Privacy-Preserving Count Aggregation

The problem

Multiple research sites each hold patient data and want to know the total count of patients matching a criterion (say “age < 50 and sex == 'F' and biomarker < 0.2”) without revealing the individual per-site counts to anyone, including the aggregator running the aggregation.

Here we use OpenFHE’s BFV scheme via the openfhe.R package. BFV operates on integer vectors with both addition and multiplication — well-suited to counting and other exact integer-valued aggregates.

This is the BFV companion to the CKKS-based real-valued master/worker vignettes (vignette("mle"), vignette("cox")). For exact integer aggregation BFV is the right choice; for real-valued sufficient statistics CKKS is the right choice.

Setup

library(openfhe.R)

set.seed(42)
site_data <- lapply(c(1000, 500, 1500), function(n) {
    data.frame(
        age       = sample(40:70, n, replace = TRUE),
        sex       = sample(c("M", "F"), n, replace = TRUE),
        biomarker = runif(n, 0, 1)
    )
})

The aggregator sets up encryption

## BFV: exact integer arithmetic mod plaintext_modulus.
cc   <- fhe_context("BFV",
                    plaintext_modulus    = 65537L,
                    multiplicative_depth = 1L)
keys <- key_gen(cc)

pk <- keys@public
sk <- keys@secret

In a real deployment the aggregator distributes the public key (and the serialized context) to each site. The secret key stays with the aggregator. We simulate this in one R session by sharing cc and pk locally.

Each site computes locally and encrypts

site_encrypt <- function(site_df, cc, pk) {
    count <- sum(site_df$age < 50 &
                 site_df$sex == "F" &
                 site_df$biomarker < 0.2)
    pt    <- make_packed_plaintext(cc, as.integer(count))
    encrypt(pk, pt, cc = cc)
}

ct_site1 <- site_encrypt(site_data[[1]], cc, pk)
ct_site2 <- site_encrypt(site_data[[2]], cc, pk)
ct_site3 <- site_encrypt(site_data[[3]], cc, pk)

These encrypted counts are opaque to the aggregator — it learns nothing about any individual site’s count.

The aggregator aggregates

## Homomorphic addition: the aggregator never decrypts intermediate values.
ct_total <- ct_site1 + ct_site2 + ct_site3

## Only the aggregator holds the secret key.
result      <- decrypt(ct_total, sk, cc = cc)
total_count <- get_packed_value(result)[1]
total_count

## [1] 105

Verification

true_count <- sum(sapply(site_data, function(df) {
    sum(df$age < 50 & df$sex == "F" & df$biomarker < 0.2)
}))
true_count

## [1] 105

stopifnot(total_count == true_count)

The aggregated count matches the cleartext computation exactly. BFV is an exact scheme over the integers: unlike the real-valued arithmetic used elsewhere in this package, it introduces no approximation error at all.

The details of what happened

The aggregator created an encryption context and distributed the public key to all sites.
Each site computed its local count in the clear, encrypted it, and sent the encrypted count to the aggregator.
The aggregator added the encrypted counts using +, which gives the same answer as adding the counts themselves.
Only the aggregator, holding the secret key, could decrypt the total.

No site revealed its individual count. The aggregator never saw any patient-level data. The total is exact.

Serializing for a real distributed protocol

In a real deployment each site needs the aggregator’s context and public key. openfhe.R provides serialization:

tdir <- tempdir()
fhe_serialize(cc, file.path(tdir, "context.bin"))
fhe_serialize(pk, file.path(tdir, "pubkey.bin"))

cc_remote <- fhe_deserialize(file.path(tdir, "context.bin"), "CryptoContext")
pk_remote <- fhe_deserialize(file.path(tdir, "pubkey.bin"), "PublicKey")

ct <- encrypt(pk_remote,
              make_packed_plaintext(cc_remote, 42L),
              cc = cc_remote)

fhe_serialize(ct, file.path(tdir, "site_count.bin"))
ct_received <- fhe_deserialize(file.path(tdir, "site_count.bin"), "Ciphertext")
result      <- decrypt(ct_received, sk, cc = cc)
get_packed_value(result)[1]

## [1] 42

Balasubramanian Narasimhan

2026-10-03