPont, Bryony ; Demirel, H. Onan ; Tumer, Irem Y. ( August 2019 , ASME International Design Engineering Technical Conferences and Computers in Engineering)

   During the design process, designers must satisfy customer needs while adequately developing engineering objectives. Among these engineering objectives, human considerations such as user interactions, safety, and comfort are indispensable during the design process. Nevertheless, traditional design engineering methodologies have significant limitations incorporating and understanding physical user interactions during early design phases. For example, Human Factors methods use checklists and guidelines applied to virtual or physical prototypes at later design stages to evaluate the concept. As a result, designers struggle to identify design deficiencies and potential failure modes caused by user-system interactions without relying on the use of detailed and costly prototypes. The Function-Human Error Design Method (FHEDM) is a novel approach to assess physical interactions during the early design stage using a functional basis approach. By applying FHEDM, designers can identify user interactions required to complete the functions of the system and to distinguish failure modes associated with such interactions, by establishing user-system associations using the information of the functional model. In this paper, we explore the use of data mining techniques to develop relationships between component, functions, flows and user interactions. We extract design information about components, functions, flows, and user interactions from a set of distinct coffee makers found in the Design Repository to build associations rules. Later, using a functional model of an electric kettle, we compared the functions, flows, and user interactions associations generated from data mining against the associations created by the authors, using the FHEDM. The results show notable similarities between the associations built from data mining and the FHEDM. We are suggesting that design information from a rich dataset can be used to extract association rules between functions, flows, components, and user interactions. This work will contribute to the design community by automating the identification of user interactions from a functional model. 

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