### get knitr just the way we like it knitr::opts_chunk$set( message = FALSE, warning = FALSE, error = FALSE, tidy = FALSE, cache = FALSE )

It is only a short way from the toy MLE example to a more useful example using Cox regression.

But first, we need the `survival`

package and the `homomopheR`

package.

if (!require("survival")) { stop("this vignette requires the survival package") } library(homomorpheR)

We generate some simulated data for the purpose of this example. We will have three sites each with patient data (sizes 1000, 500 and 1500) respectively, containing

`sex`

(0, 1) for male/female`age`

between 40 and 70- a biomarker
`bm`

- a
`time`

to some event of interest - an indicator
`event`

which is 1 if an event was observed and 0 otherwise.

It is common to fit stratified models using sites as strata since the
patient characteristics usually differ from site to site. So the
baseline hazards (`lambdaT`

) are different for each site but they
share common coefficients (`beta.1`

, `beta.2`

and `beta.3`

for `age`

,
`sex`

and `bm`

respy.) for the model. See [@survival-book] by Therneau
and Grambsch for details. So our model for each site $i$ is

$$ S(t, age, sex, bm) = [S_0^i(t)]^{\exp(\beta_1 age + \beta_2 sex + \beta_3 bm)} $$

sampleSize <- c(n1 = 1000, n2 = 500, n3 = 1500) set.seed(12345) beta.1 <- -.015; beta.2 <- .2; beta.3 <- .001; lambdaT <- c(5, 4, 3) lambdaC <- 2 coxData <- lapply(seq_along(sampleSize), function(i) { sex <- sample(c(0, 1), size = sampleSize[i], replace = TRUE) age <- sample(40:70, size = sampleSize[i], replace = TRUE) bm <- rnorm(sampleSize[i]) trueTime <- rweibull(sampleSize[i], shape = 1, scale = lambdaT[i] * exp(beta.1 * age + beta.2 * sex + beta.3 * bm )) censoringTime <- rweibull(sampleSize[i], shape = 1, scale = lambdaC) time <- pmin(trueTime, censoringTime) event <- (time == trueTime) data.frame(stratum = i, sex = sex, age = age, bm = bm, time = time, event = event) })

So here is a summary of the data for the three sites.

```
str(coxData[[1]])
```

```
str(coxData[[2]])
```

```
str(coxData[[3]])
```

If the data were all aggregated in one place, it would very simple to fit the model. Below, we row-bind the data from the three sites.

aggModel <- coxph(formula = Surv(time, event) ~ sex + age + bm + strata(stratum), data = do.call(rbind, coxData)) aggModel

Here `age`

and `sex`

are significant, but `bm`

is not. The estimates
$\hat{\beta}$ are `(-0.180, .020, .007)`

.

We can also print out the value of the (partial) log-likelihood at the MLE.

```
aggModel$loglik
```

The first is the value at the parameter value `(0, 0, 0)`

and the last
is the value at the MLE.

Assume now that the data `coxData`

is distributed between three sites
none of whom want to share actual data among each other or even with a
master computation process. They wish to keep their data secret but
are willing, together, to provide the sum of their local negative
log-likelihoods. They need to do this in a way so that the master
process will not be able to associate the contribution to the
likelihood from each site.

The overall likelihood function $l(\lambda)$ for the entire data is therefore the sum of the likelihoods at each site: $l(\lambda) = l_1(\lambda)+l_2(\lambda)+l_3(\lambda).$ How can this likelihood be computed while maintaining privacy?

Assuming that every site including the master has access to a
homomorphic computation library such as `homomorpheR`

, the likelihood
can be computed in a privacy-preserving manner using the following
scheme. We use $E(x)$ and $D(x)$ to denote the encrypted and decrypted
values of $x$ respectively.

- Master generates a public/private key pair. Master distributes the public key to all sites. (The private key is not distributed and kept only by the master.)
- Master generates a random offset $r$ to obfuscate the intial likelihood.
- Master sends $E(r)$ and a guess $\lambda_0$ to site 1. Note that $\lambda$ is not encrypted.
- Site 1 computes $l_1 = l(\lambda_0, y_1)$, the local likelihood for local data $y_1$ using parameter $\lambda_0$. It then sends on $\lambda_0$ and $E(r) + E(l_1)$ to site 2.
- Site 2 computes $l_2 = l(\lambda_0, y_2)$, the local likelihood for local data $y_2$ using parameter $\lambda_0$. It then sends on $\lambda_0$ and $E(r) + E(l_1) + E(l_2)$ to site 3.
- Site 3 computes $l_3 = l(\lambda_0, y_3)$, the local likelihood for local data $y_3$ using parameter $\lambda_0$. It then sends on $E(r) + E(l_1) + E(l_2) + E(l_3)$ back to master.
- Master retrieves $E(r) + E(l_1) + E(l_2) + E(l_3)$ which, due to the homomorphism, is exactly $E(r+l_1+l_2+l_3) = E(r+l).$ So the master computes $D(E(r+l)) - r$ to obtain the value of the overall likelihood at $\lambda_0$.
- Master updates $\lambda_0$ with a new guess $\lambda_1$ and repeats steps 1-5. This process is iterated to convergence. For added security, even steps 0-5 can be repeated, at additional computational cost.

This is pictorially shown below.

The above implementation assumes that the encryption and decryption can happen with real numbers which is not the actual situation. Instead, we use rational approximations using a large denominator, $2^{256}$, say. In the future, of course, we need to build an actual library is built with rigorous algorithms guaranteeing precision and overflow/undeflow detection. For now, this is just an ad hoc implementation.

Also, since we are only using homomorphic additive properties, a partial homomorphic scheme such as the Paillier Encryption system will be sufficient for our computations.

We define a class to encapsulate our sites that will compute the
Poisson likelihood on site data given a parameter $\lambda$. Note how
the `addNLLAndForward`

method takes care to split the result into an
integer and fractional part while performing the arithmetic
operations. (The latter is approximated by a rational number.)

We define a class to encapsulate our sites that will compute the partial log likelihood on site data given a parameter $\beta$.

In the code below, we exploit, for expository purposes, a feature of
`coxph`

: a control parameter can be passed to evaluate the
partial likelihood at a given $\beta$ value.

Site <- R6::R6Class("Site", private = list( ## name of the site name = NA, ## only master has this, NA for workers privkey = NA, ## local data data = NA, ## The next site in the communication: NA for master nextSite = NA, ## is this the master site? iAmMaster = FALSE, ## intermediate result variable intermediateResult = NA, ## Control variable for cox regression cph.control = NA ), public = list( count = NA, ## Common denominator for approximate real arithmetic den = NA, ## The public key; everyone has this pubkey = NA, initialize = function(name, data, den) { private$name <- name private$data <- data self$den <- den private$cph.control <- replace(coxph.control(), "iter.max", 0) }, setPublicKey = function(pubkey) { self$pubkey <- pubkey }, setPrivateKey = function(privkey) { private$privkey <- privkey }, ## Make me master makeMeMaster = function() { private$iAmMaster <- TRUE }, ## add neg log lik and forward to next site addNLLAndForward = function(beta, enc.offset) { if (private$iAmMaster) { ## We are master, so don't forward ## Just store intermediate result and return private$intermediateResult <- enc.offset } else { ## We are workers, so add and forward ## add negative log likelihood and forward result to next site ## Note that offset is encrypted nllValue <- self$nLL(beta) result.int <- floor(nllValue) result.frac <- nllValue - result.int result.fracnum <- gmp::as.bigq(gmp::numerator(gmp::as.bigq(result.frac) * self$den)) pubkey <- self$pubkey enc.result.int <- pubkey$encrypt(result.int) enc.result.fracnum <- pubkey$encrypt(result.fracnum) result <- list(int = pubkey$add(enc.result.int, enc.offset$int), frac = pubkey$add(enc.result.fracnum, enc.offset$frac)) private$nextSite$addNLLAndForward(beta, enc.offset = result) } ## Return a TRUE result for now. TRUE }, ## Set the next site in the communication graph setNextSite = function(nextSite) { private$nextSite <- nextSite }, ## The negative log likelihood nLL = function(beta) { if (private$iAmMaster) { ## We're master, so need to get result from sites ## 1. Generate a random offset and encrypt it pubkey <- self$pubkey offset <- list(int = random.bigz(nBits = 256), frac = random.bigz(nBits = 256)) enc.offset <- list(int = pubkey$encrypt(offset$int), frac = pubkey$encrypt(offset$frac)) ## 2. Send off to next site throwaway <- private$nextSite$addNLLAndForward(beta, enc.offset) ## 3. When the call returns, the result will be in ## the field intermediateResult, so decrypt that. sum <- private$intermediateResult privkey <- private$privkey intResult <- as.double(privkey$decrypt(sum$int) - offset$int) fracResult <- as.double(gmp::as.bigq(privkey$decrypt(sum$frac) - offset$frac) / den) intResult + fracResult } else { ## We're worker, so compute local negative log likelihood tryCatch({ m <- coxph(formula = Surv(time, event) ~ sex + age + bm, data = private$data, init = beta, control = private$cph.control) -(m$loglik[1]) }, error = function(e) NA) } }) )

We are now ready to use our sites in the computation.

We also choose a denominator for all our rational approximations.

keys <- PaillierKeyPair$new(1024) ## Generate new public and private key. den <- gmp::as.bigq(2)^256 #Our denominator for rational approximations

site1 <- Site$new(name = "Site 1", data = coxData[[1]], den = den) site2 <- Site$new(name = "Site 2", data = coxData[[2]], den = den) site3 <- Site$new(name = "Site 3", data = coxData[[3]], den = den)

The master process is also a site but has no data. So has to be thus designated.

## Master has no data! master <- Site$new(name = "Master", data = c(), den = den) master$makeMeMaster()

site1$setPublicKey(keys$pubkey) site2$setPublicKey(keys$pubkey) site3$setPublicKey(keys$pubkey) master$setPublicKey(keys$pubkey)

Only master has private key for decryption.

master$setPrivateKey(keys$getPrivateKey())

Master will always send to the first site, and then the others have to forward results in turn with the last site returning to the master.

master$setNextSite(site1) site1$setNextSite(site2) site2$setNextSite(site3) site3$setNextSite(master)

library(stats4) nll <- function(age, sex, bm) master$nLL(c(age, sex, bm)) fit <- mle(nll, start = list(age = 0, sex = 0, bm = 0))

The summary will show the results.

```
summary(fit)
```

Note how the estimated coefficients and standard errors closely match the full model summary below.

```
summary(aggModel)
```

And the log likelihood of the distributed homomorphic fit also matches as the following computation shows.

## -2 Log L -2 * logLik(fit)

The results should be the same as above.

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