LCS in Golang

Saturday, 7 March 2015

One of the fundamental algorithms in Computing Science is the LCS, or Longest Common Subsequence. This post will not attempt to explain the algorithm to any great degree. There are any number of references available to show how the algorithm works, as well as reference implementations you can obtain.

Here we will look at the implementation of a Golang version of LCS, which will would ultimately allow us to generate a Unix “unidiff” style output for two given files. As you start looking at the available implementations of LCS, you quickly find that they are basically always implemented on pairs of strings. The algorithm itself is easy enough to generalize to objects and types beyonds strings and characters, but… well, it’s just not done for you.

Usually at this point, the software engineering contingent that comes from a language with generics starts shouting about the lack of generics in Golang being a very big problem. While I agree that generics can be handy at times, I really hate them with a passion. Most of the time they are not required, and using them just because you can, usually results in grossly inefficient and bloated code. Also, I’ve yet to see an implementation of generics that is not either written in a disgustingly incomprehensible syntax, nor also suffers from run time typing issues; either by tossing type safety out the window, or using run-time checks and tossing exceptions at run time. Oh yeah, I hate exceptions as well… but that’s another topic.

So, let’s get started in having a look at the LCS implementations as given in some of the links above. I won’t bother to identify which came from which (feel free to lookup the references yourself). The first implementation looks like the following:

func LCS1(a, b string) (int, string) { arunes := []rune(a) brunes := []rune(b) aLen := len(arunes) bLen := len(brunes) lengths := make([][]int, aLen+1) for i := 0; i <= aLen; i++ { lengths[i] = make([]int, bLen+1) } // row 0 and column 0 are initialized to 0 already for i := 0; i < aLen; i++ { for j := 0; j < bLen; j++ { if arunes[i] == brunes[j] { lengths[i+1][j+1] = lengths[i][j] + 1 } else if lengths[i+1][j] > lengths[i][j+1] { lengths[i+1][j+1] = lengths[i+1][j] } else { lengths[i+1][j+1] = lengths[i][j+1] } } } // read the substring out from the matrix s := make([]rune, 0, lengths[aLen][bLen]) for x, y := aLen, bLen; x != 0 && y != 0; { if lengths[x][y] == lengths[x-1][y] { x-- } else if lengths[x][y] == lengths[x][y-1] { y-- } else { s = append(s, arunes[x-1]) x-- y-- } } // reverse string for i, j := 0, len(s)-1; i < j; i, j = i+1, j-1 { s[i], s[j] = s[j], s[i] } return len(s), string(s) }

As we can see, this version of LCS is rather specific to taking string ’s as input, and operates on rune ’s within. There are some nice properties with implementation. It works on UTF-8 characters. So it is “internationalized” right from the get go. A win for Golang in my opinion. A possibly easier to read version might be something like this:

func Max(more ...int) int { max_num := more[0] for _, elem := range more { if max_num < elem { max_num = elem } } return max_num } func LCS2(str1, str2 string) (int, string) { len1 := len(str1) len2 := len(str2) table := make([][]int, len1+1) for i := range table { table[i] = make([]int, len2+1) } i, j := 0, 0 for i = 0; i <= len1; i++ { for j = 0; j <= len2; j++ { if i == 0 || j == 0 { table[i][j] = 0 } else if str1[i-1] == str2[j-1] { table[i][j] = table[i-1][j-1] + 1 } else { table[i][j] = Max(table[i-1][j], table[i][j-1]) } } } return table[len1][len2], Back(table, str1, str2, len1-1, len2-1) } //http://en.wikipedia.org/wiki/Longest_common_subsequence_problem func Back(table [][]int, str1, str2 string, i, j int) string { if i == 0 || j == 0 { return "" } else if str1[i] == str2[j] { return Back(table, str1, str2, i-1, j-1) + string(str1[i]) } else { if table[i][j-1] > table[i-1][j] { return Back(table, str1, str2, i, j-1) } else { return Back(table, str1, str2, i-1, j) } } }

As you can see, it is very similar to the first one, but this one uses recusion to reverse the final answer. It also has a helper function Max() to make a part of the innermost loop more readable. Of course, nothing we’ve done here has helped in making this function more generic. If anything, we’ve made it worse by introducing helper functions that would need to be modified and re-implemented for each type we wish to use LCS on. One could possibly forgive this extra readability, if the performance was faster, or about the same as the slightly less readable version. As a future benchmark run will show, the difference between LCS1 and LCS2 is only about 4%, with LCS2 being slightly slower.

Let’s find a simple method to make this function more generic. I really want to use it on arrays of strings, to be able to compare two sets of files. In order to make this function generic, I’m first going to assume that we will be working with sequences of int ’s. As a method to interface (yes, the irony is not lost on me) with this new LCS3 function, we’ll define an interface like so:

type Interface interface { Keys() []int }

This tells the compiler that we will be dealing with types that implement a Keys() function that returns a slice of int ’s. Note, in Go, interfaces are implicit, in the sense that any type that implements a Keys() []int function, adheres to this interface, and can be used in places that expects this interface. IE: types that you as the implementor of LCS3() do not know about at implementation time. Let us translate the LCS function to use this new interface:

func LCS3(a, b Interface) (int, []int) { aKeys := a.Keys() bKeys := b.Keys() lengths := make([][]int, len(aKeys)+1) for i := 0; i <= len(aKeys); i++ { lengths[i] = make([]int, len(bKeys)+1) } // row 0 and column 0 are initialized to 0 already for i := 0; i < len(aKeys); i++ { for j := 0; j < len(bKeys); j++ { if aKeys[i] == bKeys[j] { lengths[i+1][j+1] = lengths[i][j] + 1 } else if lengths[i+1][j] > lengths[i][j+1] { lengths[i+1][j+1] = lengths[i+1][j] } else { lengths[i+1][j+1] = lengths[i][j+1] } } } // read the substring out from the matrix s := make([]int, 0, lengths[len(aKeys)][len(bKeys)]) for x, y := len(aKeys), len(bKeys); x != 0 && y != 0; { if lengths[x][y] == lengths[x-1][y] { x-- } else if lengths[x][y] == lengths[x][y-1] { y-- } else { s = append(s, aKeys[x-1]) x-- y-- } } ReverseIntSlice(s) return len(s), s } func ReverseIntSlice(s []int) []int { for i, j := 0, len(s)-1; i < j; i, j = i+1, j-1 { s[i], s[j] = s[j], s[i] } return s }

As you can see, it looks remarkably similar to LCS1() . The nice thing about this version is that it works exclusivly with integers. Most compilers are exceedingly good at being able to optimize working on arrays of integers. So I am hopeful that this will end up being faster. However, you say, we now need to translate every instance of this problem into an array of integers. Would this not be slower than LCS1() or LCS2() for simple string input? Also, how do you translate strings to []int to use with this? This all seems too complicated.

The key to making this usable for a set of strings lies in the interface definition we did earlier. Let’s define a new type and function:

type RuneSlice []rune func (p RuneSlice) Keys() []int { s := make([]int, 0, len(p)) for _, r := range p { s = append(s, int(r)) } return s }

We define a type RuneSlice and a Keys() []int function for this type. We can now use instances of this type to call LCS3() . Note, this function is not “fast”. It creates a []int and appends a copy of each rune to this new slice. Let’s use this type to implement LCS3String() :

func LCS3String(a, b string) (int, string) { _, runes := LCS3(RuneSlice(a), RuneSlice(b)) str := make([]rune, 0, len(runes)) for _, r := range runes { str = append(str, rune(r)) } return len(str), string(str) }

As you can see, a very small adaptor function can be created to create the necessary input and translate the output back to what is expected. But surely, this must be slower than either LCS1() and LCS2() . Fortunately, benchmarking shows that this version is about 5% faster than the previously faster LCS1 function.

So here we are, with a largely generic LCS function. How do we use this function to be able to implement an LCS function that takes []string type arguments? One thing to notice is that we can use an optimization, and instead of dealing with arrays of strings, we can use a checksum for each string instead. The implementation looks something like:

type StringSlice []string func (p StringSlice) Keys() []int { f := fnv.New32a() hash := make([]int, 0, len(p)) for i := range p { f.Reset() f.Write([]byte(p[i])) hash = append(hash, int(f.Sum32())) } return hash }

Note, this particular implementation is not generic (again!). It actually explicitly uses the 32-bit version of the fnv-a hash. If we wished, we could implement a HashKeys() version that also implemented a method to retrieve a pointer to the hash.Hash interface to use, at which point the hash function that would be used would be generic, and could be replaced by other implementations.

Below is a quick benchmark run for the various implementations. Note, BenchmarkLCS4 and BenchmarkLCS5 are implementations that test finding the LCS from arrays of strings. The benchmarks 1-3 are testing the various LCS functions that work on a set of strings (finding the longest common subsequence of runes/characters).

$ go test -bench=. github.org/weingart/lcs testing: warning: no tests to run PASS BenchmarkLCS1 10000 128831 ns/op BenchmarkLCS2 10000 134044 ns/op BenchmarkLCS3 10000 102317 ns/op BenchmarkLCS4 10000 66528 ns/op BenchmarkLCS5 10000 70554 ns/op ok github.org/weingart/lcs 5.309s

The code is not complete, and could use some cleanup for it to be more generally useful, as well as use more love on the front that generates diffs, such that it would be able to output textual diffs that are patch(1) compatible.

Tobias Weingartner.