josura c2c-sepia issues

josura / c2c-sepia

Multi agent model for perturbations in networks of networks. Used for Cell-to-cell communication with enriched pathways, using scRNA-seq or spatial data

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Remove ensemble gene names for ambiguity

#58 josura opened 1 day ago
0
Change some logging options and add an option to treat every warning as an error

#57 josura opened 2 weeks ago
0
Optimize memory usage during setup phase

#56 josura opened 2 months ago
0
Continuous intervals for the interactions between agents

#55 josura opened 2 months ago
0
Output format change

#54 josura closed 2 months ago
0
Saturation implementation is ambigous

#53 josura closed 2 months ago
2
Current implementation of time is ambiguous

#52 josura closed 2 months ago
1
graphs with no edges bring problems

#51 josura closed 2 months ago
4
Error when creating directory for output

#50 josura opened 4 months ago
1
Scaling functions could be "unique" for every node

#49 josura opened 5 months ago
1
Temporal contacts should be doubles

#48 josura closed 2 months ago
3
Using temporal networks even for the agents

#47 josura opened 6 months ago
0
Undirected edges will also be undirected between virtual nodes in the graphs

#46 josura closed 6 months ago
0
Deleting virtual inputs buffers and virtual outputs buffers leads to unknown behaviour

#45 josura closed 7 months ago
0
Zeroing virtual nodes values after every inter-propagation step

#44 josura closed 6 months ago
1
Conservation should conserve the information passed between types

#43 josura closed 2 months ago
1
Virtual nodes granularity

#42 josura closed 6 months ago
0
Add additional logging options

#41 josura opened 9 months ago
0
Integrate different contact steps for interaction between communities

#40 josura closed 6 months ago
4
Consider a stateful scaling function

#39 josura opened 9 months ago
0
Add a noheader parameter to take into account graph files (edge lists) with no header and 3 columns (start, end, weight)

#38 josura opened 10 months ago
0
MPI implementation deadlock and testing

#37 josura closed 9 months ago
1
Parametrization of nodes description

#36 josura closed 3 months ago
1
Propagation with pseudoinverse leads to inconsistence and unknown behaviour

#35 josura closed 2 months ago
1
Vector of initial values for single nodes in the graphs support

#34 josura opened 1 year ago
0
Agent visualization

#33 josura opened 1 year ago
0
Partial input vectors and partial type support makes some confusion with the concept of subtypes

#32 josura closed 11 months ago
1
Handling exceptions in the main

#31 josura opened 1 year ago
0
Add partial type support

#30 josura closed 8 months ago
1
Control for duplicate types

#29 josura closed 11 months ago
2
Add partial input supports

#28 josura closed 11 months ago
1
Use different computation model to compute propagation or perturbation values

#27 josura closed 9 months ago
1
Checkpoint creation

#26 josura closed 2 months ago
0
Feature/issue 22/parametrized scaling function

#25 josura closed 1 year ago
0
Validation of the model

#24 josura opened 1 year ago
1
Read list of graph files for every cell type

#23 josura closed 11 months ago
1
Adding parser for parametrized scaling function

#22 josura closed 1 year ago
1
Parametrize the normalization of the matrix

#21 josura opened 1 year ago
0
Refactoring of the code (main function and Computation especially)

#20 josura opened 1 year ago
3
Removing the augmented metapathways during computation causes problems

#19 josura opened 1 year ago
1
Pseudoinverse of Armadillo library doesn't seem very accurate

#18 josura closed 1 year ago
1
Perturbation growth is strictly exponential

#17 josura closed 9 months ago
1
Optimize and parallelize the code

#16 josura closed 8 months ago
1
perturbation gets too big after some iterations

#15 josura closed 1 year ago
1
Normalization in the W and W* matrix

#14 josura opened 1 year ago
1
Problems with tisch CCI data

#13 josura opened 1 year ago
0
Bug with a line of code from the standard library

#12 josura closed 1 year ago
2
Problems with github actions

#11 josura opened 1 year ago
0
Problems in the case where the first term in the iteration algorithm(the subtraction of the identity matrix and Wt) is not invertible

#10 josura closed 1 year ago
1
Remove edgesArray from Graph class

#9 josura closed 1 year ago
1