diff --git a/.gitignore b/.gitignore
index 475cb0d..32d32dc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,5 @@
 output.*.txt
 .vscode
 files
-files.*/
+files.*
+*.prof
diff --git a/main.go b/main.go
index fba1887..1f231db 100644
--- a/main.go
+++ b/main.go
@@ -9,6 +9,7 @@ import (
 	"os"
 	"path"
 	"runtime"
+	"runtime/pprof"
 	"slices"
 	"strconv"
 	"strings"
@@ -43,6 +44,16 @@ func main() {
 		start   = time.Now()
 		padding = "\n"
 	)
+
+	f, err := os.Create("cpu.prof")
+	if err != nil {
+		panic(err)
+	}
+	if err := pprof.StartCPUProfile(f); err != nil {
+		panic(err)
+	}
+	defer pprof.StopCPUProfile()
+
 	documents, output, err := run(os.Args)
 	if err != nil {
 		fmt.Fprintf(os.Stderr, "error: %v\n", err)
@@ -308,29 +319,16 @@ func (dm *DocumentManager) maybeAssociateFileWithDocument(workItem WorkItem, wor
 // on the number of line-centric differences between the contents of the two
 // files.
 func (dm *DocumentManager) compareFiles(f1Number, f2Number int) (float64, error) {
-	f1, err := dm.fcc.GetFileContents(f1Number)
+	f1, err := dm.fcc.GetLineIDsForFile(f1Number)
 	if err != nil {
 		return 0, fmt.Errorf("file %d: %w", f1Number, err)
 	}
-	f2, err := dm.fcc.GetFileContents(f2Number)
+	f2, err := dm.fcc.GetLineIDsForFile(f2Number)
 	if err != nil {
 		return 0, fmt.Errorf("file %d: %w", f2Number, err)
 	}
 
-	histogram := make(map[string]int)
-	for _, line := range f1 {
-		histogram[line]++
-	}
-	for _, line := range f2 {
-		histogram[line]--
-	}
-
-	var differences float64
-	for _, v := range histogram {
-		differences += math.Abs(float64(v))
-	}
-
-	similarity := 1 - (differences / float64(len(f1)+len(f2)))
+	similarity := compareFileLineIDs(f1, f2)
 	return similarity, nil
 }
 
@@ -382,6 +380,7 @@ func (d *Document) SortAssociatedFiles() {
 type FileContentsCache struct {
 	BaseDir string
 	cache   sync.Map
+	lineIDs sync.Map
 }
 
 // GetFileContents returns the contents of a file, excluding the first timestamp
@@ -418,6 +417,57 @@ func (fcc *FileContentsCache) GetFileContents(fileNumber int) ([]string, error)
 	return lines, nil
 }
 
+func (fcc *FileContentsCache) GetLineIDsForFile(fileNumber int) ([]uint64, error) {
+	if cachedLineIDs, ok := fcc.lineIDs.Load(fileNumber); ok {
+		return cachedLineIDs.([]uint64), nil
+	}
+
+	lines, err := fcc.GetFileContents(fileNumber)
+	if err != nil {
+		return nil, fmt.Errorf("adding line IDs for file %d: %w", fileNumber, err)
+	}
+
+	lineIDs := makeFileLinesID(lines)
+	fcc.lineIDs.Store(fileNumber, lineIDs)
+	return lineIDs, nil
+}
+
+var (
+	fileLinesCache   sync.Map
+	fileLineIDSource atomic.Uint64
+)
+
+func makeFileLinesID(fileLines []string) []uint64 {
+	fileLineIDs := make([]uint64, 0, len(fileLines))
+	for _, line := range fileLines {
+		lineID, ok := fileLinesCache.Load(line)
+		if !ok {
+			newID := fileLineIDSource.Add(1)
+			fileLinesCache.Store(line, newID)
+			fileLineIDs = append(fileLineIDs, newID)
+		} else {
+			fileLineIDs = append(fileLineIDs, lineID.(uint64))
+		}
+	}
+	slices.Sort(fileLineIDs)
+	return fileLineIDs
+}
+
+func compareFileLineIDs(f1, f2 []uint64) float64 {
+	var (
+		f2Index    int
+		similarity int
+	)
+	for _, lineID := range f1 {
+		if f2Index < len(f2) && f2[f2Index] == lineID {
+			similarity += 2
+			f2Index++
+		}
+	}
+
+	return float64(similarity) / float64(len(f1)+len(f2))
+}
+
 // ClearFilesExcept removes the contents of the fileContentsCache except for the
 // provided file numbers. This helps conserve memory by removing the contents of
 // files that are no longer of interest, which we can be sure of since we are