diff --git a/src/libhictk/balancing/include/hictk/balancing/impl/sparse_matrix_impl.hpp b/src/libhictk/balancing/include/hictk/balancing/impl/sparse_matrix_impl.hpp
index 55016ba0..a152f6f6 100644
--- a/src/libhictk/balancing/include/hictk/balancing/impl/sparse_matrix_impl.hpp
+++ b/src/libhictk/balancing/include/hictk/balancing/impl/sparse_matrix_impl.hpp
@@ -351,7 +351,7 @@ inline SparseMatrixChunked::SparseMatrixChunked(std::filesystem::path tmp_file,
       _zstd_cctx(ZSTD_createCCtx()),
       _zstd_dctx(ZSTD_createDCtx()) {
   _fs.exceptions(std::ios::badbit);
-  _fs.open(_path, std::ios::out);
+  _fs.open(_path, std::ios::out | std::ios::binary);
 }
 
 inline SparseMatrixChunked::~SparseMatrixChunked() noexcept {
@@ -388,7 +388,7 @@ inline void SparseMatrixChunked::finalize() {
   if (!_matrix.empty()) {
     write_chunk();
   }
-  _fs.open(_path, std::ios::in);
+  _fs.open(_path, std::ios::in | std::ios::binary);
 }
 
 inline void SparseMatrixChunked::marginalize(MargsVector& marg, BS::thread_pool* tpool,
@@ -397,7 +397,7 @@ inline void SparseMatrixChunked::marginalize(MargsVector& marg, BS::thread_pool*
     std::unique_ptr<ZSTD_DCtx_s> zstd_dctx(ZSTD_createDCtx());
     std::fstream fs{};
     fs.exceptions(_fs.exceptions());
-    fs.open(_path, std::ios::in);
+    fs.open(_path, std::ios::in | std::ios::binary);
     auto matrix = _matrix;
     MargsVector marg_local(marg.size());
     for (const auto offset : nonstd::span(_index).subspan(istart, iend - istart)) {
@@ -440,7 +440,7 @@ inline void SparseMatrixChunked::marginalize_nnz(MargsVector& marg, BS::thread_p
     std::unique_ptr<ZSTD_DCtx_s> zstd_dctx(ZSTD_createDCtx());
     std::fstream fs{};
     fs.exceptions(_fs.exceptions());
-    fs.open(_path, std::ios::in);
+    fs.open(_path, std::ios::in | std::ios::binary);
     auto matrix = _matrix;
     MargsVector marg_local(marg.size());
     for (const auto offset : nonstd::span(_index).subspan(istart, iend - istart)) {
@@ -484,7 +484,7 @@ inline void SparseMatrixChunked::times_outer_product_marg(MargsVector& marg,
     std::unique_ptr<ZSTD_DCtx_s> zstd_dctx(ZSTD_createDCtx());
     std::fstream fs{};
     fs.exceptions(_fs.exceptions());
-    fs.open(_path, std::ios::in);
+    fs.open(_path, std::ios::in | std::ios::binary);
     auto matrix = _matrix;
     MargsVector marg_local(marg.size());
     for (const auto offset : nonstd::span(_index).subspan(istart, iend - istart)) {
diff --git a/test/units/balancing/balancing_test.cpp b/test/units/balancing/balancing_test.cpp
index 68e01231..7c994305 100644
--- a/test/units/balancing/balancing_test.cpp
+++ b/test/units/balancing/balancing_test.cpp
@@ -55,15 +55,15 @@ static void compare_vectors(const std::vector<T>& v1, const std::vector<T>& v2)
 }
 
 // NOLINTNEXTLINE(readability-function-cognitive-complexity)
-TEST_CASE("Balancing: SparseMatrix") {
+TEST_CASE("Balancing: SparseMatrix", "[balancing][short]") {
   using SparseMatrix = hictk::balancing::SparseMatrix;
   const BinTable bins{Reference{Chromosome{0, "chr0", 50}, Chromosome{1, "chr1", 100},
                                 Chromosome{2, "chr2", 50}, Chromosome{3, "chr3", 50}},
                       50};
   // clang-format off
   const std::vector<ThinPixel<std::int32_t>> pixels{
-      {1, 0, 1}, {1, 1, 2}, {2, 1, 3},  // chr1
-      {3, 0, 4}, {3, 1, 5}};            // chr2
+      {1, 1, 1}, {1, 2, 2}, {2, 2, 3},  // chr1
+      {3, 3, 4}, {3, 4, 5}};            // chr2
   // clang-format on
 
   SECTION("accessors") { CHECK(SparseMatrix{}.empty()); }
@@ -126,15 +126,15 @@ TEST_CASE("Balancing: SparseMatrix") {
 }
 
 // NOLINTNEXTLINE(readability-function-cognitive-complexity)
-TEST_CASE("Balancing: SparseMatrixChunked") {
+TEST_CASE("Balancing: SparseMatrixChunked", "[balancing][short]") {
   using SparseMatrixChunked = hictk::balancing::SparseMatrixChunked;
   const BinTable bins{Reference{Chromosome{0, "chr0", 50}, Chromosome{1, "chr1", 100},
                                 Chromosome{2, "chr2", 50}, Chromosome{3, "chr3", 50}},
                       50};
   // clang-format off
   const std::vector<ThinPixel<std::int32_t>> pixels{
-      {1, 0, 1}, {1, 1, 2}, {2, 1, 3},  // chr1
-      {3, 0, 4}, {3, 1, 5}};            // chr2
+      {1, 1, 1}, {1, 2, 2}, {2, 2, 3},  // chr1
+      {3, 3, 4}, {3, 4, 5}};            // chr2
   // clang-format on
   const auto tmpfile = testdir() / "sparse_matrix_chunked.tmp";