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高质量的材料科学文本挖掘数据集构建方法

刘悦 刘大晖 葛献远 杨正伟 马舒畅 邹喆乂 施思齐

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高质量的材料科学文本挖掘数据集构建方法

刘悦, 刘大晖, 葛献远, 杨正伟, 马舒畅, 邹喆乂, 施思齐

A high-quality dataset construction method for text mining in materials science

Liu Yue, Liu Da-Hui, Ge Xian-Yuan, Yang Zheng-Wei, Ma Shu-Chang, Zou Zhe-Yi, Shi Si-Qi
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  • 科学文献中蕴含的大量历史数据和经验知识, 对材料设计与研发具有重要参考价值. 文本挖掘尽管能高效地探索并利用被存储在海量科学文献中的信息, 但高质量文本数据的获取困难阻碍了其在材料领域更广泛的应用. 本文从品质和数量双视角剖析了材料领域的文本数据质量问题及其相关研究工作, 提出高质量的材料科学文本挖掘数据集构建方法. 该方法通过可溯源的文献自动获取方案确保文本数据的源头可追溯; 以下游任务为驱动对文献进行预处理以提升预标注文本语料的质量; 基于材料四面体准则定义适配全体系的标签注释方案以完成对语料的高品质标注; 利用融合材料领域知识的有条件文本数据增强模型实现材料文本数据量的扩充. 在不同体系数据集上的实验结果表明, 该方法可有效地提升下游文本挖掘模型的预测精度, 其中在NASICON型固态电解质材料实体识别任务上的F1值达84%. 本文为文本挖掘在材料领域的深入应用提供理论指导和解决方案, 并有望推进数据与知识双向驱动的材料设计与研发.
    Numerous data and knowledge generated and stored as text in peer-reviewed scientific literature are important for materials research and development. Although text mining can automatically explore this information, the barriers of acquiring high-quality textual data prevent its general application in materials science. Herein, we systematically analyze the issues of textual DATA QUALITY and related research from the perspectives of data quality and quantity. Following this, we propose a pipeline to construct high-quality datasets for text mining in materials science. In this pipeline, we utilize the traceable automatic acquisition scheme of literature to ensure the traceability of textual data. Then, a data processing method driven by downstream tasks is used to generate high-quality pre-annotated corpora conditioned on the characteristics of material texts. On this basis, we define a general annotation scheme derived from materials science tetrahedron to complete high-quality annotation. Finally, a conditional data augmentation model incorporating material domain knowledge (cDA-DK) is constructed to augment the data quantity. Experimental results on datasets with various material systems demonstrate that our method can effectively improve the accuracy of downstream models and the F1-score towards the named entity recognition task in NASICON-type solid electrolyte material reaches 84%. This study provides an important insight into the general application of text mining in materials science, and is expected to advance the material design and discovery driven by data and knowledge bidirectionally.
      通信作者: 施思齐, sqshi@shu.edu.cn
    • 基金项目: 国家重点研发计划(批准号: 2021YFB3802101)和国家自然科学基金(批准号: 92270124, 52073169, 52102313)资助的课题.
      Corresponding author: Shi Si-Qi, sqshi@shu.edu.cn
    • Funds: Project supported by the National Key Research and Development Program of China (Grant No. 2021YFB3802101), and the National Natural Science Foundation of China (Grant Nos. 92270124, 52073169, 52102313).
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  • 图 1  高质量材料文本挖掘数据集构建管道

    Fig. 1.  The pipeline for constructing high-quality datasets for materials text mining.

    图 2  文献的数据与过程溯源示意图

    Fig. 2.  The illustration of the traceability of literature data and process.

    图 3  实体关系标注流程示意图

    Fig. 3.  The process of annotation on entities and relations.

    图 4  基于cDA-DK的材料文本数据增强

    Fig. 4.  Materials textual data augmentation based on cDA-DK.

    图 5  两份数据集的样本统计情况对比 (a) 三元组个数分布情况; (b) 语句长度分布情况

    Fig. 5.  Comparison of sample statistics of two datasets: (a) The distribution of numbers of triplets; (b) the distribution of length of sentence.

    图 6  实体识别模型在不同数据集上的混淆矩阵 (a) Dataset 1的混淆矩阵; (b) Dataset 2的混淆矩阵

    Fig. 6.  Confusion matrix of NER model on various datasets: (a) The confusion matrix of Dataset 1; (b) the confusion matrix of Dataset 2.

    图 7  MatBERT-BiLSTM-CRF在不同数据集上的训练及验证Loss变化曲线 (a) Dataset 1上的Loss变化曲线; (b) Dataset 2上的Loss变化曲线; (c) Dataset 4上的Loss变化曲线; (d) Dataset 5上的Loss变化曲线

    Fig. 7.  The training and validation loss function of MatBERT-BiLSTM-CRF on various datasets: (a) The loss function on Dataset 1; (b) the loss function on Dataset 2; (c) the loss function on Dataset 4; (d) the loss function on Dataset 5.

    图 8  对激活能预测起关键影响的部分描述符, 其中虚线表示尚未被研究的潜在描述符[33]

    Fig. 8.  Partial descriptor entities that are critical for predicting activation energy, of which dotted lines indicate potential ones still to be developed[33].

    表 1  材料科学文本语料获取方式对比

    Table 1.  Comparison of acquisition methods of materials scientific corpus.

    获取方式数据库文档类型访问权限文档数量参考
    索引数据库 APICAplus论文, 专利, 报告订阅www.cas.org/support/documentation/references
    DOAJ论文部分订阅doaj.org
    PubMed Central论文开放获取较少www.ncbi.nlm.nih.gov/pmc
    Science Direct论文订阅dev.elsevier.com/api_docs.html
    Scopus摘要开放获取较少
    Springer Nature论文, 书籍订阅dev.springernature.com/
    网络爬虫网页论文, 专利, 报告, 书籍开放获取requests.readthedocs.io, crummy.com/software/BeautifulSoup
    下载: 导出CSV

    表 2  化学与材料科学中常用的自然语言处理工具

    Table 2.  Common natural language processing tools in chemistry and materials science.

    名称适用范围是否开源版本迭代功能完备性难易性友好性
    OSCAR4[25]化学反应和生物化学普通
    ChemicalTagger[26]化学合成作用和条件普通
    ChemDataExtractor[27]通用化学和材料科学领域容易
    下载: 导出CSV

    表 3  已有材料文本挖掘研究中的实体标签定义对比

    Table 3.  Comparison of entity label definitions in previous materials text mining research.

    来源目标标签数标签类别适用领域应用实例
    Weston等[11]构建材料领域最新研究结果
    与历史文献的关联
    7无机材料, 相结构, 描述符, 属
    性, 应用, 合成方法, 表征方法
    无机材料目标材料检索, 文献搜索
    与总结, 元信息分析
    He等[13]从无机固相合成反应文献
    中挖掘反应前体信息
    3材料, 合成反应前体,
    目标化合物
    无机固相
    合成反应
    固相合成反应前体
    数据挖掘, 元信息分析
    Friedrich等[12]标注科学出版物中与SOFCs
    实验相关的信息
    4(SOFC) 17(SOFC-slot)实验, 材料, 数值, 应用等电池材料构建SOFCs科学语料库并用
    于多个实验信息提取任务
    Wang等[10]从文献中自动挖掘出数据驱动的材
    料设计模型所需的高质量可靠数据
    6元素, 合金命名实体, 成分含
    量, 属性描述符, 属性值, 其他
    合金材料钴基单晶高温合金${ {\rm{\gamma } } }'$
    相固溶温度预测
    Nie等[9]构建语义表示框架以探索潜在
    的锂离子电池阴极材料
    3无机材料, 锂离子电池
    阴极材料, 属性描述符
    电池材料新型锂离子电池阴
    极材料设计与寻优
    下载: 导出CSV

    表 4  面向通用领域的材料实体类型定义

    Table 4.  The definition of materials entity types in the general domain.

    实体标签定义示例
    Composition与化学式有关的内容; 描述材料内部与含量相关的内容等. NaCl, CaCl2; Na concentration, Electrons charge carriers.
    Structure晶体结构; 相; 用于刻画晶体结构的名称等. Fcc, Phase; Bottleneck, Channel, Path.
    Property带单位的可度量值; 材料表现出来定性的性质或现象;
    描述材料产生物理/化学行为或物理/化学机制的名词等.
    Conductivity, Activation, Radius; Ferroelectric, Metallic; Phase transition, Ionic reaction.
    Processing材料合成技术或加工工艺; 材料改性手段等. Solid state reaction, Annealing; Doping.
    Characterization用于表征材料的任何实验、理论、模型或公式等. XRD, STM, Photoluminescence, DFT;
    Bethe-Salpeter equation.
    Application任何高级的应用; 任何特定的器件、系统等. Cathode, Photovoltaics; Battery Management System.
    Feature样品类型、形状的特殊描述. Single crystal, Bulk, nanotube, Quantum dot.
    Condition描述材料所处的环境或外部条件. 980 $°{\rm{C}}$, 1000 MPa.
    下载: 导出CSV

    表 5  面向通用领域的材料实体关系类型定义

    Table 5.  The definition of materials relation types in the general domain.

    关系标签 (A to B)定义可能存在此关系的实体类型
    Cause-EffectA对B有影响Property-Property, Composition-Structure, Structure-Property, ...
    Component-WholeA是B的部分Composition-Composition, ...
    Feature-OfA是B的特征Feature-Composition, Feature-Application, ...
    Located-OfA占据了B位置Composition-Structure, ...
    Instance-OfA是B的实例Composition-Composition, Structure-Structure, Property-Property, ...
    Condition-OnA的条件是BProcessing-Condition, ...
    Method-OfA的表征方法是BProperty-Characterization, ...
    OtherA与B存在除上述关系类型外的其他关系
    下载: 导出CSV

    表 6  常用文本标注工具对比

    Table 6.  Comparison of common tools for text annotation.

    标注工具适配任务文本要求角色管理权限难易性友好性可扩展性参考
    Label Studio多模态信息标注严格不完善普通labelstud.io
    Brat关系标注一般完善普通github.com/nlplab/brat
    Doccano文本分类严格较完善普通github.com/doccano
    EasyData实体与关系标注一般完善容易ai.baidu.com/easydata/
    下载: 导出CSV
    算法1 数据增强方法cDA-DK
    输入 原始数据集$ {D}_{{\rm{t}}{\rm{r}}{\rm{a}}{\rm{i}}{\rm{n}}} = \{\left({x}_{1}, {y}_{1}\right), \left({x}_{2}, {y}_{2}\right), \dots , \left({x}_{n}, {y}_{n}\right)\} $    预训练语言模型模型$ {P}_{{\rm{D}}{\rm{i}}{\rm{s}}{\rm{t}}{\rm{i}}{\rm{l}}{\rm{R}}{\rm{o}}{\rm{B}}{\rm{E}}{\rm{R}}{\rm{T}}{\rm{a}}} $
       材料领域词典$ C=\{{w}_{1}, {w}_{2}, \dots , {w}_{m}\} $输出 增强数据集$ {D}_{{\rm{s}}{\rm{y}}{\rm{n}}{\rm{t}}{\rm{h}}{\rm{e}}{\rm{t}}{\rm{i}}{\rm{c}}} $
    1: 开始
    2: for $ {w}_{i}\in C $ do3:   $ {w}_{i} $输入至$ {P}_{{\rm{D}}{\rm{i}}{\rm{s}}{\rm{t}}{\rm{i}}{\rm{l}}{\rm{R}}{\rm{o}}{\rm{B}}{\rm{E}}{\rm{R}}{\rm{T}}{\rm{a}}} $的词汇表并训练其对应的词向量
    4: 在下游任务文本数据增强上微调$ {P}_{{\rm{D}}{\rm{i}}{\rm{s}}{\rm{t}}{\rm{i}}{\rm{l}}{\rm{R}}{\rm{o}}{\rm{B}}{\rm{E}}{\rm{R}}{\rm{T}}{\rm{a}}} $得到$ {F}_{{\rm{D}}{\rm{i}}{\rm{s}}{\rm{t}}{\rm{i}}{\rm{l}}{\rm{R}}{\rm{o}}{\rm{B}}{\rm{E}}{\rm{R}}{\rm{T}}{\rm{a}}} $
    5: 初始化$ {D}_{{\rm{s}}{\rm{y}}{\rm{n}}{\rm{t}}{\rm{h}}{\rm{e}}{\rm{t}}{\rm{i}}{\rm{c}}}=\left\{\right\} $
    6: for $ \left\{{x}_{i}, {y}_{i}\right\}\in {D}_{{\rm{t}}{\rm{r}}{\rm{a}}{\rm{i}}{\rm{n}}} $ do
    7:  $ ({\widehat{x}}_{i}, {\widehat{y}}_{i})={F}_{{\rm{D}}{\rm{i}}{\rm{s}}{\rm{t}}{\rm{i}}{\rm{l}}{\rm{R}}{\rm{o}}{\rm{B}}{\rm{E}}{\rm{R}}{\rm{T}}{\rm{a}}}({x}_{i}, {y}_{i}) $ // 生成新的样本
    8:  $ {D}_{{\rm{s}}{\rm{y}}{\rm{n}}{\rm{t}}{\rm{h}}{\rm{e}}{\rm{t}}{\rm{i}}{\rm{c}}}={D}_{{\rm{s}}{\rm{y}}{\rm{n}}{\rm{t}}{\rm{h}}{\rm{e}}{\rm{t}}{\rm{i}}{\rm{c}}}\cup ({\widehat{x}}_{i}, {\widehat{y}}_{i}) $ // 生成样本加入增强数据集
    9: 结束
    下载: 导出CSV

    表 7  NASICON实体关系数据集与CoNLL-2004数据集的对比

    Table 7.  Comparison of the NASICON dataset with the CoNLL-2004 dataset.

    数据集样本数实体类型实体数关系类型关系数
    CoNLL-20041, 44145, 34752, 020
    NASICON2, 43484, 85782, 297
    下载: 导出CSV

    表 8  NASICON实体关系数据集在增强前后的数据示例对比

    Table 8.  Comparison of samples before and after augmentation of NASICON dataset.

    数据集样本数实体数关系数示例
    原始数据集243448572297The (O) ionic (B-Property) conductivity (I-Property) decreases (O) with (O) increasing (O) activation (B-Property) energy (I-Property) . (O)
    cDA-DK 增强数据集484697144594The (O) electrode (B-Property) conductivity (I-Property) decreases (O) with (O) increasing (O) electric (B-Property) energy (I-Property) . (O)
    下载: 导出CSV

    表 9  实验数据集信息

    Table 9.  The details of experimental datasets.

    数据集名称应用领域重命名样本量语料规模来源
    NASICON 实体识别数据集NASICON 型固态电解质Dataset 12, 43455篇文献领域专家标注
    Dataset 22, 434数据增强
    Dataset 330535篇文献非专业人员标注
    Matscholar[11]无机材料Dataset 45, 459800份摘要领域专家标注
    Dataset 55, 459数据增强
    下载: 导出CSV

    表 10  实体识别模型在不同材料数据集上的实验结果

    Table 10.  The results of NER model on various materials datasets.

    数据集材料类别样本量PrecisionRecallF1-score
    Dataset 1NASICON 型固态电解质2, 4340.780.830.80
    Dataset 22, 4340.680.720.70
    Dataset 2+32, 7390.830.850.84
    Dataset 4无机材料5, 4590.860.900.88
    Dataset 55, 4590.750.780.77
    下载: 导出CSV
  • [1]

    Gupta T, Zaki M, Krishnan N M A, Mausam 2022 npj Comput. Mater. 8 102Google Scholar

    [2]

    Olivetti E A, Cole J M, Kim E, Kononova O, Ceder G, Han T Y J, Hiszpanski A M 2020 Appl. Phys. Rev. 7 041317Google Scholar

    [3]

    Venugopal V, Sahoo S, Zaki M, Agarwal M, Gosvami N N, Krishnan N M A 2021 Patterns 2 100290Google Scholar

    [4]

    Kononova O, He T, Huo H, Trewartha A, Olivetti E A, Ceder G 2021 iScience 24 102155Google Scholar

    [5]

    Kim E, Huang K, Saunders A, McCallum A, Ceder G, Olivetti E 2017 Chem. Mater. 29 9436Google Scholar

    [6]

    Mysore S, Jensen Z, Kim E, Huang K, Chang H S, Strubell E, Flanigan J, McCallum A, Olivetti E 2019 Proceedings of the 13th Linguistic Annotation Workshop Florence, Italy, August 1, 2019 p56

    [7]

    Tshitoyan V, Dagdelen J, Weston L, Dunn A, Rong Z, Kononova O, Persson K A, Ceder G, Jain A 2019 Nature 571 95Google Scholar

    [8]

    Vaucher A C, Zipoli F, Geluykens J, Nair V H, Schwaller P, Laino T 2020 Nat. Commun. 11 3601Google Scholar

    [9]

    Nie Z, Zheng S, Liu Y, Chen Z, Li S, Lei K, Pan F 2022 Adv. Funct. Mater. 32 2201437Google Scholar

    [10]

    Wang W R, Jiang X, Tian S H, Liu P, Dang D P, Su Y J, Lookman T, Xie J X 2022 npj Comput. Mater. 8 9Google Scholar

    [11]

    Weston L, Tshitoyan V, Dagdelen J, Kononova O, Trewartha A, Persson K A, Ceder G, Jain A 2019 J. Chem. Inf. Model. 59 3692Google Scholar

    [12]

    Friedrich A, Adel H, Tomazic F, Hingerl J, Benteau R, Maruscyk A, Lange L 2020 Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics Seattle, Washington, July 5–10, 2020 p1255

    [13]

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出版历程
  • 收稿日期:  2022-12-05
  • 修回日期:  2023-02-07
  • 上网日期:  2023-02-09
  • 刊出日期:  2023-04-05

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