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Zheng Yuan

Publications and source records attributed to Zheng Yuan.

155 records · Page 9Linked to original sources
arXiv2021

MetaHistoSeg: A Python Framework for Meta Learning in Histopathology Image Segmentation

Few-shot learning is a standard practice in most deep learning based histopathology image segmentation, given the relatively low number of digitized slides that are generally available. While many models have been developed for domain specific histopathology image segmentation, cross-domain generalization remains a key challenge for properly validating models. Here, tooling and datasets to benchmark model performance across histopathological domains are lacking. To address this limitation, we introduce MetaHistoSeg - a Python framework that implements unique scenarios in both meta learning and instance based transfer learning. Designed for easy extension to customized datasets and task sampling schemes, the framework empowers researchers with the ability of rapid model design and experimentation. We also curate a histopathology meta dataset - a benchmark dataset for training and validating models on out-of-distribution performance across a range of cancer types. In experiments we showcase the usage of MetaHistoSeg with the meta dataset and find that both meta-learning and instance based transfer learning deliver comparable results on average, but in some cases tasks can greatly benefit from one over the other.

eess.IV↗
arXiv2021

Biomedical Question Answering: A Survey of Approaches and Challenges

Automatic Question Answering (QA) has been successfully applied in various domains such as search engines and chatbots. Biomedical QA (BQA), as an emerging QA task, enables innovative applications to effectively perceive, access and understand complex biomedical knowledge. There have been tremendous developments of BQA in the past two decades, which we classify into 5 distinctive approaches: classic, information retrieval, machine reading comprehension, knowledge base and question entailment approaches. In this survey, we introduce available datasets and representative methods of each BQA approach in detail. Despite the developments, BQA systems are still immature and rarely used in real-life settings. We identify and characterize several key challenges in BQA that might lead to this issue, and discuss some potential future directions to explore.

cs.CL↗
arXiv2021

Meta Gradient Adversarial Attack

In recent years, research on adversarial attacks has become a hot spot. Although current literature on the transfer-based adversarial attack has achieved promising results for improving the transferability to unseen black-box models, it still leaves a long way to go. Inspired by the idea of meta-learning, this paper proposes a novel architecture called Meta Gradient Adversarial Attack (MGAA), which is plug-and-play and can be integrated with any existing gradient-based attack method for improving the cross-model transferability. Specifically, we randomly sample multiple models from a model zoo to compose different tasks and iteratively simulate a white-box attack and a black-box attack in each task. By narrowing the gap between the gradient directions in white-box and black-box attacks, the transferability of adversarial examples on the black-box setting can be improved. Extensive experiments on the CIFAR10 and ImageNet datasets show that our architecture outperforms the state-of-the-art methods for both black-box and white-box attack settings.

cs.CV↗
arXiv2021

CODER: Knowledge infused cross-lingual medical term embedding for term normalization

This paper proposes CODER: contrastive learning on knowledge graphs for cross-lingual medical term representation. CODER is designed for medical term normalization by providing close vector representations for different terms that represent the same or similar medical concepts with cross-lingual support. We train CODER via contrastive learning on a medical knowledge graph (KG) named the Unified Medical Language System, where similarities are calculated utilizing both terms and relation triplets from KG. Training with relations injects medical knowledge into embeddings and aims to provide potentially better machine learning features. We evaluate CODER in zero-shot term normalization, semantic similarity, and relation classification benchmarks, which show that CODERoutperforms various state-of-the-art biomedical word embedding, concept embeddings, and contextual embeddings. Our codes and models are available at https://github.com/GanjinZero/CODER.

cs.CL↗
arXiv2021

Density-Aware Federated Imitation Learning for Connected and Automated Vehicles with Unsignalized Intersection

Intelligent Transportation System (ITS) has become one of the essential components in Industry 4.0. As one of the critical indicators of ITS, efficiency has attracted wide attention from researchers. However, the next generation of urban traffic carried by multiple transport service providers may prohibit the raw data interaction among multiple regions for privacy reasons, easily ignored in the existing research. This paper puts forward a federated learning-based vehicle control framework to solve the above problem, including interactors, trainers, and an aggregator. In addition, the density-aware model aggregation method is utilized in this framework to improve vehicle control. What is more, to promote the performance of the end-to-end learning algorithm in the safety aspect, this paper proposes an imitation learning algorithm, which can obtain collision avoidance capabilities from a set of collision avoidance rules. Furthermore, a loss-aware experience selection strategy is also explored, reducing the communication overhead between the interactors and the trainers via extra computing. Finally, the experiment results demonstrate that the proposed imitation learning algorithm obtains the ability to avoid collisions and reduces discomfort by 55.71%. Besides, density-aware model aggregation can further reduce discomfort by 41.37%, and the experience selection scheme can reduce the communication overhead by 12.80% while ensuring model convergence.

cs.MA↗
arXiv2021

Improving Biomedical Pretrained Language Models with Knowledge

Pretrained language models have shown success in many natural language processing tasks. Many works explore incorporating knowledge into language models. In the biomedical domain, experts have taken decades of effort on building large-scale knowledge bases. For example, the Unified Medical Language System (UMLS) contains millions of entities with their synonyms and defines hundreds of relations among entities. Leveraging this knowledge can benefit a variety of downstream tasks such as named entity recognition and relation extraction. To this end, we propose KeBioLM, a biomedical pretrained language model that explicitly leverages knowledge from the UMLS knowledge bases. Specifically, we extract entities from PubMed abstracts and link them to UMLS. We then train a knowledge-aware language model that firstly applies a text-only encoding layer to learn entity representation and applies a text-entity fusion encoding to aggregate entity representation. Besides, we add two training objectives as entity detection and entity linking. Experiments on the named entity recognition and relation extraction from the BLURB benchmark demonstrate the effectiveness of our approach. Further analysis on a collected probing dataset shows that our model has better ability to model medical knowledge.

cs.CL↗
arXiv2020

Attributes Aware Face Generation with Generative Adversarial Networks

Recent studies have shown remarkable success in face image generations. However, most of the existing methods only generate face images from random noise, and cannot generate face images according to the specific attributes. In this paper, we focus on the problem of face synthesis from attributes, which aims at generating faces with specific characteristics corresponding to the given attributes. To this end, we propose a novel attributes aware face image generator method with generative adversarial networks called AFGAN. Specifically, we firstly propose a two-path embedding layer and self-attention mechanism to convert binary attribute vector to rich attribute features. Then three stacked generators generate $64 \times 64$, $128 \times 128$ and $256 \times 256$ resolution face images respectively by taking the attribute features as input. In addition, an image-attribute matching loss is proposed to enhance the correlation between the generated images and input attributes. Extensive experiments on CelebA demonstrate the superiority of our AFGAN in terms of both qualitative and quantitative evaluations.

cs.CV↗
arXiv2018

Construction of the Literature Graph in Semantic Scholar

We describe a deployed scalable system for organizing published scientific literature into a heterogeneous graph to facilitate algorithmic manipulation and discovery. The resulting literature graph consists of more than 280M nodes, representing papers, authors, entities and various interactions between them (e.g., authorships, citations, entity mentions). We reduce literature graph construction into familiar NLP tasks (e.g., entity extraction and linking), point out research challenges due to differences from standard formulations of these tasks, and report empirical results for each task. The methods described in this paper are used to enable semantic features in www.semanticscholar.org

cs.CL↗
arXiv2017

Artificial Error Generation with Machine Translation and Syntactic Patterns

Shortage of available training data is holding back progress in the area of automated error detection. This paper investigates two alternative methods for artificially generating writing errors, in order to create additional resources. We propose treating error generation as a machine translation task, where grammatically correct text is translated to contain errors. In addition, we explore a system for extracting textual patterns from an annotated corpus, which can then be used to insert errors into grammatically correct sentences. Our experiments show that the inclusion of artificially generated errors significantly improves error detection accuracy on both FCE and CoNLL 2014 datasets.

cs.CL↗
arXiv2017

Parallel Implementation of Lossy Data Compression for Temporal Data Sets

Many scientific data sets contain temporal dimensions. These are the data storing information at the same spatial location but different time stamps. Some of the biggest temporal datasets are produced by parallel computing applications such as simulations of climate change and fluid dynamics. Temporal datasets can be very large and cost a huge amount of time to transfer among storage locations. Using data compression techniques, files can be transferred faster and save storage space. NUMARCK is a lossy data compression algorithm for temporal data sets that can learn emerging distributions of element-wise change ratios along the temporal dimension and encodes them into an index table to be concisely represented. This paper presents a parallel implementation of NUMARCK. Evaluated with six data sets obtained from climate and astrophysics simulations, parallel NUMARCK achieved scalable speedups of up to 8788 when running 12800 MPI processes on a parallel computer. We also compare the compression ratios against two lossy data compression algorithms, ISABELA and ZFP. The results show that NUMARCK achieved higher compression ratio than ISABELA and ZFP.

cs.DC↗