Hypothesis Generation (HyGene) Model

A Julia implementation of a model of diagnostic hypothesis generation ("HyGene") and decision-making¹². The overall model is based off of Minerva 2³ and Minerva-DM⁴.

Types and Structures

HyGene.jl simulations are centered upon the structures that hold the data and parameters. The values of each structure (struct) can be changes (mutable), and each structure belongs to a custom type hierarchy. All types and structures are defined within ./src/structures.jl.

HypothesisGeneration

The HypothesisGeneration object does not hold information; rather, it is a "supertype" that encompasses all other structs in the simulation. For example, if you were to list the subtypes of HypothesisGeneration, it would look something like this:

julia> using TypeTree
julia> print(join(tt(HypothesisGeneration),""))
HypothesisGeneration
 ├─ Context
 ├─ HyGeneModel
 ├─ Hypothesis
 ├─ Observation
 └─ Trace

Thus, the rest of the structures listed below belong to the HypothesisGeneration superclass.

HypothesisGeneration is itself a subclass of a ContinuousUnivariateDistribution; however, this is mostly useful for use with Bayesian parameter estimators, such as Turing.jl and DifferentialEvolutionMCMC.jl.

HyGeneModel

This is the main structure within the HyGene.jl architecture. It holds all static and dynamic parameters (although mutable structs allow for redefinition), as well as memory stores (long-term, short-term, semantic). Information is written and directly manipulated from this structure. The information vectors that used in the simulations (such as HyGeneModel.long_term_memory) are compound vectors, or vectors of vectors. Each minivector represents a context or hypothesis, and several minivectors are chained together to form a larger representation.

Context and Hypothesis

These are similar structures that hold singular vectors of numbers representing individual contexts and hypotheses. They are mostly useful when constructing observations and traces, but are also useful for comparison to degraded representations within a HyGeneModel object.

Observation and Trace

A raw, unaltered version of an observed event is recorded as an Observation. These contain several mini-vectors, including one that provides information about the correct classification of an item (i.e., Hypothesis). When constructing a HyGeneModel object, Observation objects are translated into Trace objects, which contain degraded representations of the original item vectors with probability between 0 and 1 via HyGeneModel.decay. Trace objects are only meant to exist within memory stores in the main structure. When the model is engaged in a test trial, the contents of a new Observation object is compared to long-term memory.

Simulation Controllers

Here is a description of the functions defined in ./src/sim_controllers.jl.

Example

A short, albeit incomplete example is available in ./model/example.jl.

Footnotes and References