diff --git a/.gitmodules b/.gitmodules
index 1baeb73541..036a248070 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -7,7 +7,7 @@
 [submodule "cmake/external/emsdk"]
 	path = cmake/external/emsdk
 	url = https://github.com/emscripten-core/emsdk.git
-	branch = 3.1.37
+	branch = 3.1.44
 [submodule "cmake/external/onnxruntime-extensions"]
 	path = cmake/external/onnxruntime-extensions
 	url = https://github.com/microsoft/onnxruntime-extensions.git
diff --git a/cgmanifests/generated/cgmanifest.json b/cgmanifests/generated/cgmanifest.json
index 5faf8cd43a..f2a433ad3c 100644
--- a/cgmanifests/generated/cgmanifest.json
+++ b/cgmanifests/generated/cgmanifest.json
@@ -82,7 +82,7 @@
       "component": {
         "type": "git",
         "git": {
-          "commitHash": "b113f24842c6e97fe3e352084db09a6e278593ae",
+          "commitHash": "a896e3d066448b3530dbcaa48869fafefd738f57",
           "repositoryUrl": "https://github.com/emscripten-core/emsdk.git"
         },
         "comments": "git submodule at cmake/external/emsdk"
diff --git a/cmake/external/emsdk b/cmake/external/emsdk
index b113f24842..a896e3d066 160000
--- a/cmake/external/emsdk
+++ b/cmake/external/emsdk
@@ -1 +1 @@
-Subproject commit b113f24842c6e97fe3e352084db09a6e278593ae
+Subproject commit a896e3d066448b3530dbcaa48869fafefd738f57
diff --git a/include/onnxruntime/core/framework/data_types.h b/include/onnxruntime/core/framework/data_types.h
index 2de0f9b548..f394212807 100644
--- a/include/onnxruntime/core/framework/data_types.h
+++ b/include/onnxruntime/core/framework/data_types.h
@@ -15,14 +15,8 @@
 #include "core/framework/endian.h"
 #include "core/framework/float8.h"
 #include "core/framework/float16.h"
+#include "core/graph/onnx_protobuf.h"
 #include "core/framework/to_tensor_proto_element_type.h"
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
 
 struct OrtValue;
 
diff --git a/include/onnxruntime/core/framework/data_types_internal.h b/include/onnxruntime/core/framework/data_types_internal.h
index 1e93c7a471..fbeee8a2ae 100644
--- a/include/onnxruntime/core/framework/data_types_internal.h
+++ b/include/onnxruntime/core/framework/data_types_internal.h
@@ -17,13 +17,7 @@
 #ifndef SHARED_PROVIDER
 #include "core/common/type_list.h"
 #include "core/framework/data_types.h"
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
+#include "core/graph/onnx_protobuf.h"
 #endif
 
 namespace onnxruntime {
diff --git a/include/onnxruntime/core/framework/op_kernel.h b/include/onnxruntime/core/framework/op_kernel.h
index 36e931c2df..94c6d81ee9 100644
--- a/include/onnxruntime/core/framework/op_kernel.h
+++ b/include/onnxruntime/core/framework/op_kernel.h
@@ -24,14 +24,8 @@
 #include "core/framework/tensor.h"
 #include "core/graph/constants.h"
 #include "core/graph/graph_viewer.h"
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
+#include "core/graph/onnx_protobuf.h"
 #include "core/common/gsl.h"
-#include "onnx/onnx-operators_pb.h"
-#include "onnx/onnx_pb.h"
 namespace onnxruntime {
 class OpKernelContext;
 }
diff --git a/include/onnxruntime/core/framework/to_tensor_proto_element_type.h b/include/onnxruntime/core/framework/to_tensor_proto_element_type.h
index 9b7925e55b..21253eb4a6 100644
--- a/include/onnxruntime/core/framework/to_tensor_proto_element_type.h
+++ b/include/onnxruntime/core/framework/to_tensor_proto_element_type.h
@@ -7,7 +7,7 @@
 #include <string>
 
 #ifndef SHARED_PROVIDER
-#include "onnx/onnx_pb.h"
+#include "core/graph/onnx_protobuf.h"
 #endif
 
 #include "core/framework/float8.h"
diff --git a/include/onnxruntime/core/graph/graph.h b/include/onnxruntime/core/graph/graph.h
index 9f2ff2d409..632d79e009 100644
--- a/include/onnxruntime/core/graph/graph.h
+++ b/include/onnxruntime/core/graph/graph.h
@@ -16,15 +16,6 @@
 #pragma warning(disable : 4244)
 #endif
 
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#include "core/common/inlined_containers.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
-
 #ifdef _WIN32
 #pragma warning(pop)
 #endif
@@ -33,11 +24,15 @@
 
 #include "core/common/common.h"
 #include "core/common/const_pointer_container.h"
+#if !defined(ORT_MINIMAL_BUILD)
+#include "core/common/inlined_containers.h"
+#endif
 #include "core/common/inlined_containers_fwd.h"
 #include "core/common/path.h"
 #include "core/common/span_utils.h"
 #include "core/common/status.h"
 #include "core/common/logging/logging.h"
+#include "core/graph/onnx_protobuf.h"
 #include "core/graph/basic_types.h"
 #include "core/graph/constants.h"
 #include "core/graph/function.h"
diff --git a/include/onnxruntime/core/graph/indexed_sub_graph.h b/include/onnxruntime/core/graph/indexed_sub_graph.h
index 935ada88c6..c57db41254 100644
--- a/include/onnxruntime/core/graph/indexed_sub_graph.h
+++ b/include/onnxruntime/core/graph/indexed_sub_graph.h
@@ -8,13 +8,7 @@
 #include <vector>
 
 #include "core/graph/basic_types.h"
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
+#include "core/graph/onnx_protobuf.h"
 
 namespace onnxruntime {
 
diff --git a/include/onnxruntime/core/graph/schema_registry.h b/include/onnxruntime/core/graph/schema_registry.h
index 9982ac9434..b128e91afa 100644
--- a/include/onnxruntime/core/graph/schema_registry.h
+++ b/include/onnxruntime/core/graph/schema_registry.h
@@ -7,10 +7,8 @@
 #include <map>
 #include <sstream>
 
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
+#include "core/graph/onnx_protobuf.h"
 #include "onnx/defs/schema.h"
-
 #include "core/graph/constants.h"
 #include "core/common/common.h"
 #include "core/common/status.h"
diff --git a/onnxruntime/core/framework/kernel_type_str_resolver.h b/onnxruntime/core/framework/kernel_type_str_resolver.h
index 6655b52f41..75fc2fa894 100644
--- a/onnxruntime/core/framework/kernel_type_str_resolver.h
+++ b/onnxruntime/core/framework/kernel_type_str_resolver.h
@@ -8,7 +8,7 @@
 #include <utility>
 
 #if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
+#include "core/graph/onnx_protobuf.h"
 #endif  // !defined(ORT_MINIMAL_BUILD)
 
 #include "core/common/gsl.h"
diff --git a/onnxruntime/core/graph/contrib_ops/attn_lstm_schema_defs.h b/onnxruntime/core/graph/contrib_ops/attn_lstm_schema_defs.h
index 59f451f756..9af74fcab1 100644
--- a/onnxruntime/core/graph/contrib_ops/attn_lstm_schema_defs.h
+++ b/onnxruntime/core/graph/contrib_ops/attn_lstm_schema_defs.h
@@ -3,13 +3,7 @@
 
 #pragma once
 
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
+#include "core/graph/onnx_protobuf.h"
 
 namespace onnxruntime {
 namespace contrib {
diff --git a/onnxruntime/core/graph/contrib_ops/contrib_defs.cc b/onnxruntime/core/graph/contrib_ops/contrib_defs.cc
index 08756a66ab..a79203a94a 100644
--- a/onnxruntime/core/graph/contrib_ops/contrib_defs.cc
+++ b/onnxruntime/core/graph/contrib_ops/contrib_defs.cc
@@ -3,11 +3,8 @@
 #include "core/graph/contrib_ops/contrib_defs.h"
 
 #include <cmath>
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
+#include "core/graph/onnx_protobuf.h"
+
 #include "onnx/defs/shape_inference.h"
 #include "onnx/defs/tensor_proto_util.h"
 
diff --git a/onnxruntime/core/graph/contrib_ops/contrib_defs.h b/onnxruntime/core/graph/contrib_ops/contrib_defs.h
index 4c24b284c6..2d5b4f8e76 100644
--- a/onnxruntime/core/graph/contrib_ops/contrib_defs.h
+++ b/onnxruntime/core/graph/contrib_ops/contrib_defs.h
@@ -4,7 +4,7 @@
 #pragma once
 
 #if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
+#include "core/graph/onnx_protobuf.h"
 #include "core/graph/contrib_ops/ms_schema.h"
 #else
 #include "onnx/defs/data_type_utils.h"
diff --git a/onnxruntime/core/graph/contrib_ops/internal_nhwc_onnx_schemas.cc b/onnxruntime/core/graph/contrib_ops/internal_nhwc_onnx_schemas.cc
index b17b35ab7d..3ce7c40e75 100644
--- a/onnxruntime/core/graph/contrib_ops/internal_nhwc_onnx_schemas.cc
+++ b/onnxruntime/core/graph/contrib_ops/internal_nhwc_onnx_schemas.cc
@@ -9,6 +9,8 @@
 #include "core/graph/contrib_ops/nhwc_inference_context.h"
 #include "core/graph/contrib_ops/ms_schema.h"  // contrib::GetOpSchema
 
+#ifndef ORT_MINIMAL_BUILD
+
 namespace onnxruntime {
 namespace contrib {
 class ONNX_OPERATOR_SET_SCHEMA_CLASS_NAME(Microsoft, 1, QLinearAveragePool);
@@ -157,3 +159,5 @@ void OpSet_Internal_NHWC_ONNX::ForEachSchema(const std::function<void(ONNX_NAMES
 
 }  // namespace internal_nhwc_onnx
 }  // namespace onnxruntime
+
+#endif  // !ORT_MINIMAL_BUILD
diff --git a/onnxruntime/core/graph/contrib_ops/internal_nhwc_onnx_schemas.h b/onnxruntime/core/graph/contrib_ops/internal_nhwc_onnx_schemas.h
index c8f1f8a0c9..4c4ca0fc62 100644
--- a/onnxruntime/core/graph/contrib_ops/internal_nhwc_onnx_schemas.h
+++ b/onnxruntime/core/graph/contrib_ops/internal_nhwc_onnx_schemas.h
@@ -2,7 +2,9 @@
 // Licensed under the MIT License.
 
 #pragma once
-#include "onnx/defs/schema.h"
+#include "core/graph/onnx_protobuf.h"
+
+#ifndef ORT_MINIMAL_BUILD
 
 namespace onnxruntime {
 namespace internal_nhwc_onnx {
@@ -17,3 +19,5 @@ class OpSet_Internal_NHWC_ONNX {
 
 }  // namespace internal_nhwc_onnx
 }  // namespace onnxruntime
+
+#endif  // !ORT_MINIMAL_BUILD
diff --git a/onnxruntime/core/graph/contrib_ops/ms_opset.h b/onnxruntime/core/graph/contrib_ops/ms_opset.h
index a83f8bab9a..3c31997286 100644
--- a/onnxruntime/core/graph/contrib_ops/ms_opset.h
+++ b/onnxruntime/core/graph/contrib_ops/ms_opset.h
@@ -2,7 +2,7 @@
 // Licensed under the MIT License.
 
 #pragma once
-#include "onnx/defs/schema.h"
+#include "core/graph/onnx_protobuf.h"
 #include "core/graph/contrib_ops/ms_schema.h"
 
 namespace onnxruntime {
diff --git a/onnxruntime/core/graph/contrib_ops/ms_schema.h b/onnxruntime/core/graph/contrib_ops/ms_schema.h
index 4ecb17db25..afbb6712c7 100644
--- a/onnxruntime/core/graph/contrib_ops/ms_schema.h
+++ b/onnxruntime/core/graph/contrib_ops/ms_schema.h
@@ -3,7 +3,7 @@
 
 #pragma once
 
-#include "onnx/defs/schema.h"
+#include "core/graph/onnx_protobuf.h"
 
 namespace onnxruntime {
 namespace contrib {
@@ -12,4 +12,4 @@ namespace contrib {
 template <typename T>
 ::ONNX_NAMESPACE::OpSchema GetOpSchema();
 }  // namespace contrib
-}  // namespace onnxruntime
\ No newline at end of file
+}  // namespace onnxruntime
diff --git a/onnxruntime/core/graph/contrib_ops/onnx_deprecated_operators.cc b/onnxruntime/core/graph/contrib_ops/onnx_deprecated_operators.cc
index ee66dc614b..be39a2d7ec 100644
--- a/onnxruntime/core/graph/contrib_ops/onnx_deprecated_operators.cc
+++ b/onnxruntime/core/graph/contrib_ops/onnx_deprecated_operators.cc
@@ -1,7 +1,7 @@
 // Copyright (c) Microsoft Corporation. All rights reserved.
 // Licensed under the MIT License.
 
-#include "onnx/defs/schema.h"
+#include "core/graph/onnx_protobuf.h"
 #include "onnx/defs/shape_inference.h"
 #include "onnx/defs/tensor_proto_util.h"
 
@@ -503,4 +503,4 @@ ONNX_CONTRIB_OPERATOR_SET_SCHEMA(
 // End of ONNX exp ops(Affine, Crop, ParametricSoftplus, ImageScaler, ThresholdedRelu, DynamicSlice, ScaledTanh, MVN)
 // old version history maintenance
 }  // namespace contrib
-}  // namespace onnxruntime
\ No newline at end of file
+}  // namespace onnxruntime
diff --git a/onnxruntime/core/graph/contrib_ops/onnx_deprecated_opset.h b/onnxruntime/core/graph/contrib_ops/onnx_deprecated_opset.h
index ccc9ade10c..13341605b1 100644
--- a/onnxruntime/core/graph/contrib_ops/onnx_deprecated_opset.h
+++ b/onnxruntime/core/graph/contrib_ops/onnx_deprecated_opset.h
@@ -3,7 +3,7 @@
 
 #pragma once
 
-#include "onnx/defs/schema.h"
+#include "core/graph/onnx_protobuf.h"
 #include "core/graph/contrib_ops/ms_schema.h"
 
 // This file contains deprecated ONNX operators that have been removed from ONNX spec, but we still need to keep them
@@ -59,4 +59,4 @@ class OpSet_ONNX_Deprecated {
   }
 };
 }  // namespace contrib
-}  // namespace onnxruntime
\ No newline at end of file
+}  // namespace onnxruntime
diff --git a/onnxruntime/core/graph/contrib_ops/onnx_function_util.h b/onnxruntime/core/graph/contrib_ops/onnx_function_util.h
index 5e10cfed72..237b61aa16 100644
--- a/onnxruntime/core/graph/contrib_ops/onnx_function_util.h
+++ b/onnxruntime/core/graph/contrib_ops/onnx_function_util.h
@@ -6,8 +6,7 @@
 #include <string>
 #include <vector>
 
-#include "onnx/onnx-operators_pb.h"
-#include "onnx/defs/schema.h"
+#include "core/graph/onnx_protobuf.h"
 #include "onnx/defs/function.h"
 #include "onnx/defs/parser.h"
 
@@ -21,4 +20,4 @@ inline static FunctionBodyHelper::NodeDef Const(const std::string& name, double
   return FunctionBodyHelper::NodeDef{
       {name}, "Constant", {}, {{"value", ToTensor(value, elem_type)}}};
 }
-}  // namespace ONNX_NAMESPACE
\ No newline at end of file
+}  // namespace ONNX_NAMESPACE
diff --git a/onnxruntime/core/graph/contrib_ops/quantization_defs.h b/onnxruntime/core/graph/contrib_ops/quantization_defs.h
index c31d9e7e6c..0951a9546b 100644
--- a/onnxruntime/core/graph/contrib_ops/quantization_defs.h
+++ b/onnxruntime/core/graph/contrib_ops/quantization_defs.h
@@ -4,13 +4,7 @@
 
 #include <stdexcept>
 
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
+#include "core/graph/onnx_protobuf.h"
 
 namespace onnxruntime {
 namespace contrib {
diff --git a/onnxruntime/core/graph/contrib_ops/range_schema_defs.h b/onnxruntime/core/graph/contrib_ops/range_schema_defs.h
index 7abee0e331..c468030fbd 100644
--- a/onnxruntime/core/graph/contrib_ops/range_schema_defs.h
+++ b/onnxruntime/core/graph/contrib_ops/range_schema_defs.h
@@ -3,13 +3,7 @@
 
 #pragma once
 
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
+#include "core/graph/onnx_protobuf.h"
 
 namespace onnxruntime {
 namespace contrib {
diff --git a/onnxruntime/core/graph/contrib_ops/shape_inference_functions.cc b/onnxruntime/core/graph/contrib_ops/shape_inference_functions.cc
index 4324839c7a..eeef20e9df 100644
--- a/onnxruntime/core/graph/contrib_ops/shape_inference_functions.cc
+++ b/onnxruntime/core/graph/contrib_ops/shape_inference_functions.cc
@@ -2,6 +2,7 @@
 // Licensed under the MIT License.
 
 #include "core/graph/contrib_ops/shape_inference_functions.h"
+#include "core/graph/onnx_protobuf.h"
 #include <onnx/defs/shape_inference.h>
 #include <iostream>
 
diff --git a/onnxruntime/core/graph/dml_ops/dml_defs.h b/onnxruntime/core/graph/dml_ops/dml_defs.h
index 3fb4a4cdcd..5479005382 100644
--- a/onnxruntime/core/graph/dml_ops/dml_defs.h
+++ b/onnxruntime/core/graph/dml_ops/dml_defs.h
@@ -3,13 +3,7 @@
 
 #pragma once
 
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
+#include "core/graph/onnx_protobuf.h"
 
 namespace onnxruntime {
 namespace dml {
diff --git a/onnxruntime/core/graph/function_utils.h b/onnxruntime/core/graph/function_utils.h
index ef458d57c5..c85edbada3 100644
--- a/onnxruntime/core/graph/function_utils.h
+++ b/onnxruntime/core/graph/function_utils.h
@@ -5,7 +5,7 @@
 #include <string>
 
 #include "core/common/common.h"
-#include "onnx/onnx_pb.h"
+#include "core/graph/onnx_protobuf.h"
 #include "core/graph/graph.h"
 #include "core/graph/indexed_sub_graph.h"
 #include "core/graph/function.h"
diff --git a/onnxruntime/core/graph/graph_utils.h b/onnxruntime/core/graph/graph_utils.h
index 7f6742b845..cf76ec785f 100644
--- a/onnxruntime/core/graph/graph_utils.h
+++ b/onnxruntime/core/graph/graph_utils.h
@@ -3,16 +3,9 @@
 
 #pragma once
 
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
-
 #include "core/common/inlined_containers.h"
 #include "core/common/span_utils.h"
+#include "core/graph/onnx_protobuf.h"
 #include "core/graph/graph.h"
 
 namespace onnxruntime {
diff --git a/onnxruntime/core/graph/node_attr_utils.h b/onnxruntime/core/graph/node_attr_utils.h
index 461ec01d67..9433cfabc9 100644
--- a/onnxruntime/core/graph/node_attr_utils.h
+++ b/onnxruntime/core/graph/node_attr_utils.h
@@ -7,8 +7,7 @@
 
 #include "core/common/gsl.h"
 
-#include "onnx/onnx_pb.h"
-
+#include "core/graph/onnx_protobuf.h"
 #include "core/graph/basic_types.h"
 
 namespace onnxruntime::utils {
diff --git a/onnxruntime/core/graph/onnx_protobuf.h b/onnxruntime/core/graph/onnx_protobuf.h
index b1e109e6d5..a24ff37e76 100644
--- a/onnxruntime/core/graph/onnx_protobuf.h
+++ b/onnxruntime/core/graph/onnx_protobuf.h
@@ -2,6 +2,21 @@
 // Licensed under the MIT License.
 
 #pragma once
+#include "onnxruntime_config.h"
+
+#ifdef _WIN32
+#pragma warning(push)
+#pragma warning(disable : 4244)
+#endif
+
+#if defined(__GNUC__)
+#pragma GCC diagnostic push
+
+#ifdef HAS_SHORTEN_64_TO_32
+#pragma GCC diagnostic ignored "-Wshorten-64-to-32"
+#endif
+
+#endif
 
 #if !defined(ORT_MINIMAL_BUILD)
 #include "onnx/defs/schema.h"
@@ -11,3 +26,11 @@
 
 #include "onnx/onnx_pb.h"
 #include "onnx/onnx-operators_pb.h"
+
+#if defined(__GNUC__)
+#pragma GCC diagnostic pop
+#endif
+
+#ifdef _WIN32
+#pragma warning(pop)
+#endif
diff --git a/onnxruntime/core/graph/op.h b/onnxruntime/core/graph/op.h
index f66e1eef37..2a720a3cca 100644
--- a/onnxruntime/core/graph/op.h
+++ b/onnxruntime/core/graph/op.h
@@ -5,13 +5,7 @@
 
 #include <functional>
 #include <unordered_map>
-#if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
-#else
-#include "onnx/defs/data_type_utils.h"
-#endif
-#include "onnx/onnx_pb.h"
-#include "onnx/onnx-operators_pb.h"
+#include "core/graph/onnx_protobuf.h"
 #include "core/common/status.h"
 #include "core/graph/constants.h"
 
diff --git a/onnxruntime/core/graph/op_identifier_utils.h b/onnxruntime/core/graph/op_identifier_utils.h
index 14cec1f3f0..265364a88d 100644
--- a/onnxruntime/core/graph/op_identifier_utils.h
+++ b/onnxruntime/core/graph/op_identifier_utils.h
@@ -7,12 +7,7 @@
 
 #include "core/common/status.h"
 #include "core/graph/graph.h"
-
-#if !defined(ORT_MINIMAL_BUILD)
-
-#include "onnx/defs/schema.h"  // for ONNX_NAMESPACE::OpSchema
-
-#endif  // !defined(ORT_MINIMAL_BUILD)
+#include "core/graph/onnx_protobuf.h"
 
 namespace flatbuffers {
 class FlatBufferBuilder;
diff --git a/onnxruntime/core/optimizer/qdq_transformer/selectors_actions/shared/utils.h b/onnxruntime/core/optimizer/qdq_transformer/selectors_actions/shared/utils.h
index c64f40d0dd..246f26c176 100644
--- a/onnxruntime/core/optimizer/qdq_transformer/selectors_actions/shared/utils.h
+++ b/onnxruntime/core/optimizer/qdq_transformer/selectors_actions/shared/utils.h
@@ -10,7 +10,7 @@
 #include "core/graph/basic_types.h"
 
 #if !defined(ORT_MINIMAL_BUILD)
-#include "onnx/defs/schema.h"
+#include "core/graph/onnx_protobuf.h"
 #endif
 
 namespace onnxruntime {
@@ -85,4 +85,4 @@ Status ValidateNodeGroupDQNodes(const GraphViewer& graph_viewer,
                                 gsl::span<const Node* const> dq_nodes);
 
 }  // namespace QDQ
-}  // namespace onnxruntime
\ No newline at end of file
+}  // namespace onnxruntime
diff --git a/onnxruntime/core/platform/posix/env.cc b/onnxruntime/core/platform/posix/env.cc
index 74cb6fc7e2..7cd81d89d7 100644
--- a/onnxruntime/core/platform/posix/env.cc
+++ b/onnxruntime/core/platform/posix/env.cc
@@ -193,22 +193,6 @@ class PosixThread : public EnvThread {
       }
 
       size_t stack_size = thread_options.stack_size;
-#if defined(__wasm__)
-      // emscripten 3.1.37 has a bug which does not take build flags 'STACK_SIZE' or 'DEFAULT_PTHREAD_STACK_SIZE'.
-      // the pthread stack size will always be 64kB, which is insufficient to run some kernels.
-      // we set the stack_size to a bigger value
-      //
-      // https://github.com/emscripten-core/emscripten/issues/19302
-      //
-      // TODO: once this issue is fixed by emscripten's new release, remove this code.
-      //       future changes to DEFAULT_PTHREAD_STACK_SIZE will be in the following files
-      //       - cmake/onnxruntime_unittests.cmake (target onnxruntime_test_all)
-      //       - cmake/onnxruntime_webassembly.cmake (target onnxruntime_webassembly)
-      //
-      if (stack_size == 0) {
-        stack_size = 131072;
-      }
-#endif
       if (stack_size > 0) {
         s = pthread_attr_setstacksize(&attr, stack_size);
         if (s != 0) {
diff --git a/onnxruntime/test/onnx/pb_helper.h b/onnxruntime/test/onnx/pb_helper.h
index d2b7cdf4ee..cd73c53c19 100644
--- a/onnxruntime/test/onnx/pb_helper.h
+++ b/onnxruntime/test/onnx/pb_helper.h
@@ -33,6 +33,10 @@
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wignored-qualifiers"
 #pragma GCC diagnostic ignored "-Wunused-parameter"
+#include "onnxruntime_config.h"
+#ifdef HAS_SHORTEN_64_TO_32
+#pragma GCC diagnostic ignored "-Wshorten-64-to-32"
+#endif
 #endif
 #include <google/protobuf/message_lite.h>
 #include <google/protobuf/io/coded_stream.h>
diff --git a/tools/ci_build/build.py b/tools/ci_build/build.py
index 1e35065f95..64dae354a9 100644
--- a/tools/ci_build/build.py
+++ b/tools/ci_build/build.py
@@ -402,7 +402,7 @@ def parse_arguments():
     # WebAssembly build
     parser.add_argument("--build_wasm", action="store_true", help="Build for WebAssembly")
     parser.add_argument("--build_wasm_static_lib", action="store_true", help="Build for WebAssembly static library")
-    parser.add_argument("--emsdk_version", default="3.1.37", help="Specify version of emsdk")
+    parser.add_argument("--emsdk_version", default="3.1.44", help="Specify version of emsdk")
 
     parser.add_argument("--enable_wasm_simd", action="store_true", help="Enable WebAssembly SIMD")
     parser.add_argument("--enable_wasm_threads", action="store_true", help="Enable WebAssembly multi-threads support")
diff --git a/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml b/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml
index 7050a346b7..93945a1cb5 100644
--- a/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/linux-wasm-ci.yml
@@ -42,7 +42,7 @@ jobs:
   variables:
     EnvSetupScript: setup_env.bat
     buildArch: x64
-    CommonBuildArgs: '--parallel --config ${{ parameters.BuildConfig }} --skip_submodule_sync --build_wasm --use_xnnpack --emsdk_version releases-7c905cfc1ca6699f6ccb288ae174902cfbdcf0a2-64bit ${{ parameters.ExtraBuildArgs }}'
+    CommonBuildArgs: '--parallel --config ${{ parameters.BuildConfig }} --skip_submodule_sync --build_wasm --use_xnnpack ${{ parameters.ExtraBuildArgs }}'
     runCodesignValidationInjection: false
     TODAY: $[format('{0:dd}{0:MM}{0:yyyy}', pipeline.startTime)]
     ORT_CACHE_DIR: $(Agent.TempDirectory)/ort_ccache
@@ -92,8 +92,8 @@ jobs:
   - script: |
       set -ex
       cd '$(Build.SourcesDirectory)/cmake/external/emsdk'
-      ./emsdk install 3.1.37 ccache-git-emscripten-64bit
-      ./emsdk activate 3.1.37 ccache-git-emscripten-64bit
+      ./emsdk install 3.1.44 ccache-git-emscripten-64bit
+      ./emsdk activate 3.1.44 ccache-git-emscripten-64bit
       ln -s $(Build.SourcesDirectory)/cmake/external/emsdk/ccache/git-emscripten_64bit/bin/ccache /usr/local/bin/ccache
     displayName: 'emsdk install and activate ccache for emscripten'
     condition: eq('${{ parameters.WithCache }}', 'true')
diff --git a/tools/ci_build/github/azure-pipelines/templates/win-wasm-ci.yml b/tools/ci_build/github/azure-pipelines/templates/win-wasm-ci.yml
index 922f71614e..9d36e2dbe4 100644
--- a/tools/ci_build/github/azure-pipelines/templates/win-wasm-ci.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/win-wasm-ci.yml
@@ -42,7 +42,7 @@ jobs:
   variables:
     EnvSetupScript: setup_env.bat
     buildArch: x64
-    CommonBuildArgs: '--parallel --config ${{ parameters.BuildConfig }} --skip_submodule_sync --cmake_generator "MinGW Makefiles" --build_wasm --use_xnnpack --emsdk_version releases-7c905cfc1ca6699f6ccb288ae174902cfbdcf0a2-64bit ${{ parameters.ExtraBuildArgs }}'
+    CommonBuildArgs: '--parallel --config ${{ parameters.BuildConfig }} --skip_submodule_sync --cmake_generator "MinGW Makefiles" --build_wasm --use_xnnpack ${{ parameters.ExtraBuildArgs }}'
     runCodesignValidationInjection: false
   timeoutInMinutes: ${{ parameters.TimeoutInMinutes }}
   workspace: