Recent progress in natural language processing has been driven by advances in both model architecture and model pretraining. Transformer architectures have facilitated building higher-capacity models and pretraining has made it possible to effectively utilize this capacity for a wide variety of tasks. Transformers is an open-source library with the goal of opening up these advances to the wider machine learning community. The library consists of carefully engineered state-of-the art Transformer architectures under a unified API. Backing this library is a curated collection of pretrained models made by and available for the community. Transformers is designed to be extensible by researchers, simple for practitioners, and fast and robust in industrial deployments. The library is available at https://github.com/huggingface/transformers.

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Transformers: State-of-the-Art Natural Language Processing

Recent progress in natural language processing has been driven by advances in both model architecture and model pretraining. Transformer architectures have facilitated building higher-capacity models and pretraining has made it possible to effectively utilize this capacity for a wide variety of tasks. \textit{Transformers} is an open-source library with the goal of opening up these advances to the wider machine learning community. The library consists of carefully engineered state-of-the art Transformer architectures under a unified API. Backing this library is a curated collection of pretrained models made by and available for the community. \textit{Transformers} is designed to be extensible by researchers, simple for practitioners, and fast and robust in industrial deployments. The library is available at \url{this https URL}.

HuggingFace's Transformers: State-of-the-art Natural Language Processing.

Motivation Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. Results We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. Availability and implementation We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.

BioBERT: a pre-trained biomedical language representation model for biomedical text mining.

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures (like the dependency trees of sentences and the scene graphs of images) is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are neural models that capture the dependence of graphs via message passing between the nodes of graphs. In recent years, variants of GNNs such as graph convolutional network (GCN), graph attention network (GAT), graph recurrent network (GRN) have demonstrated ground-breaking performances on many deep learning tasks. In this survey, we propose a general design pipeline for GNN models and discuss the variants of each component, systematically categorize the applications, and propose four open problems for future research.

Graph Neural Networks: A Review of Methods and Applications

Contrastive models like CLIP have been shown to learn robust representations of images that capture both semantics and style. To leverage these representations for image generation, we propose a two-stage model: a prior that generates a CLIP image embedding given a text caption, and a decoder that generates an image conditioned on the image embedding. We show that explicitly generating image representations improves image diversity with minimal loss in photorealism and caption similarity. Our decoders conditioned on image representations can also produce variations of an image that preserve both its semantics and style, while varying the non-essential details absent from the image representation. Moreover, the joint embedding space of CLIP enables language-guided image manipulations in a zero-shot fashion. We use diffusion models for the decoder and experiment with both autoregressive and diffusion models for the prior, finding that the latter are computationally more efficient and produce higher-quality samples.

Hierarchical Text-Conditional Image Generation with CLIP Latents

We introduce Stanza, an open-source Python natural language processing toolkit supporting 66 human languages Compared to existing widely used toolkits, Stanza features a language-agnostic fully neural pipeline for text analysis, including tokenization, multi-word token expansion, lemmatization, part-of-speech and morphological feature tagging, dependency parsing, and named entity recognition We have trained Stanza on a total of 112 datasets, including the Universal Dependencies treebanks and other multilingual corpora, and show that the same neural architecture generalizes well and achieves competitive performance on all languages tested Additionally, Stanza includes a native Python interface to the widely used Java Stanford CoreNLP software, which further extends its functionality to cover other tasks such as coreference resolution and relation extraction Source code, documentation, and pretrained models for 66 languages are available at https://stanfordnlpgithubio/stanza/

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Stanza: A Python Natural Language Processing Toolkit for Many Human Languages

Dependency trees help relation extraction models capture long-range relations between words. However, existing dependency-based models either neglect crucial information (e.g., negation) by pruning the dependency trees too aggressively, or are computationally inefficient because it is difficult to parallelize over different tree structures. We propose an extension of graph convolutional networks that is tailored for relation extraction, which pools information over arbitrary dependency structures efficiently in parallel. To incorporate relevant information while maximally removing irrelevant content, we further apply a novel pruning strategy to the input trees by keeping words immediately around the shortest path between the two entities among which a relation might hold. The resulting model achieves state-of-the-art performance on the large-scale TACRED dataset, outperforming existing sequence and dependency-based neural models. We also show through detailed analysis that this model has complementary strengths to sequence models, and combining them further improves the state of the art.

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Graph Convolution over Pruned Dependency Trees Improves Relation Extraction.

Organized relational knowledge in the form of “knowledge graphs” is important for many applications. However, the ability to populate knowledge bases with facts automatically extracted from documents has improved frustratingly slowly. This paper simultaneously addresses two issues that have held back prior work. We first propose an effective new model, which combines an LSTM sequence model with a form of entity position-aware attention that is better suited to relation extraction. Then we build TACRED, a large (119,474 examples) supervised relation extraction dataset obtained via crowdsourcing and targeted towards TAC KBP relations. The combination of better supervised data and a more appropriate high-capacity model enables much better relation extraction performance. When the model trained on this new dataset replaces the previous relation extraction component of the best TAC KBP 2015 slot filling system, its F1 score increases markedly from 22.2% to 26.7%.

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Position-aware Attention and Supervised Data Improve Slot Filling

Learning visual representations of medical images is core to medical image understanding but its progress has been held back by the small size of hand-labeled datasets. Existing work commonly relies on transferring weights from ImageNet pretraining, which is suboptimal due to drastically different image characteristics, or rule-based label extraction from the textual report data paired with medical images, which is inaccurate and hard to generalize. We propose an alternative unsupervised strategy to learn medical visual representations directly from the naturally occurring pairing of images and textual data. Our method of pretraining medical image encoders with the paired text data via a bidirectional contrastive objective between the two modalities is domain-agnostic, and requires no additional expert input. We test our method by transferring our pretrained weights to 4 medical image classification tasks and 2 zero-shot retrieval tasks, and show that our method leads to image representations that considerably outperform strong baselines in most settings. Notably, in all 4 classification tasks, our method requires only 10% as much labeled training data as an ImageNet initialized counterpart to achieve better or comparable performance, demonstrating superior data efficiency.

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Contrastive Learning of Medical Visual Representations from Paired Images and Text

This paper describes Stanford’s system at the CoNLL 2018 UD Shared Task. We introduce a complete neural pipeline system that takes raw text as input, and performs all tasks required by the shared task, ranging from tokenization and sentence segmentation, to POS tagging and dependency parsing. Our single system submission achieved very competitive performance on big treebanks. Moreover, after fixing an unfortunate bug, our corrected system would have placed the 2nd, 1st, and 3rd on the official evaluation metrics LAS, MLAS, and BLEX, and would have outperformed all submission systems on low-resource treebank categories on all metrics by a large margin. We further show the effectiveness of different model components through extensive ablation studies.

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Yuhao Zhang

Papers

Stanza: A Python Natural Language Processing Toolkit for Many Human Languages

Graph Convolution over Pruned Dependency Trees Improves Relation Extraction.

Position-aware Attention and Supervised Data Improve Slot Filling

Contrastive Learning of Medical Visual Representations from Paired Images and Text

Universal Dependency Parsing from Scratch