Skip to content

Commit

Permalink
start on hippocampus
Browse files Browse the repository at this point in the history
  • Loading branch information
@rcoreilly
rcoreilly committed Dec 19, 2024
1 parent 5e99617 commit ff740e5
Show file tree
Hide file tree
Showing 10 changed files with 820 additions and 1,833 deletions.
219 changes: 107 additions & 112 deletions examples/hip/config.go
View file
Original file line number Diff line number Diff line change
@@ -1,180 +1,175 @@
// Copyright (c) 2020, The Emergent Authors. All rights reserved.
// Copyright (c) 2024, The Emergent Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.

package main

import "github.com/emer/axon/v2/axon"
import (
"github.com/emer/axon/v2/axon"
)

// ParamConfig has config parameters related to sim params
// EnvConfig has config params for environment.
type EnvConfig struct {

// Env parameters: can set any field/subfield on Env struct,
// using standard TOML formatting.
Env map[string]any

// MinDiffPct is the minimum difference between item random patterns,
// as a proportion (0-1) of total active
MinDiffPct float32 `default:"0.5"`

// DriftCtxt means use drifting context representations,
// otherwise does bit flips from prototype.
DriftCtxt bool

// CtxtFlipPct is the proportion (0-1) of active bits to flip
// for each context pattern, relative to a prototype, for non-drifting.
CtxtFlipPct float32 `default:"0.25"`

// DriftPct is percentage of active bits that drift, per step, for drifting context.
DriftPct float32 `default:"0.1"`
}

// ParamConfig has config parameters related to sim params.
type ParamConfig struct {

// network parameters
Network map[string]any
// InToEc2PCon is percent connectivity from Input to EC2.
InToEc2PCon float32 `default:"0.25"`

// ECPctAct is percent activation in EC pool, used in patgen for input generation.
ECPctAct float32 `default:"0.2"`

// Extra Param Sheet name(s) to use (space separated if multiple) -- must be valid name as listed in compiled-in params or loaded params
// Sheet is the extra params sheet name(s) to use (space separated
// if multiple). Must be valid name as listed in compiled-in params
// or loaded params.
Sheet string

// extra tag to add to file names and logs saved from this run
// Tag is an extra tag to add to file names and logs saved from this run.
Tag string

// user note -- describe the run params etc -- like a git commit message for the run
// Note is additional info to describe the run params etc,
// like a git commit message for the run.
Note string

// Name of the JSON file to input saved parameters from.
File string `nest:"+"`

// Save a snapshot of all current param and config settings in a directory named params_<datestamp> (or _good if Good is true), then quit -- useful for comparing to later changes and seeing multiple views of current params
// SaveAll will save a snapshot of all current param and config settings
// in a directory named params_<datestamp> (or _good if Good is true),
// then quit. Useful for comparing to later changes and seeing multiple
// views of current params.
SaveAll bool `nest:"+"`

// for SaveAll, save to params_good for a known good params state. This can be done prior to making a new release after all tests are passing -- add results to git to provide a full diff record of all params over time.
// Good is for SaveAll, save to params_good for a known good params state.
// This can be done prior to making a new release after all tests are passing.
// Add results to git to provide a full diff record of all params over level.
Good bool `nest:"+"`
}

// RunConfig has config parameters related to running the sim
// RunConfig has config parameters related to running the sim.
type RunConfig struct {

// mem % correct level (proportion) above which training on current list stops (switch from AB to AC or stop on AC)
StopMem float32 `default:"0.9"`

// use the GPU for computation -- generally faster even for small models if NData ~16
// GPU uses the GPU for computation, generally faster than CPU even for
// small models if NData ~16.
GPU bool `default:"true"`

// number of parallel threads for CPU computation -- 0 = use default
// NData is the number of data-parallel items to process in parallel per trial.
// Is significantly faster for both CPU and GPU. Results in an effective
// mini-batch of learning.
NData int `default:"10" min:"1"`

// NThreads is the number of parallel threads for CPU computation;
// 0 = use default.
NThreads int `default:"0"`

// starting run number -- determines the random seed -- runs counts from there -- can do all runs in parallel by launching separate jobs with each run, runs = 1
// MemThr is the threshold on proportion on / off error to count item as remembered
MemThr float64 `default:"0.34"`

// StopMem is memory pct correct level (proportion) above which training
// on current list stops (switch from AB to AC or stop on AC).
StopMem float32 `default:"0.9"`

// Run is the _starting_ run number, which determines the random seed.
// NRuns counts up from there. Can do all runs in parallel by launching
// separate jobs with each starting Run, NRuns = 1.
Run int `default:"0"`

// total number of runs to do when running Train
// Runs is the total number of runs to do when running Train, starting from Run.
Runs int `default:"5" min:"1"`

// total number of epochs per run
// Epochs is the total number of epochs per run.
Epochs int `default:"100"`

// total number of trials per epoch. Should be an even multiple of NData.
NTrials int `default:"20"`
// Trials is the total number of trials per epoch.
// Should be an even multiple of NData.
Trials int `default:"20"`

// number of data-parallel items to process in parallel per trial -- works (and is significantly faster) for both CPU and GPU. Results in an effective mini-batch of learning.
NData int `default:"10" min:"1"`
// Cycles is the total number of cycles per trial: at least 200.
Cycles int `default:"200"`

// PlusCycles is the total number of plus-phase cycles per trial. For Cycles=300, use 100.
PlusCycles int `default:"50"`

// how often to run through all the test patterns, in terms of training epochs -- can use 0 or -1 for no testing
TestInterval int `default:"1"`
// TestInterval is how often (in epochs) to run through all the test patterns,
// in terms of training epochs. Can use 0 or -1 for no testing.
TestInterval int `default:"5"`
}

// LogConfig has config parameters related to logging data
// LogConfig has config parameters related to logging data.
type LogConfig struct {

// if true, save final weights after each run
// SaveWeights will save final weights after each run.
SaveWeights bool

// if true, save train epoch log to file, as .epc.tsv typically
Epoch bool `default:"true" nest:"+"`

// if true, save run log to file, as .run.tsv typically
Run bool `default:"true" nest:"+"`

// if true, save train trial log to file, as .trl.tsv typically. May be large.
Trial bool `default:"false" nest:"+"`
// Train has the list of Train mode levels to save log files for.
Train []string `default:"['Run', 'Epoch']" nest:"+"`

// if true, save testing epoch log to file, as .tst_epc.tsv typically. In general it is better to copy testing items over to the training epoch log and record there.
TestEpoch bool `default:"false" nest:"+"`

// if true, save testing trial log to file, as .tst_trl.tsv typically. May be large.
TestTrial bool `default:"false" nest:"+"`

// if true, save network activation etc data from testing trials, for later viewing in netview
NetData bool
}

// PatConfig have the pattern parameters
type PatConfig struct {

// minimum difference between item random patterns, as a proportion (0-1) of total active
MinDiffPct float32

// use drifting context representations -- otherwise does bit flips from prototype
DriftCtxt bool

// proportion (0-1) of active bits to flip for each context pattern, relative to a prototype, for non-drifting
CtxtFlipPct float32

// percentage of active bits that drift, per step, for drifting context
DriftPct float32
}

func (pp *PatConfig) Defaults() {
pp.MinDiffPct = 0.5
pp.CtxtFlipPct = .25
// Test has the list of Test mode levels to save log files for.
Test []string `nest:"+"`
}

type ModConfig struct {

// percent connectivity from Input to EC2
InToEc2PCon float32

// percent activation in EC pool, used in patgen for input generation
// percent activation in EC pool, used in patgen for input generation
ECPctAct float32

// memory threshold
MemThr float64
}

func (mod *ModConfig) Defaults() {
// patgen
mod.ECPctAct = 0.2
// Config has the overall Sim configuration options.
type Config struct {

// input to EC2 pcon
mod.InToEc2PCon = 0.25
// Name is the short name of the sim.
Name string `display:"-" default:"Hip"`

// // theta EDL in CA1
// mod.ThetaLow = 0.9 // doesn't have strong effect at low NTrials but shouldn't go too low (e.g., 0.3)
// mod.ThetaHigh = 1
// Title is the longer title of the sim.
Title string `display:"-" default:"Axon hippocampus"`

// // EDL in CA3
// mod.MossyDel = 4
// mod.MossyDelTest = 3
// URL is a link to the online README or other documentation for this sim.
URL string `display:"-" default:"https://github.com/emer/axon/blob/main/examples/hip/README.md"`

// memory threshold
mod.MemThr = 0.34
}
// Doc is brief documentation of the sim.
Doc string `display:"-" default:"Simulates the hippocampus on basic AB-AC paired associates task."`

// Config is a standard Sim config -- use as a starting point.
type Config struct {

// specify include files here, and after configuration, it contains list of include files added
// Includes has a list of additional config files to include.
// After configuration, it contains list of include files added.
Includes []string

// open the GUI -- does not automatically run -- if false, then runs automatically and quits
// GUI means open the GUI. Otherwise it runs automatically and quits,
// saving results to log files.
GUI bool `default:"true"`

// log debugging information
// Debug reports debugging information.
Debug bool

// misc model parameters
Mod ModConfig `display:"inline"`

// Hippocampus sizing parameters
Hip axon.HipConfig
// Hip has hippocampus sizing parameters.
Hip axon.HipConfig `display:"add-fields"`

// parameters for the input patterns
Pat PatConfig
// Env has environment configuration options.
Env EnvConfig `display:"add-fields"`

// parameter related configuration options
// Params has parameter related configuration options.
Params ParamConfig `display:"add-fields"`

// sim running related configuration options
// Run has sim running related configuration options.
Run RunConfig `display:"add-fields"`

// data logging related configuration options
// Log has data logging related configuration options.
Log LogConfig `display:"add-fields"`
}

func (cfg *Config) Defaults() {
cfg.Mod.Defaults()
cfg.Hip.Defaults()
cfg.Pat.Defaults()
}

func (cfg *Config) IncludesPtr() *[]string { return &cfg.Includes }
Loading

0 comments on commit ff740e5

Please sign in to comment.