Merge branch 'main_retriver_merge_ict_eval' into 'main'

ICT zeroshot evaluation

See merge request ADLR/megatron-lm!248

examples/evaluate_ict_zeroshot_nq.sh

+#!/bin/bash
+
+# Evaluate natural question test data given Wikipedia embeddings and pretrained
+# ICT model
+
+# Datasets can be downloaded from the following link:
+# https://github.com/facebookresearch/DPR/blob/master/data/download_data.py
+
+EVIDENCE_DATA_DIR=<Specify path of Wikipedia dataset>
+EMBEDDING_PATH=<Specify path of the embeddings>
+CHECKPOINT_PATH=<Specify path of pretrained ICT model>
+
+QA_FILE=<Path of the natural question test dataset>
+
+python tasks/main.py \
+    --task ICT-ZEROSHOT-NQ \
+    --tokenizer-type BertWordPieceLowerCase \
+    --num-layers 12 \
+    --hidden-size 768 \
+    --num-attention-heads 12 \
+    --tensor-model-parallel-size 1 \
+    --micro-batch-size 128 \
+    --checkpoint-activations \
+    --seq-length 512 \
+    --max-position-embeddings 512 \
+    --load ${CHECKPOINT_PATH} \
+    --evidence-data-path ${EVIDENCE_DATA_DIR} \
+    --embedding-path ${EMBEDDING_PATH} \
+    --retriever-seq-length 256 \
+    --vocab-file  bert-vocab.txt\
+    --qa-data-test ${QA_FILE} \
+    --num-workers 2 \
+    --faiss-use-gpu \
+    --retriever-report-topk-accuracies 1 5 20 100 \
+    --fp16
+

megatron/arguments.py

@@ -712,8 +712,6 @@ def _add_biencoder_args(parser):
                         'square root of hidden size')
 
     # faiss index
-    group.add_argument('--faiss-use-gpu', action='store_true',
-                       help='Whether create the FaissMIPSIndex on GPU')
     group.add_argument('--block-data-path', type=str, default=None,
                        help='Where to save/load BlockData to/from')
     group.add_argument('--embedding-path', type=str, default=None,

megatron/data/biencoder_dataset_utils.py

@@ -24,11 +24,8 @@ def get_one_epoch_dataloader(dataset, micro_batch_size=None):
     """Specifically one epoch to be used in an indexing job."""
     args = get_args()
 
-    world_size = mpu.get_data_parallel_world_size()
-    rank = mpu.get_data_parallel_rank()
     if micro_batch_size is None:
         micro_batch_size = args.micro_batch_size
-    global_batch_size = micro_batch_size * world_size
     num_workers = args.num_workers
 
     # Use megatron's sampler with consumed samples set to 0 as

megatron/data/realm_index.py

@@ -116,18 +116,22 @@ class OpenRetreivalDataStore(object):
 
 
 class FaissMIPSIndex(object):
-    """Wrapper object for a BlockData which similarity search via FAISS under the hood"""
-    def __init__(self, embed_size, block_data=None, use_gpu=False):
+    """
+    Wrapper object for a BlockData which similarity search via FAISS under the hood
+    """
+    def __init__(self, embed_size, embed_data=None, use_gpu=False):
         self.embed_size = embed_size
-        self.block_data = block_data
+        self.embed_data = embed_data
         self.use_gpu = use_gpu
-        self.id_map = dict()
 
-        self.block_mips_index = None
-        self._set_block_index()
+        self.mips_index = None
+        self._set_mips_index()
 
-    def _set_block_index(self):
-        """Create a Faiss Flat index with inner product as the metric to search against"""
+    def _set_mips_index(self):
+        """
+        Create a Faiss Flat index with inner product as the metric
+        to search against
+        """
         try:
             import faiss
         except ImportError:
@@ -135,85 +139,86 @@ class FaissMIPSIndex(object):
 
         if mpu.is_unitialized() or mpu.get_data_parallel_rank() == 0:
             print("\n> Building index", flush=True)
-        self.block_mips_index = faiss.index_factory(self.embed_size, 'Flat', faiss.METRIC_INNER_PRODUCT)
+
+        cpu_index = faiss.IndexFlatIP(self.embed_size)
 
         if self.use_gpu:
             # create resources and config for GpuIndex
-            res = faiss.StandardGpuResources()
-            config = faiss.GpuIndexFlatConfig()
-            config.device = torch.cuda.current_device()
+            config = faiss.GpuMultipleClonerOptions()
+            config.shard = True
             config.useFloat16 = True
-
-            self.block_mips_index = faiss.GpuIndexFlat(res, self.block_mips_index, config)
+            gpu_index = faiss.index_cpu_to_all_gpus(cpu_index, co=config)
+            self.mips_index = faiss.IndexIDMap(gpu_index)
             if mpu.is_unitialized() or mpu.get_data_parallel_rank() == 0:
-                print(">> Initialized index on GPU {}".format(self.block_mips_index.getDevice()), flush=True)
+                print(">> Initialized index on GPU", flush=True)
         else:
             # CPU index supports IDs so wrap with IDMap
-            self.block_mips_index = faiss.IndexIDMap(self.block_mips_index)
+            self.mips_index = faiss.IndexIDMap(cpu_index)
             if mpu.is_unitialized() or mpu.get_data_parallel_rank() == 0:
                 print(">> Initialized index on CPU", flush=True)
 
-        # if we were constructed with a BlockData, then automatically load it when the FAISS structure is built
-        if self.block_data is not None:
-            self.add_block_embed_data(self.block_data)
+        # if we were constructed with a BlockData, then automatically load it
+        # when the FAISS structure is built
+        if self.embed_data is not None:
+            self.add_embed_data(self.embed_data)
 
     def reset_index(self):
-        """Delete existing index and create anew"""
-        del self.block_mips_index
+        """Delete existing index and create a new"""
+        del self.mips_index
 
         # reset the block data so that _set_block_index will reload it as well
-        if self.block_data is not None:
-            block_data_path = self.block_data.block_data_path
-            del self.block_data
-            self.block_data = BlockData(block_data_path)
+        if self.embed_data is not None:
+            embed_data_path = self.embed_data.embedding_path
+            del self.embed_data
+            self.embed_data = OpenRetreivalDataStore(embed_data_path)
+
+        self._set_mips_index()
+
+    def update_index(self):
+        """Delete existing index and create a new"""
+        del self.mips_index
 
-        self._set_block_index()
+        # reset the block data so that _set_mips_index will reload it as well
+        if self.embed_data is not None:
+            self.embed_data.load_from_file()
+        self._set_mips_index()
 
-    def add_block_embed_data(self, all_block_data):
+    def add_embed_data(self, all_embed_data):
         """Add the embedding of each block to the underlying FAISS index"""
 
         # this assumes the embed_data is a dict : {int: np.array<float>}
-        block_indices, block_embeds = zip(*all_block_data.embed_data.items())
+        block_indices, block_embeds = zip(*all_embed_data.embed_data.items())
 
-        # the embeddings have to be entered in as float32 even though the math internally is done with float16.
-        block_embeds_arr = np.float32(np.array(block_embeds))
-        block_indices_arr = np.array(block_indices)
-
-        # faiss GpuIndex doesn't work with IDMap wrapper so store ids to map back with
-        if self.use_gpu:
-            for i, idx in enumerate(block_indices):
-                self.id_map[i] = idx
+        # the embeddings have to be entered in as float32 even though the math
+        # internally is done with float16.
+        embeds_arr = np.float32(np.array(block_embeds))
+        indices_arr = np.array(block_indices)
 
         # we no longer need the embedding data since it's in the index now
-        all_block_data.clear()
+        all_embed_data.clear()
 
-        if self.use_gpu:
-            self.block_mips_index.add(block_embeds_arr)
-        else:
-            self.block_mips_index.add_with_ids(block_embeds_arr, block_indices_arr)
+        self.mips_index.add_with_ids(embeds_arr, indices_arr)
 
         if mpu.is_unitialized() or mpu.get_data_parallel_rank() == 0:
             print(">>> Finished adding block data to index", flush=True)
 
     def search_mips_index(self, query_embeds, top_k, reconstruct=True):
-        """Get the top-k blocks by the index distance metric.
+        """
+        Get the top-k blocks by the index distance metric.
 
-        :param reconstruct: if True: return a [num_queries x k x embed_dim] array of blocks
-                            if False: return [num_queries x k] array of distances, and another for indices
+        :param reconstruct: if True: return a [num_queries x k x embed_dim]
+                                array of blocks
+                            if False: return [num_queries x k] array of
+                                distances, and another for indices
         """
         query_embeds = np.float32(detach(query_embeds))
 
         if reconstruct:
             # get the vectors themselves
-            top_k_block_embeds = self.block_mips_index.search_and_reconstruct(query_embeds, top_k)
+            top_k_block_embeds = self.mips_index.search_and_reconstruct(\
+                query_embeds, top_k)
             return top_k_block_embeds
-
         else:
             # get distances and indices of closest vectors
-            distances, block_indices = self.block_mips_index.search(query_embeds, top_k)
-            if self.use_gpu:
-                fresh_indices = np.zeros(block_indices.shape)
-                for i, j in itertools.product(block_indices.shape):
-                    fresh_indices[i, j] = self.id_map[block_indices[i, j]]
-                block_indices = fresh_indices
+            distances, block_indices = self.mips_index.search(query_embeds, top_k)
             return distances, block_indices

tasks/main.py

@@ -47,6 +47,20 @@ def get_tasks_args(parser):
                        help='Sliding window for overlapping evaluation.')
     group.add_argument('--strict-lambada', action='store_true',
                        help='Use more difficult formulation of lambada.')
+    # Retriever args
+    group.add_argument('--qa-data-dev', type=str, default=None,
+                       help='Path to the QA dataset dev file.')
+    group.add_argument('--qa-data-test', type=str, default=None,
+                       help='Path to the QA dataset test file.')
+
+    # Faiss arguments for retriever
+    group.add_argument('--faiss-use-gpu', action='store_true',
+                       help='Whether create the FaissMIPSIndex on GPU')
+    group.add_argument('--faiss-match', type=str, default='string', \
+                        choices=['regex', 'string'], help="Answer matching '\
+                        'logic type")
+    group.add_argument('--faiss-topk-retrievals', type=int, default=100,
+                       help='Number of blocks to use as top-k during retrieval')
 
     return parser
 
@@ -62,6 +76,8 @@ if __name__ == '__main__':
         from glue.finetune import main
     elif args.task in ['LAMBADA', 'WIKITEXT103']:
         from zeroshot_gpt.evaluate import main
+    elif args.task in ['ICT-ZEROSHOT-NQ']:
+        from orqa.evaluate_orqa import main
     else:
         raise NotImplementedError('Task {} is not implemented.'.format(
             args.task))

tasks/orqa/evaluate_orqa.py

+# coding=utf-8
+# Copyright (c) 2020, NVIDIA CORPORATION.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Main tasks functionality."""
+
+import os
+import sys
+
+from megatron import get_args
+from tasks.orqa.evaluate_utils import ORQAEvaluator
+
+def main():
+    """
+    Main program
+    """
+
+    args = get_args()
+
+    # Set up the model and evaluator
+    evaluator = ORQAEvaluator()
+
+    # Run evaluation
+    if args.qa_data_dev is not None:
+        evaluator.evaluate(args.qa_data_dev, "DEV")
+
+    if args.qa_data_test is not None:
+        evaluator.evaluate(args.qa_data_test, "TEST")
+

tasks/orqa/evaluate_utils.py

+# coding=utf-8
+# Copyright (c) 2020, NVIDIA CORPORATION.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import torch
+
+from megatron import get_args, print_rank_0
+from megatron.checkpointing import load_biencoder_checkpoint
+from megatron.data.orqa_wiki_dataset import get_open_retrieval_wiki_dataset
+from tasks.orqa.natural_questions.nq import get_nq_dataset
+from tasks.orqa.natural_questions.nq import get_one_epoch_nq_dataloader
+from tasks.orqa.natural_questions.nq import process_nq_batch
+from tasks.orqa.natural_questions.qa_utils import calculate_matches
+from megatron.data.realm_index import OpenRetreivalDataStore, FaissMIPSIndex
+from megatron.model.biencoder_model import biencoder_model_provider
+from megatron.training import get_model
+
+class ORQAEvaluator(object):
+    def __init__(self):
+        args = get_args()
+        self.embedding_size = args.hidden_size
+        self.faiss_use_gpu = args.faiss_use_gpu
+        self.evidence_embedder_obj = None
+        self.evidence_dataset = None
+        self.mips_index = None
+        self.eval_dataset = None
+
+        # Get Evidence (Wikipedia) dataset
+        self.get_evidence_dataset()
+
+        # Load query encoder checkpoint
+        only_query_model = True
+        if args.biencoder_shared_query_context_model:
+            only_query_model = False
+
+        model = get_model(lambda: biencoder_model_provider(only_query_model=\
+            only_query_model, biencoder_shared_query_context_model=\
+            args.biencoder_shared_query_context_model))
+
+        self.model = load_biencoder_checkpoint(model,
+                only_query_model=only_query_model)
+
+        assert len(self.model) == 1
+        self.model[0].eval()
+
+        # Load faiss indexer
+        self.faiss_wrapper()
+
+    def get_evidence_embedding(self):
+        # This will load the embedding from the embedding path
+        self.evidence_embedder_obj = OpenRetreivalDataStore(load_from_path=True)
+
+    def get_evidence_dataset(self):
+        self.evidence_dataset = get_open_retrieval_wiki_dataset()
+
+    def faiss_wrapper(self):
+        # Initialize FAISS wrapper on local rank = 0 as the evidence embeddings
+        # is distributed over all the GPUs in a node and FAISS is not 
+        # thread-safe
+        args = get_args()
+        if args.local_rank == 0:
+            # Get evidence embeddings computed using context encoder
+            self.get_evidence_embedding()
+
+            assert self.evidence_embedder_obj is not None
+            self.mips_index = FaissMIPSIndex(embed_size=self.embedding_size,
+                                        embed_data=self.evidence_embedder_obj,
+                                        use_gpu=self.faiss_use_gpu)
+
+        # Wait for the FAISS index to be initialized in all the nodes
+        torch.distributed.barrier()
+
+    def generate_query_vectors(self, qa_data, split):
+
+        self.eval_dataset = get_nq_dataset(qa_data, split)
+        dataloader = get_one_epoch_nq_dataloader(self.eval_dataset)
+
+        query_vectors = []
+        reference_list = []
+
+        for batch in dataloader:
+            # batch also has query_tokens and query_pad_data
+            query_tokens, query_mask, query_types, \
+                query_len, reference = process_nq_batch(batch)
+
+            assert len(self.model) == 1
+            unwrapped_model = self.model[0]
+            while not hasattr(unwrapped_model, 'embed_text'):
+                unwrapped_model = unwrapped_model.module
+
+            with torch.no_grad():
+                query_logits = unwrapped_model.embed_text(
+                    unwrapped_model.query_model, query_tokens, 
+                    query_mask, query_types)
+
+            reference_list.extend(reference)
+            query_vectors.extend(query_logits.split(1, dim=0))
+            if len(query_vectors) % 100 == 0:
+                print_rank_0('Encoded queries {}'.format(len(query_vectors)))
+
+        query_tensor = torch.cat(query_vectors, dim=0)
+        print_rank_0('Total encoded queries tensor {}'.format(query_tensor.size()))
+
+        assert query_tensor.size(0) == len(self.eval_dataset)
+        return query_tensor, reference_list
+
+    def evaluate(self, qa_data, split):
+        args = get_args()
+        query_tensor, reference_list = self.generate_query_vectors(qa_data, \
+                                                                    split)
+        local_rank = args.local_rank
+        rank = torch.distributed.get_rank()
+        device_count = torch.cuda.device_count()
+        num_nodes = torch.distributed.get_world_size() // device_count
+        node_id = rank // device_count
+
+        for node in range(num_nodes):
+            start_rank = node * device_count
+            end_rank = (node + 1) * device_count
+            ranks_list = list(range(start_rank, end_rank))
+            node_group = torch.distributed.new_group(ranks=ranks_list)
+
+            if node_id == node:
+                device_start_rank = start_rank
+                group = node_group
+        
+        input_ = torch.empty_like(query_tensor).copy_(query_tensor).detach_()
+        tensor_list = [torch.empty_like(input_) for _ in range(device_count)]
+        torch.distributed.all_gather(tensor_list, query_tensor, group=group)
+
+        if local_rank == 0 and self.mips_index is not None:
+            all_query_tensor = torch.cat(tensor_list, dim=0).contiguous()
+
+            distance, topkindex = self.mips_index.search_mips_index(
+                all_query_tensor, top_k=args.faiss_topk_retrievals, 
+                reconstruct=False)
+            distance = torch.from_numpy(distance).cuda()
+            topkindex = torch.LongTensor(topkindex).cuda()
+
+        if local_rank != 0:
+            distance = torch.empty(device_count * len(query_tensor), \
+                args.faiss_topk_retrievals, dtype=torch.float32).cuda()
+            topkindex = torch.empty(device_count * len(query_tensor), \
+                args.faiss_topk_retrievals, dtype=torch.int64).cuda()
+
+        torch.distributed.broadcast(distance, src=device_start_rank, \
+            group=group)
+        torch.distributed.broadcast(topkindex, src=device_start_rank, \
+            group=group)
+
+        distance = torch.split(distance, len(query_tensor), dim=0)\
+            [local_rank]
+        topkindex = torch.split(topkindex, len(query_tensor), dim=0)\
+            [local_rank]
+
+        top_ids_and_scores = []
+        for darray, topkarray in zip(distance, topkindex):
+            top_ids_and_scores.append((topkarray.tolist(), darray.tolist()))
+
+        passages = self.evidence_dataset.id2text
+        match_stats = calculate_matches(passages,
+                                        reference_list,
+                                        top_ids_and_scores,
+                                        workers_num=args.num_workers,
+                                        match_type=args.faiss_match)
+        top_k_hits = match_stats.top_k_hits
+
+        print_rank_0("{} SET RESULTS".format(split))
+        print_rank_0("topk-{} documents hits {}".format(
+            args.faiss_topk_retrievals, top_k_hits))
+        top_k_hits = [v / len(top_ids_and_scores) for v in top_k_hits]
+        print_rank_0("top-k documents hits accuracy {}".format(top_k_hits))
+
+        for i in args.retriever_report_topk_accuracies:
+            print_rank_0("top-{}: {:.2f}".format(i, top_k_hits[i-1] * 100))
+
+        return

tasks/orqa/natural_questions/nq.py

+# coding=utf-8
+# Copyright (c) 2020, NVIDIA CORPORATION.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+ Data Loader for Google NQ dataset
+"""
+
+from abc import ABC
+import csv
+from collections import OrderedDict
+import numpy as np
+
+import torch
+from torch.utils.data import DataLoader
+from torch.utils.data import Dataset, BatchSampler
+
+from megatron import print_rank_0, get_args, get_tokenizer, mpu
+from megatron.data.biencoder_dataset_utils import make_attention_mask
+
+def get_nq_dataset(qa_data, split):
+    args = get_args()
+    tokenizer = get_tokenizer()
+
+    dataset = NQDataset('Google NQ {} Split'.format(split),
+                        'Google Natural Questions',
+                        qa_data,
+                        tokenizer,
+                        args.retriever_seq_length)
+    return dataset
+
+
+def process_nq_batch(batch):
+    query_tokens = batch['token_ids'].long().cuda()
+    query_mask = (batch['token_mask'] < 0.5).cuda()
+    query_types = batch['token_types'].long().cuda()
+    query_len = batch['seq_len'].long().cuda()
+    reference = batch['reference']
+
+    return query_tokens, query_mask, query_types, query_len, reference
+
+
+class CustomDataLoader(DataLoader):
+    def __init__(self, dataset, eval=False, **kwargs):
+        if kwargs.get('collate_fn', None) is None:
+            kwargs['collate_fn'] = self._collate_fn
+        self.eval = eval
+        super().__init__(dataset, **kwargs)
+
+    def _collate_fn(self, batch_data):
+        # generate batch
+        batch_size = len(batch_data)
+        tensorized = OrderedDict()
+        for d in batch_data:
+            for k, v in d.items():
+                tensorized.setdefault(k, []).append(v)
+        assert len(tensorized) == 5
+
+        tensorized['token_ids'] = torch.LongTensor(tensorized['token_ids'])
+        tensorized['token_mask'] = torch.LongTensor(tensorized['token_mask'])
+        tensorized['token_types'] = torch.LongTensor(tensorized['token_types'])
+        tensorized['seq_len'] = torch.LongTensor(tensorized['seq_len'])
+        return tensorized
+
+
+def get_one_epoch_nq_dataloader(dataset, micro_batch_size=None):
+    """Data loader. Note that batch-size is the local (per GPU) batch-size.
+       NOTE: This dataloader is not distributed !!!
+    """
+
+    args = get_args()
+    if micro_batch_size is None:
+        micro_batch_size = args.micro_batch_size
+    num_workers = args.num_workers
+
+    sampler = torch.utils.data.SequentialSampler(dataset)
+    # importantly, drop_last must be False to get all the data.
+    batch_sampler = BatchSampler(sampler,
+                                 batch_size=micro_batch_size,
+                                 drop_last=False)
+
+    # Data loader. Note that batch size is the per GPU batch size.
+    data_loader = CustomDataLoader(dataset,
+                                   batch_sampler=batch_sampler,
+                                   num_workers=num_workers,
+                                   pin_memory=True)
+    return data_loader
+
+
+def build_tokens_types_paddings_from_text(src_text, tokenizer, max_seq_length):
+    """Build token types and paddings, trim if needed, and pad if needed."""
+
+    src_text_ids = tokenizer.tokenize(src_text)
+
+    return build_tokens_types_paddings_from_ids(src_text_ids,
+                                                max_seq_length,
+                                                tokenizer.cls,
+                                                tokenizer.sep,
+                                                tokenizer.pad)
+
+
+def build_tokens_types_paddings_from_ids(src_ids, max_seq_length, cls_id, \
+    sep_id, pad_id):
+    """
+    Build token types and paddings, trim if needed, and pad if needed.
+
+    TODO: Design modular interface to reuse this function. This is getting
+    repeated multiple times in different tasks
+    """
+
+    enc_ids = []
+    tokentypes_enc = []
+
+    # [CLS].
+    enc_ids.append(cls_id)
+    tokentypes_enc.append(0)
+
+    # A.
+    len_src = len(src_ids)
+    enc_ids.extend(src_ids)
+    tokentypes_enc.extend([0] * len_src)
+
+    # Cap the size.
+    if len(enc_ids) > max_seq_length - 1:
+        enc_ids = enc_ids[0: max_seq_length - 1]
+        tokentypes_enc = tokentypes_enc[0: max_seq_length - 1]
+
+    # [SEP].
+    enc_ids.append(sep_id)
+    tokentypes_enc.append(0)
+
+    num_tokens_enc = len(enc_ids)
+    # Padding.
+    padding_length = max_seq_length - len(enc_ids)
+    if padding_length > 0:
+        enc_ids.extend([pad_id] * padding_length)
+        tokentypes_enc.extend([pad_id] * padding_length)
+
+    return enc_ids, tokentypes_enc, num_tokens_enc
+
+
+def build_sample(token_ids, token_types, num_tokens, reference):
+    """
+    Convert to numpy and return a sample consumed by the
+    batch producer.
+    """
+
+    token_ids = np.array(token_ids, dtype=np.int64)
+    token_types = np.array(token_types, dtype=np.int64)
+    token_mask = make_attention_mask(token_ids, token_ids)
+
+    sample = ({
+        'token_ids': token_ids,
+        'token_mask': token_mask,
+        'token_types': token_types,
+        'seq_len': num_tokens,
+        'reference': reference
+    })
+    return sample
+
+
+class NQDataset(ABC, Dataset):
+    """
+    Open Retrieval Question Answering evaluation using Google NQ dataset.
+    """
+
+    def __init__(self, task_name, dataset_name, datapath,
+                 tokenizer, max_seq_length):
+        # Store inputs.
+        self.task_name = task_name
+        self.dataset_name = dataset_name
+        self.tokenizer = tokenizer
+        self.max_seq_length = max_seq_length
+        print_rank_0(' > building {} dataset for {}:'.format(self.task_name,
+                                                             self.dataset_name))
+        print_rank_0(datapath)
+        self.samples = self.process_samples_from_single_path(datapath)
+        print_rank_0('  >> total number of samples: {}'.format(\
+                                                        len(self.samples)))
+
+    def __len__(self):
+        return len(self.samples)
+
+    def __getitem__(self, idx):
+        raw_sample = self.samples[idx]
+
+        ques_tokens, tokentypes_enc, num_tokens_ques = \
+            build_tokens_types_paddings_from_text(raw_sample['question'],
+                self.tokenizer, self.max_seq_length)
+
+        sample = build_sample(ques_tokens,
+                              tokentypes_enc,
+                              num_tokens_ques,
+                              raw_sample['answers'])
+        return sample
+
+    @staticmethod
+    def process_samples_from_single_path(filename):
+        print_rank_0(' > Processing {} ...'.format(filename))
+        samples = []
+        total = 0
+
+        with open(filename, 'r') as ifile:
+            reader = csv.reader(ifile, delimiter='\t')
+            for row in reader:
+                question = row[0]
+                answers = eval(row[1])
+
+                sample = {'question': question, 'answers': answers}
+                total += 1
+                samples.append(sample)
+
+                if total % 1000 == 0:
+                    print_rank_0('  > processed {} so far ...'.format(total))
+
+        print_rank_0(' >> processed {} samples.'.format(len(samples)))
+        return samples

tasks/orqa/natural_questions/qa_utils.py

+#!/usr/bin/env python3
+# Copyright (c) Facebook, Inc. and its affiliates.
+# All rights reserved.
+#
+
+# The following code has been taken from
+# https://github.com/facebookresearch/DPR, which is CC-BY-NC 4.0
+# licensed as of now. More details on the license can be found
+# at https://github.com/facebookresearch/DPR/blob/master/LICENSE
+
+"""
+ Set of utilities for Q&A results validation tasks - Retriver passage
+ validation and Reader predicted answer validation
+"""
+
+import collections
+import logging
+import string
+import unicodedata
+from functools import partial
+from multiprocessing import Pool as ProcessPool
+from typing import Tuple, List, Dict
+
+import regex as re
+from tasks.orqa.natural_questions.tokenizers import SimpleTokenizer
+
+logger = logging.getLogger(__name__)
+
+QAMatchStats = collections.namedtuple('QAMatchStats', ['top_k_hits',\
+                                        'questions_doc_hits'])
+
+def calculate_matches(all_docs: Dict[object, Tuple[str, str]], 
+    answers: List[List[str]], closest_docs: List[Tuple[List[object], 
+    List[float]]], workers_num: int, match_type: str) -> QAMatchStats:
+    """
+    Evaluates answers presence in the set of documents. This function is 
+    supposed to be used with a large collection of documents and results. 
+    It internally forks multiple sub-processes for evaluation and then 
+    merges results
+    :param all_docs: dictionary of the entire documents database. 
+        doc_id -> (doc_text, title)
+    :param answers: list of answers's list. One list per question
+    :param closest_docs: document ids of the top results along with their
+        scores
+    :param workers_num: amount of parallel threads to process data
+    :param match_type: type of answer matching. Refer to has_answer code for
+        available options
+    :return: matching information tuple.
+    top_k_hits - a list where the index is the amount of top documents retrieved
+        and the value is the total amount of valid matches across an entire
+        dataset.
+    questions_doc_hits - more detailed info with answer matches for every
+        question and every retrieved document
+    """
+    global dpr_all_documents
+    dpr_all_documents = all_docs
+
+    tok_opts = {}
+    tokenizer = SimpleTokenizer(**tok_opts)
+
+    processes = ProcessPool(
+        processes=workers_num,
+    )
+
+    logger.info('Matching answers in top docs...')
+
+    get_score_partial = partial(check_answer, match_type=match_type,
+                                    tokenizer=tokenizer)
+
+    questions_answers_docs = zip(answers, closest_docs)
+
+    scores = processes.map(get_score_partial, questions_answers_docs)
+
+    logger.info('Per question validation results len=%d', len(scores))
+
+    n_docs = len(closest_docs[0][0])
+    top_k_hits = [0] * n_docs
+    for question_hits in scores:
+        best_hit = next((i for i, x in enumerate(question_hits) if x), None)
+        if best_hit is not None:
+            top_k_hits[best_hit:] = [v + 1 for v in top_k_hits[best_hit:]]
+
+    return QAMatchStats(top_k_hits, scores)
+
+
+def check_answer(questions_answers_docs, tokenizer, match_type) -> List[bool]:
+    """
+    Search through all the top docs to see if they have any of the answers.
+    """
+    answers, (doc_ids, doc_scores) = questions_answers_docs
+
+    global dpr_all_documents
+    hits = []
+
+    for i, doc_id in enumerate(doc_ids):
+        doc = dpr_all_documents[doc_id]
+        text = doc[0]
+
+        answer_found = False
+        if text is None:  # cannot find the document for some reason
+            logger.warning("no doc in db")
+            hits.append(False)
+            continue
+
+        if has_answer(answers, text, tokenizer, match_type):
+            answer_found = True
+        hits.append(answer_found)
+    return hits
+
+
+def has_answer(answers, text, tokenizer, match_type) -> bool:
+    """
+    Check if a document contains an answer string.
+    If `match_type` is string, token matching is done between the text 
+        and answer.
+    If `match_type` is regex, we search the whole text with the regex.
+    """
+    text = _normalize(text)
+
+    if match_type == 'string':
+        # Answer is a list of possible strings
+        text = tokenizer.tokenize(text).words(uncased=True)
+
+        for single_answer in answers:
+            single_answer = _normalize(single_answer)
+            single_answer = tokenizer.tokenize(single_answer)
+            single_answer = single_answer.words(uncased=True)
+
+            for i in range(0, len(text) - len(single_answer) + 1):
+                if single_answer == text[i: i + len(single_answer)]:
+                    return True
+
+    elif match_type == 'regex':
+        # Answer is a regex
+        for single_answer in answers:
+            single_answer = _normalize(single_answer)
+            if regex_match(text, single_answer):
+                return True
+    return False
+
+
+def regex_match(text, pattern):
+    """Test if a regex pattern is contained within a text."""
+    try:
+        pattern = re.compile(
+            pattern,
+            flags=re.IGNORECASE + re.UNICODE + re.MULTILINE,
+        )
+    except BaseException:
+        return False
+    return pattern.search(text) is not None
+
+
+# function for the reader model answer validation
+def exact_match_score(prediction, ground_truth):
+    return _normalize_answer(prediction) == _normalize_answer(ground_truth)
+
+
+def _normalize_answer(s):
+    def remove_articles(text):
+        return re.sub(r'\b(a|an|the)\b', ' ', text)
+
+    def white_space_fix(text):
+        return ' '.join(text.split())
+
+    def remove_punc(text):
+        exclude = set(string.punctuation)
+        return ''.join(ch for ch in text if ch not in exclude)
+
+    def lower(text):
+        return text.lower()
+
+    return white_space_fix(remove_articles(remove_punc(lower(s))))
+
+
+def _normalize(text):
+    return unicodedata.normalize('NFD', text)

tasks/orqa/natural_questions/tokenizers.py

+#!/usr/bin/env python3
+# Copyright (c) Facebook, Inc. and its affiliates.
+# All rights reserved.
+#
+
+# The following code has been taken from
+# https://github.com/facebookresearch/DPR, which is CC-BY-NC 4.0
+# licensed as of now. More details on the license can be found
+# at https://github.com/facebookresearch/DPR/blob/master/LICENSE
+
+"""
+Most of the tokenizers code here is copied from DrQA codebase to avoid adding extra dependency
+"""
+
+import copy
+import logging
+
+import regex
+import spacy
+
+logger = logging.getLogger(__name__)
+
+
+class Tokens(object):
+    """A class to represent a list of tokenized text."""
+    TEXT = 0
+    TEXT_WS = 1
+    SPAN = 2
+    POS = 3
+    LEMMA = 4
+    NER = 5
+
+    def __init__(self, data, annotators, opts=None):
+        self.data = data
+        self.annotators = annotators
+        self.opts = opts or {}
+
+    def __len__(self):
+        """The number of tokens."""
+        return len(self.data)
+
+    def slice(self, i=None, j=None):
+        """Return a view of the list of tokens from [i, j)."""
+        new_tokens = copy.copy(self)
+        new_tokens.data = self.data[i: j]
+        return new_tokens
+
+    def untokenize(self):
+        """Returns the original text (with whitespace reinserted)."""
+        return ''.join([t[self.TEXT_WS] for t in self.data]).strip()
+
+    def words(self, uncased=False):
+        """Returns a list of the text of each token
+
+        Args:
+            uncased: lower cases text
+        """
+        if uncased:
+            return [t[self.TEXT].lower() for t in self.data]
+        else:
+            return [t[self.TEXT] for t in self.data]
+
+    def offsets(self):
+        """Returns a list of [start, end) character offsets of each token."""
+        return [t[self.SPAN] for t in self.data]
+
+    def pos(self):
+        """Returns a list of part-of-speech tags of each token.
+        Returns None if this annotation was not included.
+        """
+        if 'pos' not in self.annotators:
+            return None
+        return [t[self.POS] for t in self.data]
+
+    def lemmas(self):
+        """Returns a list of the lemmatized text of each token.
+        Returns None if this annotation was not included.
+        """
+        if 'lemma' not in self.annotators:
+            return None
+        return [t[self.LEMMA] for t in self.data]
+
+    def entities(self):
+        """Returns a list of named-entity-recognition tags of each token.
+        Returns None if this annotation was not included.
+        """
+        if 'ner' not in self.annotators:
+            return None
+        return [t[self.NER] for t in self.data]
+
+    def ngrams(self, n=1, uncased=False, filter_fn=None, as_strings=True):
+        """Returns a list of all ngrams from length 1 to n.
+
+        Args:
+            n: upper limit of ngram length
+            uncased: lower cases text
+            filter_fn: user function that takes in an ngram list and returns
+              True or False to keep or not keep the ngram
+            as_string: return the ngram as a string vs list
+        """
+
+        def _skip(gram):
+            if not filter_fn:
+                return False
+            return filter_fn(gram)
+
+        words = self.words(uncased)
+        ngrams = [(s, e + 1)
+                  for s in range(len(words))
+                  for e in range(s, min(s + n, len(words)))
+                  if not _skip(words[s:e + 1])]
+
+        # Concatenate into strings
+        if as_strings:
+            ngrams = ['{}'.format(' '.join(words[s:e])) for (s, e) in ngrams]
+
+        return ngrams
+
+    def entity_groups(self):
+        """Group consecutive entity tokens with the same NER tag."""
+        entities = self.entities()
+        if not entities:
+            return None
+        non_ent = self.opts.get('non_ent', 'O')
+        groups = []
+        idx = 0
+        while idx < len(entities):
+            ner_tag = entities[idx]
+            # Check for entity tag
+            if ner_tag != non_ent:
+                # Chomp the sequence
+                start = idx
+                while (idx < len(entities) and entities[idx] == ner_tag):
+                    idx += 1
+                groups.append((self.slice(start, idx).untokenize(), ner_tag))
+            else:
+                idx += 1
+        return groups
+
+
+class Tokenizer(object):
+    """Base tokenizer class.
+    Tokenizers implement tokenize, which should return a Tokens class.
+    """
+
+    def tokenize(self, text):
+        raise NotImplementedError
+
+    def shutdown(self):
+        pass
+
+    def __del__(self):
+        self.shutdown()
+
+
+class SimpleTokenizer(Tokenizer):
+    ALPHA_NUM = r'[\p{L}\p{N}\p{M}]+'
+    NON_WS = r'[^\p{Z}\p{C}]'
+
+    def __init__(self, **kwargs):
+        """
+        Args:
+            annotators: None or empty set (only tokenizes).
+        """
+        self._regexp = regex.compile(
+            '(%s)|(%s)' % (self.ALPHA_NUM, self.NON_WS),
+            flags=regex.IGNORECASE + regex.UNICODE + regex.MULTILINE
+        )
+        if len(kwargs.get('annotators', {})) > 0:
+            logger.warning('%s only tokenizes! Skipping annotators: %s' %
+                           (type(self).__name__, kwargs.get('annotators')))
+        self.annotators = set()
+
+    def tokenize(self, text):
+        data = []
+        matches = [m for m in self._regexp.finditer(text)]
+        for i in range(len(matches)):
+            # Get text
+            token = matches[i].group()
+
+            # Get whitespace
+            span = matches[i].span()
+            start_ws = span[0]
+            if i + 1 < len(matches):
+                end_ws = matches[i + 1].span()[0]
+            else:
+                end_ws = span[1]
+
+            # Format data
+            data.append((
+                token,
+                text[start_ws: end_ws],
+                span,
+            ))
+        return Tokens(data, self.annotators)
+
+
+class SpacyTokenizer(Tokenizer):
+
+    def __init__(self, **kwargs):
+        """
+        Args:
+            annotators: set that can include pos, lemma, and ner.
+            model: spaCy model to use (either path, or keyword like 'en').
+        """
+        model = kwargs.get('model', 'en')
+        self.annotators = copy.deepcopy(kwargs.get('annotators', set()))
+        nlp_kwargs = {'parser': False}
+        if not any([p in self.annotators for p in ['lemma', 'pos', 'ner']]):
+            nlp_kwargs['tagger'] = False
+        if 'ner' not in self.annotators:
+            nlp_kwargs['entity'] = False
+        self.nlp = spacy.load(model, **nlp_kwargs)
+
+    def tokenize(self, text):
+        # We don't treat new lines as tokens.
+        clean_text = text.replace('\n', ' ')
+        tokens = self.nlp.tokenizer(clean_text)
+        if any([p in self.annotators for p in ['lemma', 'pos', 'ner']]):
+            self.nlp.tagger(tokens)
+        if 'ner' in self.annotators:
+            self.nlp.entity(tokens)
+
+        data = []
+        for i in range(len(tokens)):
+            # Get whitespace
+            start_ws = tokens[i].idx
+            if i + 1 < len(tokens):
+                end_ws = tokens[i + 1].idx
+            else:
+                end_ws = tokens[i].idx + len(tokens[i].text)
+
+            data.append((
+                tokens[i].text,
+                text[start_ws: end_ws],
+                (tokens[i].idx, tokens[i].idx + len(tokens[i].text)),
+                tokens[i].tag_,
+                tokens[i].lemma_,
+                tokens[i].ent_type_,
+            ))
+
+        # Set special option for non-entity tag: '' vs 'O' in spaCy
+        return Tokens(data, self.annotators, opts={'non_ent': ''})