Upgrade to new FARM / Transformers / PyTorch versions (#212)

haystack/reader/farm.py

@@ -6,8 +6,10 @@ import numpy as np
 from farm.data_handler.data_silo import DataSilo
 from farm.data_handler.processor import SquadProcessor
 from farm.data_handler.dataloader import NamedDataLoader
-from farm.infer import Inferencer
+from farm.data_handler.inputs import QAInput, Question
+from farm.infer import QAInferencer
 from farm.modeling.optimization import initialize_optimizer
+from farm.modeling.predictions import QAPred, QACandidate
 from farm.train import Trainer
 from farm.eval import Evaluator
 from farm.utils import set_all_seeds, initialize_device_settings
@@ -85,7 +87,7 @@ class FARMReader(BaseReader):
         else:
             self.return_no_answers = True
         self.top_k_per_candidate = top_k_per_candidate
-        self.inferencer = Inferencer.load(model_name_or_path, batch_size=batch_size, gpu=use_gpu,
+        self.inferencer = QAInferencer.load(model_name_or_path, batch_size=batch_size, gpu=use_gpu,
                                           task_type="question_answering", max_seq_len=max_seq_len,
                                           doc_stride=doc_stride, num_processes=num_processes)
         self.inferencer.model.prediction_heads[0].context_window_size = context_window_size
@@ -231,18 +233,16 @@ class FARMReader(BaseReader):
         """
 
         # convert input to FARM format
-        input_dicts = []
+        inputs = []
         for doc in documents:
-            cur = {
-                "text": doc.text,
-                "questions": [question],
-                "document_id": doc.id
-            }
-            input_dicts.append(cur)
+            cur = QAInput(doc_text=doc.text,
+                          questions=Question(text=question,
+                                             uid=doc.id))
+            inputs.append(cur)
 
         # get answers from QA model
-        predictions = self.inferencer.inference_from_dicts(
-            dicts=input_dicts, return_json=True, multiprocessing_chunksize=1
+        predictions = self.inferencer.inference_from_objects(
+            objects=inputs, return_json=False, multiprocessing_chunksize=1
         )
         # assemble answers from all the different documents & format them.
         # For the "no answer" option, we collect all no_ans_gaps and decide how likely
@@ -250,29 +250,28 @@ class FARMReader(BaseReader):
         answers = []
         no_ans_gaps = []
         best_score_answer = 0
-        # TODO once FARM returns doc ids again we can revert to using them inside the preds and remove
-        for pred, inp in zip(predictions, input_dicts):
+        for pred, inp in zip(predictions, inputs):
             answers_per_document = []
-            no_ans_gaps.append(pred["predictions"][0]["no_ans_gap"])
-            for ans in pred["predictions"][0]["answers"]:
+            no_ans_gaps.append(pred.no_answer_gap)
+            for ans in pred.prediction:
                 # skip "no answers" here
                 if self._check_no_answer(ans):
                     pass
                 else:
-                    cur = {"answer": ans["answer"],
-                           "score": ans["score"],
+                    cur = {"answer": ans.answer,
+                           "score": ans.score,
                            # just a pseudo prob for now
-                           "probability": float(expit(np.asarray([ans["score"]]) / 8)),  # type: ignore
-                           "context": ans["context"],
-                           "offset_start": ans["offset_answer_start"] - ans["offset_context_start"],
-                           "offset_end": ans["offset_answer_end"] - ans["offset_context_start"],
-                           "offset_start_in_doc": ans["offset_answer_start"],
-                           "offset_end_in_doc": ans["offset_answer_end"],
-                           "document_id": inp["document_id"]} #TODO revert to ans["docid"] once it is populated
+                           "probability": float(expit(np.asarray([ans.score]) / 8)),  # type: ignore
+                           "context": ans.context_window,
+                           "offset_start": ans.offset_answer_start - ans.offset_context_window_start,
+                           "offset_end": ans.offset_answer_end - ans.offset_context_window_start,
+                           "offset_start_in_doc": ans.offset_answer_start,
+                           "offset_end_in_doc": ans.offset_answer_end,
+                           "document_id": pred.id}
                     answers_per_document.append(cur)
 
-                    if ans["score"] > best_score_answer:
-                        best_score_answer = ans["score"]
+                    if ans.score > best_score_answer:
+                        best_score_answer = ans.score
             # only take n best candidates. Answers coming back from FARM are sorted with decreasing relevance.
             answers += answers_per_document[:self.top_k_per_candidate]
 
@@ -299,7 +298,7 @@ class FARMReader(BaseReader):
         Returns a dict containing the following metrics:
             - "EM": exact match score
             - "f1": F1-Score
-            - "top_n_recall": Proportion of predicted answers that overlap with correct answer
+            - "top_n_accuracy": Proportion of predicted answers that match with correct answer
 
         :param data_dir: The directory in which the test set can be found
         :type data_dir: Path or str
@@ -329,7 +328,7 @@ class FARMReader(BaseReader):
         results = {
             "EM": eval_results[0]["EM"],
             "f1": eval_results[0]["f1"],
-            "top_n_recall": eval_results[0]["top_n_recall"]
+            "top_n_accuracy": eval_results[0]["top_n_accuracy"]
         }
         return results
 
@@ -347,7 +346,7 @@ class FARMReader(BaseReader):
         Returns a dict containing the following metrics:
             - "EM": Proportion of exact matches of predicted answers with their corresponding correct answers
             - "f1": Average overlap between predicted answers and their corresponding correct answers
-            - "top_n_recall": Proportion of predicted answers that overlap with correct answer
+            - "top_n_accuracy": Proportion of predicted answers that match with correct answer
 
         :param document_store: The ElasticsearchDocumentStore containing the evaluation documents
         :type document_store: ElasticsearchDocumentStore
@@ -404,23 +403,23 @@ class FARMReader(BaseReader):
         results = {
             "EM": eval_results[0]["EM"],
             "f1": eval_results[0]["f1"],
-            "top_n_recall": eval_results[0]["top_n_recall"]
+            "top_n_accuracy": eval_results[0]["top_n_accuracy"]
         }
         return results
 
 
     @staticmethod
-    def _check_no_answer(d: dict):
+    def _check_no_answer(c: QACandidate):
         # check for correct value in "answer"
-        if d["offset_answer_start"] == 0 and d["offset_answer_end"] == 0:
-            assert d["answer"] == "is_impossible", f"Check for no answer is not working"
-
-        # check weather the model thinks there is no answer
-        if d["answer"] == "is_impossible":
+        if c.offset_answer_start == 0 and c.offset_answer_end == 0:
+            if c.answer != "no_answer":
+                logger.error("Invalid 'no_answer': Got a prediction for position 0, but answer string is not 'no_answer'")
+        if c.answer == "no_answer":
             return True
         else:
             return False
 
+
     @staticmethod
     def _calc_no_answer(no_ans_gaps: List[float], best_score_answer: float):
         # "no answer" scores and positive answers scores are difficult to compare, because
@@ -476,5 +475,5 @@ class FARMReader(BaseReader):
                              are "gpu_tensor_core" (GPUs with tensor core like V100 or T4),
                              "gpu_without_tensor_core" (most other GPUs), and "cpu".
         """
-        inferencer = Inferencer.load(model_name_or_path, task_type="question_answering")
+        inferencer = QAInferencer.load(model_name_or_path, task_type="question_answering")
         inferencer.model.convert_to_onnx(output_path=Path("onnx-export"), opset_version=opset_version, optimize_for=optimize_for)

haystack/reader/transformers.py

@@ -1,6 +1,6 @@
 from typing import List, Optional
 
-from transformers import pipeline
+from haystack.reader.transformers_utils import pipeline
 
 from haystack.database.base import Document
 from haystack.reader.base import BaseReader
@@ -40,10 +40,11 @@ class TransformersReader(BaseReader):
         :param use_gpu: < 0  -> use cpu
                         >= 0 -> ordinal of the gpu to use
         """
-        self.model = pipeline("question-answering", model=model, tokenizer=tokenizer, device=use_gpu)
+        self.model = pipeline('question-answering', model=model, tokenizer=tokenizer, device=use_gpu)
         self.context_window_size = context_window_size
         self.n_best_per_passage = n_best_per_passage
         #TODO param to modify bias for no_answer
+        # TODO context_window_size behaviour different from behavior in FARMReader
 
     def predict(self, question: str, documents: List[Document], top_k: Optional[int] = None):
         """
@@ -76,6 +77,9 @@ class TransformersReader(BaseReader):
         for doc in documents:
             query = {"context": doc.text, "question": question}
             predictions = self.model(query, topk=self.n_best_per_passage)
+            # for single preds (e.g. via top_k=1) transformers returns a dict instead of a list
+            if type(predictions) == dict:
+                predictions = [predictions]
             # assemble and format all answers
             for pred in predictions:
                 if pred["answer"]:

requirements.txt

@@ -1,4 +1,4 @@
-farm==0.4.5
+farm==0.4.6
 --find-links=https://download.pytorch.org/whl/torch_stable.html
 fastapi
 uvicorn

test/conftest.py

@@ -1,3 +1,4 @@
+
 import tarfile
 import time
 import urllib.request
@@ -10,6 +11,7 @@ from elasticsearch import Elasticsearch
 from haystack.reader.farm import FARMReader
 from haystack.reader.transformers import TransformersReader
 
+from haystack.database.base import Document
 from haystack.database.sql import SQLDocumentStore
 from haystack.database.memory import InMemoryDocumentStore
 from haystack.database.elasticsearch import ElasticsearchDocumentStore
@@ -72,6 +74,39 @@ def reader(request):
                                   use_gpu=-1)
 
 
+# TODO Fix bug in test_no_answer_output when using
+# @pytest.fixture(params=["farm", "transformers"])
+@pytest.fixture(params=["farm"])
+def no_answer_reader(request):
+    if request.param == "farm":
+        return FARMReader(model_name_or_path="deepset/roberta-base-squad2",
+                          use_gpu=False, top_k_per_sample=5, no_ans_boost=0, num_processes=0)
+    if request.param == "transformers":
+        return TransformersReader(model="deepset/roberta-base-squad2",
+                                  tokenizer="deepset/roberta-base-squad2",
+                                  use_gpu=-1, n_best_per_passage=5)
+
+
+@pytest.fixture()
+def prediction(reader, test_docs_xs):
+    docs = []
+    for d in test_docs_xs:
+        doc = Document(id=d["meta"]["name"], text=d["text"], meta=d["meta"])
+        docs.append(doc)
+    prediction = reader.predict(question="Who lives in Berlin?", documents=docs, top_k=5)
+    return prediction
+
+
+@pytest.fixture()
+def no_answer_prediction(no_answer_reader, test_docs_xs):
+    docs = []
+    for d in test_docs_xs:
+        doc = Document(id=d["meta"]["name"], text=d["text"], meta=d["meta"])
+        docs.append(doc)
+    prediction = no_answer_reader.predict(question="What is the meaning of life?", documents=docs, top_k=5)
+    return prediction
+
+
 @pytest.fixture(params=["sql", "memory", "elasticsearch"])
 def document_store_with_docs(request, test_docs_xs, elasticsearch_fixture):
     if request.param == "sql":

test/test_finder.py

@@ -28,17 +28,17 @@ def test_finder_offsets(reader, document_store_with_docs):
                                     top_k_reader=5)
 
     assert prediction["answers"][0]["offset_start"] == 11
-    #TODO enable again when FARM is upgraded incl. the new offset calc
-#    assert prediction["answers"][0]["offset_end"] == 16
+    assert prediction["answers"][0]["offset_end"] == 16
     start = prediction["answers"][0]["offset_start"]
     end = prediction["answers"][0]["offset_end"]
-    #assert prediction["answers"][0]["context"][start:end] == prediction["answers"][0]["answer"]
+    assert prediction["answers"][0]["context"][start:end] == prediction["answers"][0]["answer"]
 
 
 def test_finder_get_answers_single_result(reader, document_store_with_docs):
     retriever = TfidfRetriever(document_store=document_store_with_docs)
     finder = Finder(reader, retriever)
-    prediction = finder.get_answers(question="testing finder", top_k_retriever=1,
+    query = "testing finder"
+    prediction = finder.get_answers(question=query, top_k_retriever=1,
                                     top_k_reader=1)
     assert prediction is not None
     assert len(prediction["answers"]) == 1

test/test_reader.py

@@ -1,7 +1,10 @@
-import pytest
+import math
 
-from haystack.reader.base import BaseReader
 from haystack.database.base import Document
+from haystack.reader.base import BaseReader
+from haystack.reader.farm import FARMReader
+from haystack.reader.transformers import TransformersReader
+
 
 
 def test_reader_basic(reader):
@@ -9,20 +12,89 @@ def test_reader_basic(reader):
     assert isinstance(reader, BaseReader)
 
 
-def test_output(reader, test_docs_xs):
+def test_output(prediction):
+    assert prediction is not None
+    assert prediction["question"] == "Who lives in Berlin?"
+    assert prediction["answers"][0]["answer"] == "Carla"
+    assert prediction["answers"][0]["offset_start"] == 11
+    assert prediction["answers"][0]["offset_end"] == 16
+    assert prediction["answers"][0]["probability"] <= 1
+    assert prediction["answers"][0]["probability"] >= 0
+    assert prediction["answers"][0]["context"] == "My name is Carla and I live in Berlin"
+    assert prediction["answers"][0]["document_id"] == "filename1"
+    assert len(prediction["answers"]) == 5
+
+
+def test_no_answer_output(no_answer_prediction):
+    assert no_answer_prediction is not None
+    assert no_answer_prediction["question"] == "What is the meaning of life?"
+    assert math.isclose(no_answer_prediction["no_ans_gap"], -14.4729533, rel_tol=0.0001)
+    assert no_answer_prediction["answers"][0]["answer"] is None
+    assert no_answer_prediction["answers"][0]["offset_start"] == 0
+    assert no_answer_prediction["answers"][0]["offset_end"] == 0
+    assert no_answer_prediction["answers"][0]["probability"] <= 1
+    assert no_answer_prediction["answers"][0]["probability"] >= 0
+    assert no_answer_prediction["answers"][0]["context"] == None
+    assert no_answer_prediction["answers"][0]["document_id"] == None
+    answers = [x["answer"] for x in no_answer_prediction["answers"]]
+    assert answers.count(None) == 1
+    assert len(no_answer_prediction["answers"]) == 5
+
+# TODO Directly compare farm and transformers reader outputs
+# TODO checks to see that model is responsive to input arguments e.g. context_window_size - topk
+
+def test_prediction_attributes(prediction):
+    # TODO FARM's prediction also has no_ans_gap
+    attributes_gold = ["question", "answers"]
+    for ag in attributes_gold:
+        assert ag in prediction
+
+
+def test_answer_attributes(prediction):
+    # TODO Transformers answer also has meta key
+    # TODO FARM answer has offset_start_in_doc, offset_end_in_doc
+    answer = prediction["answers"][0]
+    attributes_gold = ['answer', 'score', 'probability', 'context', 'offset_start', 'offset_end', 'document_id']
+    for ag in attributes_gold:
+        assert ag in answer
+
+
+def test_context_window_size(test_docs_xs):
+    # TODO parametrize window_size and farm/transformers reader using pytest
     docs = []
     for d in test_docs_xs:
         doc = Document(id=d["meta"]["name"], text=d["text"], meta=d["meta"])
         docs.append(doc)
-    results = reader.predict(question="Who lives in Berlin?", documents=docs, top_k=5)
-    assert results is not None
-    assert results["question"] == "Who lives in Berlin?"
-    assert results["answers"][0]["answer"] == "Carla"
-    assert results["answers"][0]["offset_start"] == 11
-    #TODO enable again when FARM is upgraded incl. the new offset calc
-    # assert results["answers"][0]["offset_end"] == 16
-    assert results["answers"][0]["probability"] <= 1
-    assert results["answers"][0]["probability"] >= 0
-    assert results["answers"][0]["context"] == "My name is Carla and I live in Berlin"
-    assert results["answers"][0]["document_id"] == "filename1"
-    assert len(results["answers"]) == 5
+    for window_size in [10, 15, 20]:
+        farm_reader = FARMReader(model_name_or_path="distilbert-base-uncased-distilled-squad",
+                              use_gpu=False, top_k_per_sample=5, no_ans_boost=None, context_window_size=window_size)
+        prediction = farm_reader.predict(question="Who lives in Berlin?", documents=docs, top_k=5)
+        for answer in prediction["answers"]:
+            # If the extracted answer is larger than the context window, the context window is expanded.
+            # If the extracted answer is odd in length, the resulting context window is one less than context_window_size
+            # due to rounding (See FARM's QACandidate)
+            # TODO Currently the behaviour of context_window_size in FARMReader and TransformerReader is different
+            if len(answer["answer"]) <= window_size:
+                assert len(answer["context"]) in [window_size, window_size-1]
+            else:
+                assert len(answer["answer"]) == len(answer["context"])
+
+        # TODO Need to test transformers reader
+        # TODO Currently the behaviour of context_window_size in FARMReader and TransformerReader is different
+
+
+def test_top_k(test_docs_xs):
+    # TODO parametrize top_k and farm/transformers reader using pytest
+    # TODO transformers reader was crashing when tested on this
+    docs = []
+    for d in test_docs_xs:
+        doc = Document(id=d["meta"]["name"], text=d["text"], meta=d["meta"])
+        docs.append(doc)
+    farm_reader = FARMReader(model_name_or_path="distilbert-base-uncased-distilled-squad",
+                             use_gpu=False, top_k_per_sample=4, no_ans_boost=None, top_k_per_candidate=4)
+    for top_k in [2, 5, 10]:
+        prediction = farm_reader.predict(question="Who lives in Berlin?", documents=docs, top_k=top_k)
+        assert len(prediction["answers"]) == top_k
+
+
+

tutorials/Tutorial5_Evaluation.py

@@ -76,8 +76,8 @@ if eval_reader_only:
     # Evaluation of Reader can also be done directly on a SQuAD-formatted file without passing the data to Elasticsearch
     #reader_eval_results = reader.eval_on_file("../data/natural_questions", "dev_subset.json", device=device)
 
-    ## Reader Top-N-Recall is the proportion of predicted answers that overlap with their corresponding correct answer
-    print("Reader Top-N-Recall:", reader_eval_results["top_n_recall"])
+    ## Reader Top-N-Accuracy is the proportion of predicted answers that match with their corresponding correct answer
+    print("Reader Top-N-Accuracy:", reader_eval_results["top_n_accuracy"])
     ## Reader Exact Match is the proportion of questions where the predicted answer is exactly the same as the correct answer
     print("Reader Exact Match:", reader_eval_results["EM"])
     ## Reader F1-Score is the average overlap between the predicted answers and the correct answers