Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Improving models for student retention and graduation using Markov chains.

ABSTRACT: Graduation rates are a key measure of the long-term efficacy of academic interventions. However, challenges to using traditional estimates of graduation rates for underrepresented students include inherently small sample sizes and high data requirements. Here, we show that a Markov model increases confidence and reduces biases in estimated graduation rates for underrepresented minority and first-generation students. We use a Learning Assistant program to demonstrate the Markov model's strength for assessing program efficacy. We find that Learning Assistants in gateway science courses are associated with a 9% increase in the six-year graduation rate. These gains are larger for underrepresented minority (21%) and first-generation students (18%). Our results indicate that Learning Assistants can improve overall graduation rates and address inequalities in graduation rates for underrepresented students.

SUBMITTER: Tedeschi MN

PROVIDER: S-EPMC10292706 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Improving models for student retention and graduation using Markov chains.

Tedeschi Mason N MN Hose Tiana M TM Mehlman Emily K EK Franklin Scott S Wong Tony E TE

PloS one 20230626 6

Graduation rates are a key measure of the long-term efficacy of academic interventions. However, challenges to using traditional estimates of graduation rates for underrepresented students include inherently small sample sizes and high data requirements. Here, we show that a Markov model increases confidence and reduces biases in estimated graduation rates for underrepresented minority and first-generation students. We use a Learning Assistant program to demonstrate the Markov model's strength f ...[more]

PMID: 37363904

Similar Datasets

Combining chains of Bayesian models with Markov melding.

Project description:A challenge for practitioners of Bayesian inference is specifying a model that incorporates multiple relevant, heterogeneous data sets. It may be easier to instead specify distinct submodels for each source of data, then join the submodels together. We consider chains of submodels, where submodels directly relate to their neighbours via common quantities which may be parameters or deterministic functions thereof. We propose chained Markov melding, an extension of Markov melding, a generic method to combine chains of submodels into a joint model. One challenge we address is appropriately capturing the prior dependence between common quantities within a submodel, whilst also reconciling differences in priors for the same common quantity between two adjacent submodels. Estimating the posterior of the resulting overall joint model is also challenging, so we describe a sampler that uses the chain structure to incorporate information contained in the submodels in multiple stages, possibly in parallel. We demonstrate our methodology using two examples. The first example considers an ecological integrated population model, where multiple data sets are required to accurately estimate population immigration and reproduction rates. We also consider a joint longitudinal and time-to-event model with uncertain, submodel-derived event times. Chained Markov melding is a conceptually appealing approach to integrating submodels in these settings.

| S-EPMC7614958 | biostudies-literature

Multilocus association mapping using variable-length Markov chains.

Project description:I propose a new method for association-based gene mapping that makes powerful use of multilocus data, is computationally efficient, and is straightforward to apply over large genomic regions. The approach is based on the fitting of variable-length Markov chain models, which automatically adapt to the degree of linkage disequilibrium (LD) between markers to create a parsimonious model for the LD structure. Edges of the fitted graph are tested for association with trait status. This approach can be thought of as haplotype testing with sophisticated windowing that accounts for extent of LD to reduce degrees of freedom and number of tests while maximizing information. I present analyses of two published data sets that show that this approach can have better power than single-marker tests or sliding-window haplotypic tests.

| S-EPMC1474089 | biostudies-literature

Inferring animal densities from tracking data using Markov chains.

Project description:The distributions and relative densities of species are keys to ecology. Large amounts of tracking data are being collected on a wide variety of animal species using several methods, especially electronic tags that record location. These tracking data are effectively used for many purposes, but generally provide biased measures of distribution, because the starts of the tracks are not randomly distributed among the locations used by the animals. We introduce a simple Markov-chain method that produces unbiased measures of relative density from tracking data. The density estimates can be over a geographical grid, and/or relative to environmental measures. The method assumes that the tracked animals are a random subset of the population in respect to how they move through the habitat cells, and that the movements of the animals among the habitat cells form a time-homogenous Markov chain. We illustrate the method using simulated data as well as real data on the movements of sperm whales. The simulations illustrate the bias introduced when the initial tracking locations are not randomly distributed, as well as the lack of bias when the Markov method is used. We believe that this method will be important in giving unbiased estimates of density from the growing corpus of animal tracking data.

| S-EPMC3632542 | biostudies-literature

Analysing ill-conditioned Markov chains.

Project description:Discrete state Markov chains in discrete or continuous time are widely used to model phenomena in the social, physical and life sciences. In many cases, the model can feature a large state space, with extreme differences between the fastest and slowest transition timescales. Analysis of such ill-conditioned models is often intractable with finite precision linear algebra techniques. In this contribution, we propose a solution to this problem, namely partial graph transformation, to iteratively eliminate and renormalize states, producing a low-rank Markov chain from an ill-conditioned initial model. We show that the error induced by this procedure can be minimized by retaining both the renormalized nodes that represent metastable superbasins, and those through which reactive pathways concentrate, i.e. the dividing surface in the discrete state space. This procedure typically returns a much lower rank model, where trajectories can be efficiently generated with kinetic path sampling. We apply this approach to an ill-conditioned Markov chain for a model multi-community system, measuring the accuracy by direct comparison with trajectories and transition statistics. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

| S-EPMC10200351 | biostudies-literature

Microbial gene identification using interpolated Markov models.

Project description:This paper describes a new system, GLIMMER, for finding genes in microbial genomes. In a series of tests on Haemophilus influenzae , Helicobacter pylori and other complete microbial genomes, this system has proven to be very accurate at locating virtually all the genes in these sequences, outperforming previous methods. A conservative estimate based on experiments on H.pylori and H. influenzae is that the system finds >97% of all genes. GLIMMER uses interpolated Markov models (IMMs) as a framework for capturing dependencies between nearby nucleotides in a DNA sequence. An IMM-based method makes predictions based on a variable context; i.e., a variable-length oligomer in a DNA sequence. The context used by GLIMMER changes depending on the local composition of the sequence. As a result, GLIMMER is more flexible and more powerful than fixed-order Markov methods, which have previously been the primary content-based technique for finding genes in microbial DNA.

| S-EPMC147303 | biostudies-other

Stochastic model of Alzheimer's Disease progression using two-state Markov chains.

Project description:In 2016, Hao and Friedman developed a deterministic model of Alzheimer's disease progression using a system of partial differential equations. This model describes the general behavior of the disease, however, it does not incorporate the molecular and cellular stochasticity intrinsic to the underlying disease processes. Here we extend the Hao and Friedman model by modeling each event in disease progression as a stochastic Markov process. This model identifies stochasticity in disease progression, as well as changes to the mean dynamics of key agents. We find that the pace of neuron death increases whereas the production of the two key measures of progression, Tau and Amyloid beta proteins, decelerates when stochasticity is incorporated into the model. These results suggest that the non-constant reactions and time-steps have a significant effect on the overall progression of the disease.

| S-EPMC10327163 | biostudies-literature

Stochastic model of Alzheimer's disease progression using two-state Markov chains.

| S-EPMC10798450 | biostudies-literature

Using Markov state models to study self-assembly.

Project description:Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to construct MSMs that is applicable to modeling a broad class of multi-molecular assembly reactions. Distinct structures formed during assembly are distinguished by their undirected graphs, which are defined by strong subunit interactions. Spatial inhomogeneities of free subunits are accounted for using a recently developed Gaussian-based signature. Simplifications to this state identification are also investigated. The feasibility of this approach is demonstrated on two different coarse-grained models for virus self-assembly. We find good agreement between the dynamics predicted by the MSMs and long, unbiased simulations, and that the MSMs can reduce overall simulation time by orders of magnitude.

| S-EPMC4048447 | biostudies-other

Redefining CpG islands using hidden Markov models.

Project description:The DNA of most vertebrates is depleted in CpG dinucleotide: a C followed by a G in the 5' to 3' direction. CpGs are the target for DNA methylation, a chemical modification of cytosine (C) heritable during cell division and the most well-characterized epigenetic mechanism. The remaining CpGs tend to cluster in regions referred to as CpG islands (CGI). Knowing CGI locations is important because they mark functionally relevant epigenetic loci in development and disease. For various mammals, including human, a readily available and widely used list of CGI is available from the UCSC Genome Browser. This list was derived using algorithms that search for regions satisfying a definition of CGI proposed by Gardiner-Garden and Frommer more than 20 years ago. Recent findings, enabled by advances in technology that permit direct measurement of epigenetic endpoints at a whole-genome scale, motivate the need to adapt the current CGI definition. In this paper, we propose a procedure, guided by hidden Markov models, that permits an extensible approach to detecting CGI. The main advantage of our approach over others is that it summarizes the evidence for CGI status as probability scores. This provides flexibility in the definition of a CGI and facilitates the creation of CGI lists for other species. The utility of this approach is demonstrated by generating the first CGI lists for invertebrates, and the fact that we can create CGI lists that substantially increases overlap with recently discovered epigenetic marks. A CGI list and the probability scores, as a function of genome location, for each species are available at http://www.rafalab.org.

| S-EPMC2883304 | biostudies-literature

Inferring Adaptive Introgression Using Hidden Markov Models.

Project description:Adaptive introgression-the flow of adaptive genetic variation between species or populations-has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.

| S-EPMC8097282 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data