jcrozum/biobalm issues and pull requests

#128 - pruned redundant paths in control succession search

Pull Request - State: closed - Opened by jcrozum about 2 months ago - 5 comments

#127 - Further DNF optimizations

Issue - State: open - Opened by daemontus about 2 months ago

#126 - Minor things to tidy up

Issue - State: closed - Opened by jcrozum 2 months ago - 1 comment

#125 - Skip nodes

Pull Request - State: closed - Opened by daemontus 2 months ago - 1 comment

#124 - Alternative two-way reachability method

Pull Request - State: closed - Opened by daemontus 3 months ago - 2 comments

#123 - Add a fallback to the fully symbolic attractor detection if the NFVS search fails

Pull Request - State: closed - Opened by daemontus 3 months ago - 1 comment

#122 - Fast-forward source node expansion anywhere in the succession diagram

Pull Request - State: closed - Opened by daemontus 3 months ago - 3 comments

#121 - Expansion limits

Pull Request - State: closed - Opened by daemontus 3 months ago - 2 comments

#120 - Remove duplicate computation from block expansion

Pull Request - State: closed - Opened by daemontus 3 months ago - 2 comments

#119 - Block (scc) expansion

Pull Request - State: closed - Opened by daemontus 6 months ago - 3 comments

#118 - Refactor SCC expansion

Pull Request - State: closed - Opened by daemontus 6 months ago - 1 comment

#117 - SCC Expansion Bug

Issue - State: closed - Opened by jcrozum 6 months ago - 1 comment
Labels: Priority: High, Type: Bug

#116 - Attractor detection refactoring

Pull Request - State: closed - Opened by daemontus 8 months ago - 6 comments

#100 - Drivers docs

Pull Request - State: closed - Opened by jcrozum 9 months ago - 2 comments

#99 - mole site down

Issue - State: closed - Opened by jcrozum 9 months ago - 3 comments

#98 - Documentation pipeline

Pull Request - State: closed - Opened by jcrozum 9 months ago - 4 comments

#97 - remove analysis and random models

Pull Request - State: closed - Opened by kyuhyongpark 9 months ago - 1 comment

#96 - Succession diagram exposure

Pull Request - State: closed - Opened by jcrozum 10 months ago - 2 comments

#95 - Balm goes brrrrrr

Pull Request - State: closed - Opened by daemontus 10 months ago - 3 comments

#94 - Aeon 1.0

Pull Request - State: closed - Opened by daemontus 10 months ago - 4 comments

#93 - Simplify `SuccessionDiagram` API

Issue - State: open - Opened by jcrozum 10 months ago - 2 comments
Labels: Type: Feature Improvement, Priority: Low

#92 - Move analysis to separate repository

Issue - State: closed - Opened by jcrozum 11 months ago - 6 comments
Labels: Priority: High, Experiments

#91 - Standardize documentation

Issue - State: open - Opened by jcrozum 11 months ago - 6 comments
Labels: Priority: High, Type: Documentation Addition, Type: Feature Addition

#90 - Unused code

Issue - State: closed - Opened by jcrozum 12 months ago - 2 comments
Labels: Priority: Medium

#89 - Clean up repository

Issue - State: closed - Opened by jcrozum 12 months ago
Labels: Priority: Medium, Type: Documentation Error, Type: More Information Needed

#88 - Usability improvments

Pull Request - State: closed - Opened by jcrozum 12 months ago - 3 comments

#87 - rename package to balm

Pull Request - State: closed - Opened by jcrozum 12 months ago - 2 comments

#86 - Percolation optimizations

Pull Request - State: closed - Opened by jcrozum 12 months ago - 3 comments

#85 - AEON stubs outdated?

Issue - State: closed - Opened by jcrozum 12 months ago - 5 comments
Labels: Type: Documentation Error, Type: More Information Needed

#84 - Percolation is very slow

Issue - State: closed - Opened by jcrozum 12 months ago - 12 comments
Labels: Type: Feature Improvement, Priority: Low

#83 - fix edge motifs (back-merge)

Pull Request - State: closed - Opened by jcrozum 12 months ago - 1 comment

#82 - Remaining tasks to run

Issue - State: closed - Opened by kyuhyongpark 12 months ago - 2 comments
Labels: Experiments

#81 - User friendliness improvements

Issue - State: closed - Opened by jcrozum about 1 year ago - 5 comments
Labels: Priority: Medium, Type: Documentation Addition, Type: Feature Addition, Type: Feature Improvement

#80 - Control optimization

Issue - State: open - Opened by jcrozum about 1 year ago - 2 comments
Labels: Priority: Medium, Type: Feature Improvement

#79 - Source SCC based expansion

Issue - State: closed - Opened by kyuhyongpark about 1 year ago - 15 comments
Labels: Type: Feature Addition, Type: Feature Improvement

#78 - Add models with randomly sampled inputs

Pull Request - State: closed - Opened by daemontus about 1 year ago - 2 comments

#77 - Succession diagram size bigger than expected

Issue - State: closed - Opened by kyuhyongpark about 1 year ago - 1 comment
Labels: Type: Bug, Priority: Low

#76 - Random models for benchmarks

Pull Request - State: closed - Opened by kyuhyongpark over 1 year ago - 2 comments

#75 - Investigate using constant nodes as drivers

Issue - State: open - Opened by jcrozum over 1 year ago
Labels: Priority: Medium, Type: Feature Improvement, Type: More Information Needed

#74 - reconciling #71 and #73 for #69

Pull Request - State: closed - Opened by jcrozum over 1 year ago - 5 comments

#73 - Control of succession

Pull Request - State: closed - Opened by jcrozum over 1 year ago - 2 comments

#72 - Storing Succession Diagrams

Issue - State: closed - Opened by kyuhyongpark over 1 year ago - 2 comments
Labels: Type: Feature Addition, Priority: Low

#71 - Lazy succession diagram

Pull Request - State: closed - Opened by daemontus over 1 year ago - 6 comments

#70 - Optimize preprocessing ssf

Pull Request - State: closed - Opened by giang-trinh over 1 year ago - 4 comments

#69 - Tracking issue for control

Issue - State: closed - Opened by jcrozum over 1 year ago - 5 comments
Labels: Priority: High, Type: Feature Addition

#68 - We might need to define the different types of asynchronous updating ("plain", "generalised"/"set", "interval", "linear", and "most permissive"). However, I am delaying this task until we are sure we actually have some viable results in this regard.

Issue - State: closed - Opened by giang-trinh over 1 year ago - 1 comment

#67 - Analysis of Succession Diagrams

Issue - State: closed - Opened by kyuhyongpark over 1 year ago - 3 comments
Labels: Experiments

#66 - Style improvements and safety

Pull Request - State: closed - Opened by jcrozum over 1 year ago - 5 comments

#65 - Meta analysis of update functions in BBM real-world networks

Issue - State: closed - Opened by daemontus over 1 year ago - 3 comments
Labels: Paper, Experiments

#64 - Find a network with locally-monotonic functions and motif-avoidant attractor...

Issue - State: closed - Opened by daemontus over 1 year ago - 8 comments
Labels: Paper

#63 - Find a network with interval update that has a motif-avoidant attractor...

Issue - State: closed - Opened by daemontus over 1 year ago - 2 comments
Labels: Paper

#62 - Add Graphviz or tikz export for succession diagram

Issue - State: closed - Opened by daemontus over 1 year ago - 1 comment
Labels: Priority: Medium, Type: Feature Addition

#61 - Compute attractors and SDs of real-world networks

Issue - State: closed - Opened by daemontus over 1 year ago - 2 comments
Labels: Paper, Experiments

#60 - Generate random models

Issue - State: closed - Opened by daemontus over 1 year ago - 4 comments
Labels: Paper, Experiments

#59 - Write "Partial Succession Diagrams"

Issue - State: closed - Opened by daemontus over 1 year ago - 2 comments
Labels: Paper

#58 - Write "Random models of Boolean networks"

Issue - State: closed - Opened by daemontus over 1 year ago - 1 comment
Labels: Paper

#57 - Write "Influence graphs of Boolean networks"

Issue - State: closed - Opened by daemontus over 1 year ago - 1 comment
Labels: Paper

#56 - Write "Basics of Boolean modeling"

Issue - State: closed - Opened by daemontus over 1 year ago - 4 comments
Labels: Paper

#55 - Publication tracking issue

Issue - State: closed - Opened by daemontus over 1 year ago - 1 comment
Labels: Paper

#54 - Small type hint and style issues

Issue - State: closed - Opened by jcrozum over 1 year ago - 2 comments
Labels: Type: Documentation Addition, Type: Feature Improvement, Priority: Low

#53 - State bdd optimizations

Pull Request - State: closed - Opened by jcrozum over 1 year ago - 3 comments

#52 - Types and speed for percolation

Pull Request - State: closed - Opened by jcrozum over 1 year ago - 2 comments

#51 - Error with trap spaces and drivers

Issue - State: closed - Opened by jcrozum over 1 year ago - 1 comment
Labels: Priority: High, Type: Bug

#50 - potential percolation error

Issue - State: closed - Opened by jcrozum over 1 year ago - 6 comments
Labels: Priority: Critical, Type: Bug

#49 - dict to bdd conversion is very slow

Issue - State: closed - Opened by jcrozum over 1 year ago - 1 comment
Labels: Priority: Medium, Type: Feature Improvement, Type: Benchmarks and Validation

#48 - Terminal restriction space

Pull Request - State: closed - Opened by kyuhyongpark over 1 year ago - 1 comment

#47 - Make specification document

Issue - State: closed - Opened by jcrozum over 1 year ago - 2 comments
Labels: Priority: Medium, Type: Documentation Addition

#46 - Simplified succession diagram

Pull Request - State: closed - Opened by daemontus over 1 year ago - 3 comments

#45 - Benchmarking

Pull Request - State: closed - Opened by daemontus over 1 year ago - 1 comment

#44 - Single-node driver and terminal restriction space optimization

Issue - State: closed - Opened by jcrozum over 1 year ago - 3 comments
Labels: Priority: Medium, Type: Feature Improvement

#43 - Initial implementation of a lazy `SuccessionDiagram`

Pull Request - State: closed - Opened by daemontus over 1 year ago - 6 comments

#42 - Minor improvements to motif avoidant attractor detection

Pull Request - State: closed - Opened by daemontus over 1 year ago - 1 comment

#41 - Support Petri net as input in Trappist directly

Pull Request - State: closed - Opened by daemontus over 1 year ago - 1 comment

#40 - Fix `int` vs `str` problems when representing spaces

Pull Request - State: closed - Opened by daemontus over 1 year ago - 2 comments

#39 - Remove non-determinism from `find_minimum_NFVS`

Pull Request - State: closed - Opened by daemontus over 1 year ago - 2 comments

#38 - Fix automata network generator for empty condition lists.

Pull Request - State: closed - Opened by daemontus over 1 year ago - 2 comments

#37 - Function `detect_motif_avoidant_attractors` fails for petri nets with constant nodes

Issue - State: closed - Opened by daemontus over 1 year ago

#36 - Function `find_minimum_NFVS` is not deterministic

Issue - State: closed - Opened by daemontus over 1 year ago - 5 comments
Labels: Type: Benchmarks and Validation

#35 - Infinite succession loop fix

Pull Request - State: closed - Opened by jcrozum over 1 year ago - 7 comments

#34 - An infinite loop in Succession Diagram construction

Issue - State: closed - Opened by jcrozum over 1 year ago - 5 comments
Labels: Priority: Critical, Type: Bug

#33 - Merger to make working algorithm

Pull Request - State: closed - Opened by jcrozum almost 2 years ago - 4 comments

#32 - Percolation convention

Issue - State: closed - Opened by jcrozum almost 2 years ago - 3 comments
Labels: Type: Feature Improvement, Priority: Low, Type: More Information Needed

#31 - Self negating tr trapspaces

Pull Request - State: closed - Opened by kyuhyongpark almost 2 years ago - 1 comment

#30 - Add Trappist tests for reverse_time, ensure_subspace and avoid_subspaces

Issue - State: closed - Opened by kyuhyongpark almost 2 years ago - 1 comment
Labels: Priority: Medium, Type: Benchmarks and Validation

#29 - Properly compute terminal restriction space

Issue - State: closed - Opened by kyuhyongpark almost 2 years ago

#28 - Succession diagram storage

Pull Request - State: closed - Opened by jcrozum almost 2 years ago - 5 comments

#27 - Replace Pint with something else?

Issue - State: closed - Opened by jcrozum almost 2 years ago - 7 comments
Labels: Priority: High, Type: Feature Improvement

#26 - Meta issue: Basic data structures

Issue - State: closed - Opened by daemontus almost 2 years ago - 7 comments
Labels: Type: Feature Improvement, Priority: Low

#25 - Create an asynchronous automaton

Issue - State: closed - Opened by giang-trinh almost 2 years ago - 1 comment

#24 - Motif-avoidant checking

Pull Request - State: closed - Opened by giang-trinh almost 2 years ago - 2 comments

#23 - Compute the candidate set of states

Pull Request - State: closed - Opened by giang-trinh almost 2 years ago - 3 comments

#22 - Store succession diagram

Issue - State: closed - Opened by jcrozum almost 2 years ago - 1 comment
Labels: Priority: Medium, Type: Feature Addition

#21 - New code of for computing negative feedback vertex sets

Pull Request - State: closed - Opened by giang-trinh almost 2 years ago - 6 comments

#20 - Improve `trappist` integration with `nfvsmotifs`

Pull Request - State: closed - Opened by daemontus almost 2 years ago - 1 comment

#19 - Finding single node drivers of stable motifs

Pull Request - State: closed - Opened by kyuhyongpark almost 2 years ago - 3 comments
Labels: Type: Feature Addition

#18 - Feedback vertex set and idependent cycles computation

Pull Request - State: closed - Opened by daemontus almost 2 years ago - 1 comment

#17 - Add GitHub actions workflow to continuously check for errors

Pull Request - State: closed - Opened by daemontus about 2 years ago - 2 comments

#16 - Add routine for inferring the signed interaction graph of a BN

Pull Request - State: closed - Opened by daemontus about 2 years ago - 3 comments

#15 - A better more general implementation of percolation.

Pull Request - State: closed - Opened by daemontus about 2 years ago - 7 comments

#14 - Add function to compute logical percolation

Issue - State: closed - Opened by jcrozum about 2 years ago - 2 comments
Labels: Priority: High, Type: Feature Addition

GitHub / jcrozum/biobalm issues and pull requests