diff --git a/BUILD.md b/BUILD.md
index 8db4a7fc52416..6b270ef3ec16d 100644
--- a/BUILD.md
+++ b/BUILD.md
@@ -37,14 +37,21 @@ OS/Compiler Matrix:
 ONNX Runtime python binding only supports Python 3.x. Please use python 3.5+.
 
 ## Build
-Install cmake-3.11 or better from https://cmake.org/download/.
+1. Checkout the source tree:
+   ```
+   git clone --recursive https://github.com/Microsoft/onnxruntime
+   cd onnxruntime
+   ```
+2. Install cmake-3.11 or better from https://cmake.org/download/.
+3. (optional) Install protobuf 3.6.1 from source code(cmake/external/protobuf). CMake flag protobuf\_BUILD\_SHARED\_LIBS must be turned off. After the installation, you should have the 'protoc' executable in your PATH.
+4. (optional) Install onnx from source code(cmake/external/onnx)
+    ```
+    export ONNX_ML=1
+    python3 setup.py bdist_wheel
+    pip3 install --upgrade dist/*.whl
+    ```
+5. Run './build.sh --config RelWithDebInfo --build\_wheel' for Linux (or './build.bat --config RelWithDebInfo --build\_wheel' for Windows)
 
-Checkout the source tree:
-```
-git clone --recursive https://github.com/Microsoft/onnxruntime
-cd onnxruntime
-./build.sh for Linux (or ./build.bat for Windows)
-```
 The build script runs all unit tests by default.
 
 The complete list of build options can be found by running `./build.sh (or ./build.bat) --help`
diff --git a/onnxruntime/test/python/onnx_backend_test_series.py b/onnxruntime/test/python/onnx_backend_test_series.py
index f1be2cd97acc7..80f7f6c81f34d 100644
--- a/onnxruntime/test/python/onnx_backend_test_series.py
+++ b/onnxruntime/test/python/onnx_backend_test_series.py
@@ -12,49 +12,79 @@
 
 backend_test = onnx.backend.test.BackendTest(c2, __name__)
 
-# Current status
-# Ran 930 tests in 0.948s OK (skipped=574)
-
-# We should investigate.
-
-# dimension issue
-# Error message is: Input X must be 4-dimensional. X: {1,1,3}
-# ONNX Runtime expects a 4-dimension vector for operator ConvTranspose.
-# file onnxruntime/core/providers/cpu/nn/conv_transpose.cc
-backend_test.exclude(r'(convtranspose)')
 
 # Type not supported
 backend_test.exclude(r'(FLOAT16)')
 
-# Operator not supported
-backend_test.exclude(r'(test_expand)')
-backend_test.exclude(r'(maxpool)')
-backend_test.exclude(r'(AvgPool)')
-backend_test.exclude(r'(max_one_input)|(max_example_cpu)|(max_two_inputs)')
-backend_test.exclude(r'(min_one_input)|(min_example_cpu)|(min_two_inputs)')
-backend_test.exclude(r'(mean_example)|(mean_one_input)|(mean_two_inputs)')
-backend_test.exclude(r'(sum_example)|(sum_one_input)|(sum_two_inputs)')
-backend_test.exclude(r'(BatchNorm)')
-backend_test.exclude(r'(GLU)|(PReLU)|(PoissonNLLLLoss)|(Softsign)')
-backend_test.exclude(r'(Linear_cpu)')
-backend_test.exclude(r'(broadcast)')
-backend_test.exclude(r'(addconstant)|(addmm)|(basic)|(lstm)')
-backend_test.exclude(r'(_mm)|(non_float)|(test_operator_params_cpu)')
-backend_test.exclude(r'(pow_cpu)|(rnn_cpu)|(rnn_single)|(_gru_)')
-backend_test.exclude("(precomputed_((pads)|(strides)))")
-
-# Exclude deep learning
-backend_test.exclude(r'(test_vgg19|test_vgg)')  # Too long.
-backend_test.exclude(r'(alexnet)')  # Too long.
-backend_test.exclude(r'(densenet)')  # Too long.
-backend_test.exclude(r'(inception)')  # Too long.
-backend_test.exclude(r'(resnet)')  # Too long.
-backend_test.exclude(r'(shufflenet)')  # Too long.
-backend_test.exclude(r'(squeezenet)')  # Too long.
-backend_test.exclude(r'(zfnet)')  # Too long.
-
-# Exclude experimental
-backend_test.exclude(r'(test_mvn_cpu)')
+backend_test.exclude(r'(test_acosh_cpu.*'
+'|test_acosh_example_cpu.*'
+'|test_asinh_cpu.*'
+'|test_asinh_example_cpu.*'
+'|test_atanh_cpu.*'
+'|test_atanh_example_cpu.*'
+'|test_convtranspose_1d_cpu.*'
+'|test_convtranspose_3d_cpu.*'
+'|test_cosh_cpu.*'
+'|test_cosh_example_cpu.*'
+'|test_dynamic_slice_cpu.*'
+'|test_dynamic_slice_default_axes_cpu.*'
+'|test_dynamic_slice_end_out_of_bounds_cpu.*'
+'|test_dynamic_slice_neg_cpu.*'
+'|test_dynamic_slice_start_out_of_bounds_cpu.*'
+'|test_eyelike_populate_off_main_diagonal_cpu.*'
+'|test_eyelike_with_dtype_cpu.*'
+'|test_eyelike_without_dtype_cpu.*'
+'|test_gru_seq_length_cpu.*'
+'|test_maxunpool_export_with_output_shape_cpu.*'
+'|test_maxunpool_export_without_output_shape_cpu.*'
+'|test_onehot_with_axis_cpu.*'
+'|test_onehot_without_axis_cpu.*'
+'|test_scan_sum_cpu.*'
+'|test_scatter_with_axis_cpu.*'
+'|test_scatter_without_axis_cpu.*'
+'|test_sign_cpu.*'
+'|test_sinh_cpu.*'
+'|test_sinh_example_cpu.*'
+'|test_AvgPool1d_cpu.*'
+'|test_AvgPool1d_stride_cpu.*'
+'|test_AvgPool2d_cpu.*'
+'|test_AvgPool2d_stride_cpu.*'
+'|test_AvgPool3d_cpu.*'
+'|test_AvgPool3d_stride1_pad0_gpu_input_cpu.*'
+'|test_AvgPool3d_stride_cpu.*'
+'|test_BatchNorm1d_3d_input_eval_cpu.*'
+'|test_BatchNorm2d_eval_cpu.*'
+'|test_BatchNorm2d_momentum_eval_cpu.*'
+'|test_BatchNorm3d_eval_cpu.*'
+'|test_BatchNorm3d_momentum_eval_cpu.*'
+'|test_GLU_cpu.*'
+'|test_GLU_dim_cpu.*'
+'|test_Linear_cpu.*'
+'|test_PReLU_1d_cpu.*'
+'|test_PReLU_1d_multiparam_cpu.*'
+'|test_PReLU_2d_cpu.*'
+'|test_PReLU_2d_multiparam_cpu.*'
+'|test_PReLU_3d_cpu.*'
+'|test_PReLU_3d_multiparam_cpu.*'
+'|test_PoissonNLLLLoss_no_reduce_cpu.*'
+'|test_Softsign_cpu.*'
+'|test_operator_add_broadcast_cpu.*'
+'|test_operator_add_size1_broadcast_cpu.*'
+'|test_operator_add_size1_right_broadcast_cpu.*'
+'|test_operator_add_size1_singleton_broadcast_cpu.*'
+'|test_operator_addconstant_cpu.*'
+'|test_operator_addmm_cpu.*'
+'|test_operator_basic_cpu.*'
+'|test_operator_lstm_cpu.*'
+'|test_operator_mm_cpu.*'
+'|test_operator_non_float_params_cpu.*'
+'|test_operator_params_cpu.*'
+'|test_operator_pow_cpu.*'
+'|test_operator_rnn_cpu.*'
+'|test_operator_rnn_single_layer_cpu.*'
+'|test_sign_model_cpu.*'
+'|test_mvn.*' #No schema registered for 'MeanVarianceNormalization'!
+')')
 
 # import all test cases at global scope to make
 # them visible to python.unittest.
diff --git a/tools/ci_build/build.py b/tools/ci_build/build.py
index 2dce493f2d6d4..813356bdb36c6 100755
--- a/tools/ci_build/build.py
+++ b/tools/ci_build/build.py
@@ -109,7 +109,7 @@ def get_config_build_dir(build_dir, config):
     # build directory per configuration
     return os.path.join(build_dir, config)
 
-def run_subprocess(args, cwd=None, capture=False, dll_path=None, check=True):
+def run_subprocess(args, cwd=None, capture=False, dll_path=None):
     log.debug("Running subprocess in '{0}'\n{1}".format(cwd or os.getcwd(), args))
     my_env = os.environ.copy()
     if dll_path:
@@ -122,9 +122,9 @@ def run_subprocess(args, cwd=None, capture=False, dll_path=None, check=True):
                 my_env["LD_LIBRARY_PATH"] = dll_path
 
     if (capture):
-        result = subprocess.run(args, cwd=cwd, check=check, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, env=my_env)
+        result = subprocess.run(args, cwd=cwd, check=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, env=my_env)
     else:
-        result = subprocess.run(args, cwd=cwd, check=check, env=my_env)
+        result = subprocess.run(args, cwd=cwd, check=True, env=my_env)
 
     return result
 
@@ -409,8 +409,8 @@ def run_onnxruntime_tests(args, source_dir, ctest_path, build_dir, configs, enab
                 run_subprocess([sys.executable, 'onnxruntime_test_python_backend.py'], cwd=cwd, dll_path=dll_path)
                 run_subprocess([sys.executable, os.path.join(source_dir,'onnxruntime','test','onnx','gen_test_models.py'),'--output_dir','test_models'], cwd=cwd)
                 run_subprocess([os.path.join(cwd,'onnx_test_runner'), 'test_models'], cwd=cwd)
-                #The following one may fail
-                run_subprocess([sys.executable, 'onnx_backend_test_series.py'], cwd=cwd, dll_path=dll_path, check=False)
+                if config != 'Debug':
+                    run_subprocess([sys.executable, 'onnx_backend_test_series.py'], cwd=cwd, dll_path=dll_path)
             try:
                 import onnxmltools
                 import keras
diff --git a/tools/ci_build/github/linux/docker/scripts/install_deps.sh b/tools/ci_build/github/linux/docker/scripts/install_deps.sh
index e1987194ebacd..364cbb8bf8d19 100755
--- a/tools/ci_build/github/linux/docker/scripts/install_deps.sh
+++ b/tools/ci_build/github/linux/docker/scripts/install_deps.sh
@@ -33,8 +33,8 @@ else
   #Install ONNX
   #5af210ca8a1c73aa6bae8754c9346ec54d0a756e is v1.2.3
   #bae6333e149a59a3faa9c4d9c44974373dcf5256 is v1.3.0
-  #eb4b7c2cc2a0d34c0127e26c2c1cb5e712467e1e is v1.3.0 latest
-  for onnx_version in "5af210ca8a1c73aa6bae8754c9346ec54d0a756e" "bae6333e149a59a3faa9c4d9c44974373dcf5256" "eb4b7c2cc2a0d34c0127e26c2c1cb5e712467e1e"; do
+  #0a4d5abdf4939ab0842a5eadcc16a3bf0738f901 is v1.3.0 latest
+  for onnx_version in "5af210ca8a1c73aa6bae8754c9346ec54d0a756e" "bae6333e149a59a3faa9c4d9c44974373dcf5256" "0a4d5abdf4939ab0842a5eadcc16a3bf0738f901"; do
     if [ -z ${lastest_onnx_version+x} ]; then
       echo "first pass";
     else