Extended asymmetric division function by davidlzhou · Pull Request #1 · davidlzhou/PhysiCell

davidlzhou · 2025-04-28T02:02:16Z

Additions to encode alternative asymmetric division functions, where daughter cells can both be different types from parent.

Implementation of extended asymmetric division, where cell type A can yield daughter cell types B and C through mitosis. Will need to double-check robustness of pair hash function (collisions?), and add Studio support for this.

drbergman

I think this looks really great! A very promising start to this, and so much more than just a start. I think we're already at just the software polishing stage. So, really well done! I think the only outstanding concern not under the polish umbrella is if you've fully accounted for the ordering business. I think we either make synonyms (add extra keys to the behavior_to_int dicts so that no matter how the user inputs the rules, we process them correctly.

Otherwise, just a couple polishing details that will minorly improve the code.

Great job!!

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drbergman

Nice update here. I think you have a good hash function now. The Cantor function I suggested is not necessary. What you have here is perfect.

I do think (from my own testing) that we'll still need to set an equality for the unordered map. If there is a hash collision (two keys produce the same hash), equality is then checked to determine which value is being requested. Without defining our own equality, it will not see (3,5) and (5,3) as the same even though they have the same has.

drbergman · 2025-05-16T18:48:43Z

Great! changes look good! I think one final thing is to add a new sample project that demos this. Give it a name. Add it to Makefile and sample_projects/Makefile-default. Let's make sure that we have cells that have the config use both orders (lower index cell type first and higher index cell type first), and have cells that do the same but for rules. Also, sym div into a new cell type (A -> B+B).

drbergman

Looks really good! A couple bugs to address and some cleaning up. I'm happy to help directly on the code. I realize I'm probably driving you crazy with all these comments!

drbergman · 2025-05-31T03:10:19Z

 !user_projects/empty.txt
 Studio.zip
 /studio
+.vscode/settings.json


I agree with adding .vscode here (don't need to specify just the settings.json).

However, let's not touch the custom_modules or output folders since those are kind of part of the main repo

drbergman · 2025-05-31T03:11:22Z

-        <number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">0</number_of_cells>
+        <number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">5</number_of_cells>
    </user_parameters>
 </PhysiCell_settings>


Make sure to undo all these changes

drbergman · 2025-05-31T03:15:54Z

+				auto first_search = cell_definition_indices_by_name.find(first_target_name);
+				auto second_search = cell_definition_indices_by_name.find(second_target_name);
+				// safety first!
+				if( first_search != cell_definition_indices_by_name.end() || second_search != cell_definition_indices_by_name.end() )


I think the logic here needs to be fixed. Also, a nice trick is to put the error in the if block and then what you currently have in the if block can just go after that error-handling block without the extra indentation.

I think we need && instead of ||, but if you take my suggestion about flipping then just be careful to negate correctly :)

drbergman · 2025-05-31T03:17:17Z

+				node_eadp = node_eadp.next_sibling("extended_asymmetric_division_probability");
+			}
+			std::cout << "Extended asymmetric division probabilities for " << pCD->name << ": ";
+			for (int i = 0; i < pEAD->asymmetric_division_probabilities.size(); i++)


Delete this line

drbergman · 2025-05-31T03:18:36Z

+			for (int i = 0; i < pEAD->asymmetric_division_probabilities.size(); i++)
+			for (auto it = pEAD->asymmetric_division_probabilities.begin(); it != pEAD->asymmetric_division_probabilities.end(); ++it)
+			{
+				std::cout << it->first.first << " " << it->first.second << ": " << it->second << " ";


I feel like this print statement would look kinda cluttered...

Can you share a screenshot if you like it? I'd think we'd want something like
Extended asymmetric division probabilities for rgc:

rgc + rgc : 0.2

rgc + neuron : 0.1
...

Something Like that. Or just get rid of this altogether. We print too much stuff at the top of simulations as it is

I think an issue we run into here is that we'd have to get the daughter cell type names from the IDs, but if one of the daughter types haven't been processed/created yet, cell_definitions_by_index[ID] won't find the correct cell definition and cause seg fault.

Maybe just get rid?

drbergman · 2025-05-31T03:37:52Z

+		for( int j = i; j < n; j++ )
+		{ extended_asym_index_to_upper_triangle.push_back( std::make_pair(i,j) ); }
+	};
+	*/


drbergman · 2025-05-31T11:19:39Z

+		{
+			if (it->first.first != parent_type) // only convert if the parent is not already the correct type
+			{ pCell_daughter->convert_to_cell_definition( *cell_definitions_by_index[it->first.first] ); }
+			if (it->first.second != pCell_daughter->type) // only convert if the daughter is not already the correct type


Need to check against the parent type as above

drbergman · 2025-05-31T11:22:35Z

@@ -0,0 +1 @@
+1.14.2


Delete this file

drbergman · 2025-05-31T11:22:59Z

@@ -0,0 +1,249 @@
+<PhysiCell_settings version="devel-version">


Don't need a backup in the sample project. Delete file

drbergman · 2025-05-31T11:26:27Z

+type0,time,increases,extended asymmetric division to type1 and type2,0.5,600,256,0
+type0,time,decreases,extended asymmetric division to type1 and type2,0.0,1200,256,0
+type0,time,increases,extended asymmetric division to type3 and type4,0.5,1200,256,0


Let's also show off symmetric division (1 -> 1 + 1 AND 1 -> 2 + 2) and show that the order doesn't matter (1 -> 4 + 3)

It would be kinda cute to arrange 10 cells in the upper triangular pattern and use the cells.csv to get them to show off each of the possible asymmetric div outcomes. I can help with the csv to make that happen. Let me know

Yeah that sounds like a cool demo! If the initial 10 cells are of the same type though, how should we have them follow different division fates?

Also definitely feel free to directly edit the files! I completely understand that is sometimes easier than getting someone else to properly understand and implement code ideas :)

drbergman · 2025-09-05T16:23:40Z

Feel free to close, David. I cannot. See here: #2 (comment)

davidlzhou added 5 commits April 26, 2025 00:12

Update with extended asymmetric division behaviors

ec80145

Implementation of extended asymmetric division, where cell type A can yield daughter cell types B and C through mitosis. Will need to double-check robustness of pair hash function (collisions?), and add Studio support for this.

Update .gitignore

b31949e

main for extended div

edd40e9

Delete empty.txt

d669670

Update PhysiCell_settings.xml

ddab2bd

drbergman reviewed Apr 28, 2025

View reviewed changes

revised extended asym

065d9e8

drbergman reviewed May 9, 2025

View reviewed changes

Comment thread core/PhysiCell_phenotype.h

Comment thread core/PhysiCell_phenotype.h Outdated

Comment thread core/PhysiCell_signal_behavior.cpp Outdated

Extended asym div updates for equality and map indexing

3a193d5

drbergman reviewed May 16, 2025

View reviewed changes

Comment thread core/PhysiCell_phenotype.h

davidlzhou added 3 commits May 30, 2025 15:16

more changes for EAD

82e469f

EAD: change to index-to-pair function

4be4256

Adding basic EAD sample project

b81aa37

drbergman suggested changes May 31, 2025

View reviewed changes

davidlzhou added 3 commits May 31, 2025 16:16

EAD sample project; bugfixes

09fb30d

more updates

5dcece2

Restore random seed to PhysiCell_settings.xml

80d46c1

		@@ -0,0 +1,249 @@
		<PhysiCell_settings version="devel-version">

		@@ -0,0 +1 @@
		1.14.2 No newline at end of file

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davidlzhou commented Apr 28, 2025

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drbergman commented May 16, 2025

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drbergman commented Sep 5, 2025

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