MemoryPool

Manages long-lived memory cells that can be recalled when distribution shifts are detected. Implements the immunological distinction between short-lived effector cells and long-lived memory cells.

Public fields

memory_cells

Numeric matrix of archived memory antibodies.

memory_metadata

Data frame of metadata for memory cells.

archive_threshold

Affinity threshold for archiving (only high-quality antibodies become memory).

max_memory

Maximum number of memory cells to store.

recall_threshold

Threshold for triggering memory recall.

Methods

Public methods

• MemoryPool$new()

• MemoryPool$archive()

• MemoryPool$recall()

• MemoryPool$size()

• MemoryPool$print()

• MemoryPool$clone()

---

Method new()

Create a new MemoryPool.

Usage

MemoryPool$new(
  archive_threshold = 0.5,
  max_memory = 100,
  recall_threshold = 0.3
)

Arguments

archive_threshold

Numeric. Minimum average affinity to archive.

max_memory

Integer. Maximum memory cells.

recall_threshold

Numeric. Minimum affinity to recall a memory.

---

Method archive()

Archive high-performing antibodies as memory cells.

Usage

MemoryPool$archive(
  repertoire,
  X,
  affinityFunc = "gaussian",
  affinityParams = list(alpha = 1, c = 1, p = 2)
)

Arguments

repertoire

An ImmuneRepertoire.

X

Training data matrix.

affinityFunc

Character. Affinity function.

affinityParams

List. Affinity parameters.

Returns

Integer. Number of new memory cells archived.

---

Method recall()

Recall memory cells relevant to current data.

Usage

MemoryPool$recall(
  X,
  affinityFunc = "gaussian",
  affinityParams = list(alpha = 1, c = 1, p = 2)
)

Arguments

X

Data matrix to match against memory.

affinityFunc

Character. Affinity function.

affinityParams

List. Affinity parameters.

Returns

Numeric matrix of recalled memory cells (may be empty).

---

Method size()

Get current memory pool size.

Usage

MemoryPool$size()

Returns

Integer.

---

Method print()

Print summary.

Usage

MemoryPool$print(...)

Arguments

...

Not used.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

MemoryPool$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Archive and recall memory cells
data(iris)
X <- as.matrix(iris[, 1:4])
A <- X[sample(150, 10), ]
mp <- MemoryPool$new(archive_threshold = 0.01)
rep <- ImmuneRepertoire$new(A)
mp$archive(rep, X)
#> [1] 10
mp$size()  # number of archived memories
#> [1] 10
recalled <- mp$recall(X[1:5, ])
nrow(recalled)  # memories relevant to query
#> [1] 5