I'm getting a timeout for those no matter what in Java. I'm not sure I can optimize this solution much more and I'm starting to think it's not my fault that I'm timing out.

Same for Swift. And same for PHP solutions.

I'm using two NSCountedSets and have tried minimizing the boilerplate code as much as possible to no success.

Same here. 2 Hashmaps so no .contains() or anything. In fact not function calls aside from append() is used. Still no go. No one on leaderboard got full point in Swift

yeah i am also getting timeout for 9-13 testcases.

I tried running the barebones boilerplate code and I am still getting timeouts

I was experiencing the same issue. It turns out that the boilerplate code is the problem, because if you set freqQuery(queries: [[Int]])->[Int] to simply return [], it still fails some of the tests with timeout.

So, in the boilerplate, I replaced:

let queries: [[Int]] = AnyIterator{ readLine()?.replacingOccurrences(of: "\\s+$", with: "", options: .regularExpression) }.prefix(q).map {
    let queriesRow: [Int] = $0.split(separator: " ").map {
        if let queriesItem = Int($0) {
            return queriesItem
        } else { fatalError("Bad input") }
    }

    guard queriesRow.count == 2 else { fatalError("Bad input") }

    return queriesRow
}

with:

var queries = [[Int]]()
while let raw = readLine() {
    guard raw.count >= 3, raw[raw.index(raw.startIndex, offsetBy: 1)] == " " else { fatalError("Bad input") }
    guard let op = Int("\(raw[raw.startIndex])"),
        let val = Int("\(raw[raw.index(raw.startIndex, offsetBy: 2)..<raw.endIndex])")
    else {
        fatalError("Bad input")
    }
    queries.append([op, val])
}

And then all my tests passed. I'll submit this as a suggestion for them to fix as well. Cheers!