SHMEngine

Somatic Hypermutation Engine implementing five biologically- inspired mutation strategies for the bHIVE artificial immune system.

Details

The five strategies are:

uniform

Classic random Gaussian noise. Mutation rate = (1-affinity) * decay^(iter-1). This is the original bHIVE behavior.

airs

AIRS-style affinity-proportional mutation. Rate = c * exp(-affinity / T). From Watkins & Timmis (AIRS2), achieving 50% better data reduction than uniform.

hotspot

Feature-importance-weighted mutation. Features with higher gradient magnitude mutate more, analogous to AID targeting WRCY motifs in real SHM.

energy

Energy-budget-constrained mutation. Total mutation magnitude bounded by E = E_0 * (1-affinity)^2, inspired by Kleinstein's E_SHM ~ N_Mut^2 model.

adaptive

Per-feature adaptive mutation rate with moment tracking, directly implementing SHM as the Adam optimizer.

Public fields

method

Character. One of "uniform", "airs", "hotspot", "energy", "adaptive".

params

Named list of method-specific parameters.

m1_state

First moment state matrix (for adaptive method).

m2_state

Second moment state matrix (for adaptive method).

Methods

Public methods

• SHMEngine$new()

• SHMEngine$init_state()

• SHMEngine$reset_state()

• SHMEngine$print()

• SHMEngine$clone()

---

Method new()

Create a new SHMEngine.

Usage

SHMEngine$new(
  method = "uniform",
  decay = 1,
  mutationMin = 0.01,
  c_rate = 1,
  temperature = 0.5,
  E_0 = 1,
  base_rate = 0.1,
  beta1 = 0.9,
  beta2 = 0.999,
  adam_epsilon = 1e-08
)

Arguments

method

Character. Mutation strategy.

decay

Numeric. Per-iteration mutation rate decay (uniform method).

mutationMin

Numeric. Minimum mutation rate floor.

c_rate

Numeric. Scaling constant (airs method).

temperature

Numeric. Temperature parameter (airs method).

E_0

Numeric. Energy budget base (energy method).

base_rate

Numeric. Base mutation rate (hotspot, adaptive methods).

beta1

Numeric. First moment decay (adaptive method, like Adam).

beta2

Numeric. Second moment decay (adaptive method, like Adam).

adam_epsilon

Numeric. Numerical stability (adaptive method).

---

Method init_state()

Initialize internal state for adaptive method.

Usage

SHMEngine$init_state(nAntibodies, nFeatures)

Arguments

nAntibodies

Integer. Number of antibodies.

nFeatures

Integer. Number of features.

---

Method reset_state()

Reset moment states (e.g., after suppression changes antibody count).

Usage

SHMEngine$reset_state(nAntibodies, nFeatures, kept_idx = NULL)

Arguments

nAntibodies

Integer. New number of antibodies.

nFeatures

Integer. Number of features.

kept_idx

Integer vector. Indices of antibodies that were kept.

---

Method print()

Print summary.

Usage

SHMEngine$print(...)

Arguments

...

Not used.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SHMEngine$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Create different SHM engines
shm_uniform  <- SHMEngine$new(method = "uniform")
shm_adaptive <- SHMEngine$new(method = "adaptive", base_rate = 0.1)
shm_airs     <- SHMEngine$new(method = "airs", temperature = 0.3)
print(shm_adaptive)
#> <SHMEngine> method='adaptive'
#>   base_rate: 0.1
#>   beta1: 0.9
#>   beta2: 0.999