v0.1.0

MatrixProductBP v0.1.0

Merged pull requests:

• Pair observations and inference (#1) (@stecrotti)
• Re-organization as a Julia module (#2) (@stecrotti)
• add readme (#3) (@stecrotti)
• observations also at time zero (#4) (@stecrotti)
• convergence based on messages instead of beliefs (#5) (@stecrotti)
• use Tullio in SIS (#10) (@abraunst)
• Pair observations moved to only outgoing messages (#11) (@stecrotti)
• Simplifications via Tullio in SIS (#12) (@abraunst)
• replace p0 with phi (#13) (@stecrotti)
• remove two lines (#14) (@abraunst)
• Make the code for SimpleBPFactors more general (#15) (@stecrotti)
• WIP: Cavities (#17) (@abraunst)
• WIP: add codecov (#19) (@stecrotti)
• Trigger coverage when merging PR to main (#20) (@stecrotti)
• interface to SIB is in notebook (#21) (@stecrotti)
• ignore jupyter in language stats (#22) (@stecrotti)
• WIP: more than one factor simultaneously, variable number of variable states (#23) (@abraunst)
• Multithread (#25) (@abraunst)
• SIRS model, comparison with sib on SIR (#26) (@abraunst)
• Small bugfix (#27) (@stecrotti)
• avoid kron2 (#29) (@abraunst)
• Optionally print log of SVD truncations (#30) (@stecrotti)
• Equilibrium results, Erdos-Renyi, more notebooks, some small fixes (#33) (@stecrotti)
• Glauber ± J and the generalizations needed to make it work (#34) (@stecrotti)
• use @cast instead of reshape as it's nicer to read (#35) (@abraunst)
• fix multithread bug (#36) (@abraunst)
• use cavity from CavityTools (#37) (@abraunst)
• CompatHelper: add new compat entry for CavityTools at version 0.1, (keep existing compat) (#38) (@github-actions[bot])
• RFIM, plots for paper (#39) (@stecrotti)
• Plots for paper (#40) (@stecrotti)
• [WIP] Smarter free energy (#43) (@stecrotti)
• logging through logger (#44) (@abraunst)
• [WIP] Epidemics inference (#45) (@stecrotti)
• Callback enhanced with svd info (#46) (@stecrotti)
• Nicer plots, notebooks on AUC (#48) (@stecrotti)
• Large deviations + optional info string to print during progress (#49) (@stecrotti)
• import loop vectorization for Tullio usage (#50) (@abraunst)
• CompatHelper: add new compat entry for LoopVectorization at version 0.12, (keep existing compat) (#52) (@github-actions[bot])
• CompatHelper: bump compat for CavityTools to 0.2, (keep existing compat) (#53) (@github-actions[bot])
• Karate, SIRS, damping, equilibrium, TruncBondThresh, SIS vs softmargin (#54) (@stecrotti)
• CompatHelper: add new compat entry for CavityTools at version 0.2, (keep existing compat) (#55) (@github-actions[bot])
• Plots + large deviations SIS (#56) (@stecrotti)
• Effect of discarding dead epidemics, restore corrupted SIRS notebook (#57) (@stecrotti)
• Fix bug with ising ±J (#60) (@stecrotti)
• Spin glass (#61) (@stecrotti)
• "d-" for "discretized" in legend (#62) (@stecrotti)
• Asymmetric graphs (#63) (@stecrotti)
• Impose compat for LoopVectorization (#65) (@stecrotti)
• Plots with discrete CME (#67) (@stecrotti)
• Generalize marginals to MPTrain (#68) (@stecrotti)
• Equilibrium energy for infinite RRG (#69) (@stecrotti)
• Glauber correlations on infinite graph (#70) (@stecrotti)
• Update CavityTools (#71) (@stecrotti)
• Asymmetric dynamics (#72) (@stecrotti)
• Sample from MatrixProductTrain (#73) (@stecrotti)
• Use LogarithmicNumbers algebra (#74) (@stecrotti)
• Get rid of getT(::MPEM) (#75) (@stecrotti)
• [WIP] Use core code from TensorTrains.jl (#76) (@stecrotti)
• Fix small bug in arg (#77) (@stecrotti)
• Add notebook about convergence of messages (#78) (@stecrotti)
• Some stuff to reply to reviewers (#79) (@stecrotti)
• Fix issue with sampling (#80) (@stecrotti)
• Compat from julia 1.8 on (#81) (@stecrotti)
• Move recursive and test factors to main module (#84) (@stecrotti)
• Use TensorTrains v0.6 (#85) (@stecrotti)
• TensorTrains >= 0.6.1 (#87) (@stecrotti)
• Update on star graph plot (#88) (@stecrotti)
• TensorTrains v 0.7 (#89) (@stecrotti)
• Compute energy of ising model (#90) (@stecrotti)
• CompatHelper: bump compat for IndexedGraphs to 0.4, (keep existing compat) (#91) (@github-actions[bot])
• silence avx warnings (#93) (@abraunst)
• Update readme (#94) (@stecrotti)
• Optimization (#95) (@abraunst)
• Tidy up repo (#96) (@stecrotti)
• Misc (#97) (@stecrotti)
• Infected -> infectious (#98) (@stecrotti)
• CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#99) (@github-actions[bot])
• Generic BP adapted to work with periodic time, with test (#100) (@stecrotti)
• Add link to pnas and errata (#101) (@stecrotti)
• Add bounded compats (#104) (@stecrotti)
• Add license file, tagbot (#105) (@stecrotti)

Closed issues:

• Put pair observations only on outgoing messages (#6)
• Cavity computations (#7)
• Generalize code for SimpleBPFactors (#8)
• Replace time zero prior with observation (#9)
• Introduce MPEM1s ? (#16)
• Add codecov to github actions (#18)
• Add paralellization (#24)
• More general RecursiveBPFactors (#31)
• Warning from LoopVectorization (#58)