Nonstationary Markov Modeling: An Application to Wage-Influenced Industrial Relocation

Abstract Motivation Position-specific probability matrices (PPMs, also called position-specific weight matrices) have been the dominating model for transcription factor (TF)-binding motifs in DNA. There is, however, increasing recent evidence of better performance of higher order models such as Markov models of order one, also called adjacent dinucleotide matrices (ADMs). ADMs can model dependencies between adjacent nucleotides, unlike PPMs. A modeling technique and software tool that would estimate such models simultaneously both for monomers and their dimers have been missing. Results We present an ADM-based mixture model for monomeric and dimeric TF-binding motifs and an expectation maximization algorithm MODER2 for learning such models from training data and seeds. The model is a mixture that includes monomers and dimers, built from the monomers, with a description of the dimeric structure (spacing, orientation). The technique is modular, meaning that the co-operative effect of dimerization is made explicit by evaluating the difference between expected and observed models. The model is validated using HT-SELEX and generated datasets, and by comparing to some earlier PPM and ADM techniques. The ADM models explain data slightly better than PPM models for 314 tested TFs (or their DNA-binding domains) from four families (bHLH, bZIP, ETS and Homeodomain), the ADM mixture models by MODER2 being the best on average. Availability and implementation Software implementation is available from https://github.com/jttoivon/moder2. Supplementary information Supplementary data are available at Bioinformatics online.

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Deriving Effective Decision-Making Strategies of Prosthetists: Using Hidden Markov Modeling and Qualitative Analysis to Compare Experts and Novices

Human Factors The Journal of the Human Factors and Ergonomics Society ◽

10.1177/00187208211032860 ◽

2021 ◽

pp. 001872082110328

Author(s):

Pratima Saravanan ◽

Jessica Menold

Keyword(s):

Decision Making ◽

Qualitative Analysis ◽

Clinical Decision Making ◽

Hidden Markov ◽

Activity Level ◽

Markov Modeling ◽

Support Tool ◽

Case Complexity ◽

Hidden Markov Modeling ◽

Expert And Novice

Objective This research focuses on studying the clinical decision-making strategies of expert and novice prosthetists for different case complexities. Background With an increasing global amputee population, there is an urgent need for improved amputee care. However, current prosthetic prescription standards are based on subjective expertise, making the process challenging for novices, specifically during complex patient cases. Hence, there is a need for studying the decision-making strategies of prosthetists. Method An interactive web-based survey was developed with two case studies of varying complexities. Navigation between survey pages and time spent were recorded for 28 participants including experts ( n = 20) and novices ( n = 8). Using these data, decision-making strategies, or patterns of decisions, during prosthetic prescription were derived using hidden Markov modeling. A qualitative analysis of participants’ rationale regarding decisions was used to add a deep contextualized understanding of decision-making strategies derived from the quantitative analysis. Results Unique decision-making strategies were observed across expert and novice participants. Experts tended to focus on the personal details, activity level, and state of the residual limb prior to prescription, and this strategy was independent of case complexity. Novices tended to change strategies dependent upon case complexity, fixating on certain factors when case complexity was high. Conclusion The decision-making strategies of experts stayed the same across the two cases, whereas the novices exhibited mixed strategies. Application By modeling the decision-making strategies of experts and novices, this study builds a foundation for development of an automated decision-support tool for prosthetic prescription, advancing novice training, and amputee care.

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