shak360
commented
5 years ago 2nd version submitted! Still needs work with figures, results, and discussion.
Closed shak360 closed 5 years ago
shak360
commented
5 years ago 2nd version submitted! Still needs work with figures, results, and discussion.
https://1drv.ms/w/s!AncRvdvF6gtNgdJqtfqU68JJSkR1SQ OBSOLETE
https://1drv.ms/w/s!AncRvdvF6gtNgdJ7Y_TqAhLuHQA1CA USE THIS
Above is a link to an editable Word document (moved away from Overleaf due to limited times we can share a document). Some of the
LaTeXdidn't move well so we have to change it.Here is a list of figures (sub-figures) that we decided should be implemented (see Slack and Meeting notes for more detail):
[ ] Graphical abstract of our method. Message: Summarize our method/paper.
[ ] Cells (images of cells, tracking images, segmentation, scale bars, resolutions, etc.) Message: Our experimental setup, and could be an example of the type of setup a user might want to use our model with.
[ ] Plot a synthesized lineage, plot lineage from wet-lab data. Message: Examples of possible inputs to our model. What would a user need to use our model. This figure may not be necessary.
[ ] Graphical Model of our tHMM/ Graphical model of our transitions (state transition diagram). See:
[x] Percent classified (some measure of accuracy) vs. Divergence of cell phenotypes (i.e. show how different cells have to be (how far apart must the Bernoulli and Gompertz parameters be) to get accurate classification/state change). Utilize KL-divergence. Message: How far apart do our underlying distributions have to be for MLE (one state model) to fail? for BW/Viterbi (>1 state model) to succeed?
[x] Percent classified (some measure of accuracy) vs. Tree length (i.e. how does tree length affect accurate classification/state change) Message: How does the experiment time affect the accuracy of MLE? of BW/Viterbi?
[x] Percent classified vs. Number of lineages (i.e. how do number of lineages affect inference) Message: How many lineages do I need to accurately obtain the state parameters for MLE (1 state model)? for BW/Viterbi (2 state model)? Averaging the fitted state parameters over several lineages should do better than just using 1 lineage of a cell type/state.
[ ] A heat-map of a single lineage (or more) showing how the state change is altered over time. Plot the
gammas, i.e. the smoothed-probabilities, as a tree. This figure may not be necessary.If we have time:
[ ] If there are x% of cells in 1 state and (1-x)% in the other state, how many cells and/or lineages are required to appropriately classify this?
[x] Explore Akaike Information Criterion (AIC) for multi-state models.
Feel free to edit the above. If you make changes to the document, please use track changes or just add a summary of your edits here. You can also make edits to the Google Drive document and then we can move that here.