diff --git a/src/modelling/embedding_utils.jl b/src/modelling/embedding_utils.jl
index 8d7507a..a3de520 100644
--- a/src/modelling/embedding_utils.jl
+++ b/src/modelling/embedding_utils.jl
@@ -178,19 +178,16 @@ end
 
 function _clear_masked_embeddings!(D::AbstractArray{Float32, 3},
         integer_ids::AbstractMatrix{Int32}, skiplist::Vector{Int})
-    @assert isequal(size(D)[2:end], size(integer_ids))
-    "size(D): $(size(D)), size(integer_ids): $(size(integer_ids))"
-
+    isequal(size(D)[2:end], size(integer_ids)) ||
+        throw(DomainError("The number of embeddings in D and tokens " *
+                          "in integer_ids must be equal!"))
     # set everything to true
     mask = similar(integer_ids, Bool)                       # respects the device as well
     mask .= true
     mask_skiplist!(mask, integer_ids, skiplist)             # (doc_maxlen, current_batch_size)
     mask = reshape(mask, (1, size(mask)...))                # (1, doc_maxlen, current_batch_size)
 
-    @assert isequal(size(mask)[2:end], size(D)[2:end])
-    "size(mask): $(size(mask)), size(D): $(size(D))"
-    @assert mask isa AbstractArray{Bool} "$(typeof(mask))"
-
+    # clear embeddings
     D .= D .* mask                                          # clear embeddings of masked tokens
     mask
 end
@@ -201,6 +198,8 @@ end
 
 function _remove_masked_tokens(
         D::AbstractMatrix{Float32}, mask::AbstractMatrix{Bool})
-    D[:, reshape(mask, prod(size(mask)))]
+    size(D, 2) == prod(size(mask)) ||
+        throw(DimensionMismatch("The total number of embeddings " * "
+        in D must be equal to the total number of tokens represented by mask!"))
+    D[:, vec(mask)]
 end
-
diff --git a/test/modelling/checkpoint.jl b/test/modelling/checkpoint.jl
index 6f9544f..e69de29 100644
--- a/test/modelling/checkpoint.jl
+++ b/test/modelling/checkpoint.jl
@@ -1,10 +0,0 @@
-@testset "doc_tokenization.jl" begin
-    
-end
-
-@testset "query_tokenization.jl" begin
-end
-
-@testset "checkpoint.jl" begin
-    # use the defaults for the config; gpu tests will be separate
-end
diff --git a/test/modelling/embedding_utils.jl b/test/modelling/embedding_utils.jl
new file mode 100644
index 0000000..a1e10a8
--- /dev/null
+++ b/test/modelling/embedding_utils.jl
@@ -0,0 +1,156 @@
+using ColBERT: mask_skiplist!, _clear_masked_embeddings!, _flatten_embeddings,
+               _remove_masked_tokens
+
+@testset "mask_skiplist!" begin
+    # Test Case 1: Simple case with no skips
+    mask = trues(3, 3)
+    integer_ids = Int32[1 2 3; 4 5 6; 7 8 9]
+    skiplist = Int[]
+    expected_mask = trues(3, 3)
+    mask_skiplist!(mask, integer_ids, skiplist)
+    @test mask == expected_mask
+
+    # Test Case 2: Skip one value
+    mask = trues(3, 3)
+    integer_ids = Int32[1 2 3; 4 5 6; 7 8 9]
+    skiplist = [5]
+    expected_mask = [true true true; true false true; true true true]
+    mask_skiplist!(mask, integer_ids, skiplist)
+    @test mask == expected_mask
+
+    # Test Case 3: Skip multiple values
+    mask = trues(3, 3)
+    integer_ids = Int32[1 2 3; 4 5 6; 7 8 9]
+    skiplist = [2, 6, 9]
+    expected_mask = [true false true; true true false; true true false]
+    mask_skiplist!(mask, integer_ids, skiplist)
+    @test mask == expected_mask
+
+    # Test Case 4: All values in skiplist
+    mask = trues(3, 3)
+    integer_ids = Int32[1 2 3; 4 5 6; 7 8 9]
+    skiplist = [1, 2, 3, 4, 5, 6, 7, 8, 9]
+    expected_mask = falses(3, 3)
+    mask_skiplist!(mask, integer_ids, skiplist)
+    @test mask == expected_mask
+
+    # Test Case 5: Empty integer_ids matrix
+    mask = trues(0, 0)
+    integer_ids = rand(Int32, 0, 0)
+    skiplist = [1]
+    expected_mask = trues(0, 0)
+    mask_skiplist!(mask, integer_ids, skiplist)
+    @test mask == expected_mask
+
+    # Test Case 6: Skiplist with no matching values
+    mask = trues(3, 3)
+    integer_ids = Int32[1 2 3; 4 5 6; 7 8 9]
+    skiplist = [10, 11]
+    expected_mask = trues(3, 3)
+    mask_skiplist!(mask, integer_ids, skiplist)
+    @test mask == expected_mask
+end
+
+@testset "_clear_masked_embeddings!" begin
+    # Test Case 1: No skiplist entries
+    dim, len, bsize = rand(1:20, 3)
+    D = rand(Float32, dim, len, bsize)
+    integer_ids = rand(Int32, len, bsize)
+    skiplist = Int[]
+    expected_D = copy(D)
+    _clear_masked_embeddings!(D, integer_ids, skiplist)
+    @test D == expected_D
+
+    # Test Case 2: Single skiplist entry
+    dim, len, bsize = rand(1:20, 3)
+    D = rand(Float32, dim, len, bsize)
+    integer_ids = rand(Int32, len, bsize)
+    skiplist = Int[integer_ids[rand(1:(len * bsize))]]
+    expected_D = copy(D)
+    expected_D[:, findall(in(skiplist), integer_ids)] .= 0.0f0
+    _clear_masked_embeddings!(D, integer_ids, skiplist)
+    @test D == expected_D
+
+    # Test Case 3: Multiple skiplist entries
+    dim, len, bsize = rand(1:20, 3)
+    D = rand(Float32, dim, len, bsize)
+    integer_ids = rand(Int32, len, bsize)
+    skiplist = unique(Int.(rand(vec(integer_ids), rand(1:(len * bsize)))))
+    expected_D = copy(D)
+    expected_D[:, findall(in(skiplist), integer_ids)] .= 0.0f0
+    _clear_masked_embeddings!(D, integer_ids, skiplist)
+    @test D == expected_D
+
+    # Test Case 4: Skip all tokens
+    dim, len, bsize = rand(1:20, 3)
+    D = rand(Float32, dim, len, bsize)
+    integer_ids = rand(int32, len, bsize)
+    skiplist = unique(Int.(vec(integer_ids)))
+    expected_D = similar(D)
+    expected_D .= 0.0f0
+    _clear_masked_embeddings!(D, integer_ids, skiplist)
+    @test D == expected_D
+
+    # Test Case 5: Skiplist with no matching tokens
+    dim, len, bsize = rand(1:20, 3)
+    D = rand(Float32, dim, len, bsize)
+    integer_ids = Int32.(rand(1:100, len, bsize))
+    skiplist = unique(rand(101:1000, rand(1:20)))
+    expected_D = copy(D)
+    _clear_masked_embeddings!(D, integer_ids, skiplist)
+    @test D == expected_D
+
+    # Test 6: Types and shapes
+    dim, len, bsize = rand(1:20, 3)
+    D = rand(Float32, dim, len, bsize)
+    integer_ids = rand(Int32, len, bsize)
+    skiplist = unique(rand(Int, rand(1:20)))
+    mask = _clear_masked_embeddings!(D, integer_ids, skiplist)
+    @test mask isa Array{Bool, 3}
+    @test isequal(size(mask), (1, size(D)[2:end]...))
+end
+
+@testset "_flatten_embeddings" begin
+    # Test Case 1: Generic case; len will correspond to a vector of constants
+    dim, len, bsize = rand(1:20, 3)
+    D = Array{Float32}(undef, dim, len, bsize)
+    for idx in 1:len
+        D[:, idx, :] .= idx
+    end
+    expected = Matrix{Float32}(undef, dim, len * bsize)
+    for idx in 1:len
+        expected[:, [idx + k * len for k in 0:(bsize - 1)]] .= idx
+    end
+    @test _flatten_embeddings(D) == expected
+
+    # Test Case 2: Edge case with 0x3x2 array (should return 0x6 array)
+    D = Float32[]
+    D = reshape(D, 0, 3, 2)
+    expected_output = reshape(Float32[], 0, 6)
+    @test _flatten_embeddings(D) == expected_output
+end
+
+@testset "_remove_masked_tokens" begin
+    # Test 1: Generic case; build a skiplist, and manually build the expected tensor
+    dim, len, bsize = rand(1:20, 3)
+    mask = trues(len, bsize)
+    skiplist = unique(rand(1:len, rand(1:len)))
+    for id in skiplist
+        mask[id, :] .= false
+    end
+    D = Matrix{Float32}(undef, dim, len * bsize)
+    for idx in 1:len
+        D[:, [idx + k * len for k in 0:(bsize - 1)]] .= idx
+    end
+    expected = rand(Float32, dim, 0)
+    for emb_id in 1:size(D, 2)
+        if !(D[1, emb_id] in skiplist)
+            expected = hcat(expected, D[:, emb_id])
+        end
+    end
+    @test _remove_masked_tokens(D, mask) == expected
+
+    # Test 2: Test for errors
+    @test_throws DimensionMismatch _remove_masked_tokens(
+        rand(Float32, 12, 20), rand(Bool, 4, 4))
+end
diff --git a/test/runtests.jl b/test/runtests.jl
index cc56925..ec4d48a 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -9,5 +9,12 @@ const INT_TYPES = [
 const FLOAT_TYPES = [Float16, Float32, Float64]
 
 # include("Aqua.jl")
+
+# indexing operations
 include("indexing/codecs/residual.jl")
+
+# modelling operations 
+include("modelling/embedding_utils.jl")
+
+# utils
 include("utils.jl")