We report the preliminary work on cleansing and
classifying a scholarly big dataset containing 10+ million academic
documents released by CiteSeerX. We design novel approaches
to match paper entities in CiteSeerX to reference
datasets, including DBLP, Web of Science, and Medline, resulting
in 4.2M unique matches, whose metadata can be cleansed. We
also investigate traditional machine learning and neural network
methods to classify abstracts into 6 subject categories. The
classification results reveal that the current CiteSeerX dataset is
highly multidisciplinary, containing papers well beyond computer
and information sciences.
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Large Scale Subject Category Classification of Scholarly Papers With Deep Attentive Neural Networks
Subject categories of scholarly papers generally refer to the knowledge domain(s) to which the papers belong, examples being computer science or physics. Subject category classification is a prerequisite for bibliometric studies, organizing scientific publications for domain knowledge extraction, and facilitating faceted searches for digital library search engines. Unfortunately, many academic papers do not have such information as part of their metadata. Most existing methods for solving this task focus on unsupervised learning that often relies on citation networks. However, a complete list of papers citing the current paper may not be readily available. In particular, new papers that have few or no citations cannot be classified using such methods. Here, we propose a deep attentive neural network (DANN) that classifies scholarly papers using only their abstracts. The network is trained using nine million abstracts from Web of Science (WoS). We also use the WoS schema that covers 104 subject categories. The proposed network consists of two bi-directional recurrent neural networks followed by an attention layer. We compare our model against baselines by varying the architecture and text representation. Our best model achieves micro- F 1 measure of 0.76 with F 1 of individual subject categories ranging from 0.50 to 0.95. The results showed the importance of retraining word embedding models to maximize the vocabulary overlap and the effectiveness of the attention mechanism. The combination of word vectors with TFIDF outperforms character and sentence level embedding models. We discuss imbalanced samples and overlapping categories and suggest possible strategies for mitigation. We also determine the subject category distribution in CiteSeerX by classifying a random sample of one million academic papers.
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- Award ID(s):
- 1823288
- NSF-PAR ID:
- 10272152
- Date Published:
- Journal Name:
- Frontiers in Research Metrics and Analytics
- Volume:
- 5
- ISSN:
- 2504-0537
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Table of Contents: Foreword by the CI 2016 Workshop Chairs …………………………………vi Foreword by the CI 2016 Steering Committee ..…………………………..…..viii List of Organizing Committee ………………………….……....x List of Registered Participants .………………………….……..xi Acknowledgement of Sponsors ……………………………..…xiv Hackathon and Workshop Agenda .………………………………..xv Hackathon Summary .………………………….…..xviii Invited talks - abstracts and links to presentations ………………………………..xxi Proceedings: 34 short research papers ……………………………….. 1-135 Papers 1. BAYESIAN MODELS FOR CLIMATE RECONSTRUCTION FROM POLLEN RECORDS ..................................... 1 Lasse Holmström, Liisa Ilvonen, Heikki Seppä, Siim Veski 2. ON INFORMATION CRITERIA FOR DYNAMIC SPATIO-TEMPORAL CLUSTERING ..................................... 5 Ethan D. Schaeffer, Jeremy M. Testa, Yulia R. Gel, Vyacheslav Lyubchich 3. DETECTING MULTIVARIATE BIOSPHERE EXTREMES ..................................... 9 Yanira Guanche García, Erik Rodner, Milan Flach, Sebastian Sippel, Miguel Mahecha, Joachim Denzler 4. SPATIO-TEMPORAL GENERATIVE MODELS FOR RAINFALL OVER INDIA ..................................... 13 Adway Mitra 5. A NONPARAMETRIC COPULA BASED BIAS CORRECTION METHOD FOR STATISTICAL DOWNSCALING ..................................... 17 Yi Li, Adam Ding, Jennifer Dy 6. DETECTING AND PREDICTING BEAUTIFUL SUNSETS USING SOCIAL MEDIA DATA ..................................... 21 Emma Pierson 7. OCEANTEA: EXPLORING OCEAN-DERIVED CLIMATE DATA USING MICROSERVICES ..................................... 25 Arne N. Johanson, Sascha Flögel, Wolf-Christian Dullo, Wilhelm Hasselbring 8. IMPROVED ANALYSIS OF EARTH SYSTEM MODELS AND OBSERVATIONS USING SIMPLE CLIMATE MODELS ..................................... 29 Balu Nadiga, Nathan Urban 9. SYNERGY AND ANALOGY BETWEEN 15 YEARS OF MICROWAVE SST AND ALONG-TRACK SSH ..................................... 33 Pierre Tandeo, Aitor Atencia, Cristina Gonzalez-Haro 10. PREDICTING EXECUTION TIME OF CLIMATE-DRIVEN ECOLOGICAL FORECASTING MODELS ..................................... 37 Scott Farley and John W. Williams 11. SPATIOTEMPORAL ANALYSIS OF SEASONAL PRECIPITATION OVER US USING CO-CLUSTERING ..................................... 41 Mohammad Gorji–Sefidmazgi, Clayton T. Morrison 12. PREDICTION OF EXTREME RAINFALL USING HYBRID CONVOLUTIONAL-LONG SHORT TERM MEMORY NETWORKS ..................................... 45 Sulagna Gope, Sudeshna Sarkar, Pabitra Mitra 13. SPATIOTEMPORAL PATTERN EXTRACTION WITH DATA-DRIVEN KOOPMAN OPERATORS FOR CONVECTIVELY COUPLED EQUATORIAL WAVES ..................................... 49 Joanna Slawinska, Dimitrios Giannakis 14. COVARIANCE STRUCTURE ANALYSIS OF CLIMATE MODEL OUTPUT ..................................... 53 Chintan Dalal, Doug Nychka, Claudia Tebaldi 15. SIMPLE AND EFFICIENT TENSOR REGRESSION FOR SPATIOTEMPORAL FORECASTING ..................................... 57 Rose Yu, Yan Liu 16. TRACKING OF TROPICAL INTRASEASONAL CONVECTIVE ANOMALIES ..................................... 61 Bohar Singh, James L. Kinter 17. ANALYSIS OF AMAZON DROUGHTS USING SUPERVISED KERNEL PRINCIPAL COMPONENT ANALYSIS ..................................... 65 Carlos H. R. Lima, Amir AghaKouchak 18. A BAYESIAN PREDICTIVE ANALYSIS OF DAILY PRECIPITATION DATA ..................................... 69 Sai K. Popuri, Nagaraj K. Neerchal, Amita Mehta 19. INCORPORATING PRIOR KNOWLEDGE IN SPATIO-TEMPORAL NEURAL NETWORK FOR CLIMATIC DATA ..................................... 73 Arthur Pajot, Ali Ziat, Ludovic Denoyer, Patrick Gallinari 20. DIMENSIONALITY-REDUCTION OF CLIMATE DATA USING DEEP AUTOENCODERS ..................................... 77 Juan A. Saenz, Nicholas Lubbers, Nathan M. Urban 21. MAPPING PLANTATION IN INDONESIA ..................................... 81 Xiaowei Jia, Ankush Khandelwal, James Gerber, Kimberly Carlson, Paul West, Vipin Kumar 22. FROM CLIMATE DATA TO A WEIGHTED NETWORK BETWEEN FUNCTIONAL DOMAINS ..................................... 85 Ilias Fountalis, Annalisa Bracco, Bistra Dilkina, Constantine Dovrolis 23. EMPLOYING SOFTWARE ENGINEERING PRINCIPLES TO ENHANCE MANAGEMENT OF CLIMATOLOGICAL DATASETS FOR CORAL REEF ANALYSIS ..................................... 89 Mark Jenne, M.M. Dalkilic, Claudia Johnson 24. Profiler Guided Manual Optimization for Accelerating Cholesky Decomposition on R Environment ..................................... 93 V.B. Ramakrishnaiah, R.P. Kumar, J. Paige, D. Hammerling, D. Nychka 25. GLOBAL MONITORING OF SURFACE WATER EXTENT DYNAMICS USING SATELLITE DATA ..................................... 97 Anuj Karpatne, Ankush Khandelwal and Vipin Kumar 26. TOWARD QUANTIFYING TROPICAL CYCLONE RISK USING DIAGNOSTIC INDICES .................................... 101 Erica M. Staehling and Ryan E. Truchelut 27. OPTIMAL TROPICAL CYCLONE INTENSITY ESTIMATES WITH UNCERTAINTY FROM BEST TRACK DATA .................................... 105 Suz Tolwinski-Ward 28. EXTREME WEATHER PATTERN DETECTION USING DEEP CONVOLUTIONAL NEURAL NETWORK .................................... 109 Yunjie Liu, Evan Racah, Prabhat, Amir Khosrowshahi, David Lavers, Kenneth Kunkel, Michael Wehner, William Collins 29. INFORMATION TRANSFER ACROSS TEMPORAL SCALES IN ATMOSPHERIC DYNAMICS .................................... 113 Nikola Jajcay and Milan Paluš 30. Identifying precipitation regimes in China using model-based clustering of spatial functional data .................................... 117 Haozhe Zhang, Zhengyuan Zhu, Shuiqing Yin 31. RELATIONAL RECURRENT NEURAL NETWORKS FOR SPATIOTEMPORAL INTERPOLATION FROM MULTI-RESOLUTION CLIMATE DATA .................................... 121 Guangyu Li, Yan Liu 32. OBJECTIVE SELECTION OF ENSEMBLE BOUNDARY CONDITIONS FOR CLIMATE DOWNSCALING .................................... 124 Andrew Rhines, Naomi Goldenson 33. LONG-LEAD PREDICTION OF EXTREME PRECIPITATION CLUSTER VIA A SPATIO-TEMPORAL CONVOLUTIONAL NEURAL NETWORK .................................... 128 Yong Zhuang, Wei Ding 34. MULTIPLE INSTANCE LEARNING FOR BURNED AREA MAPPING USING MULTI –TEMPORAL REFLECTANCE DATA .................................... 132 Guruprasad Nayak, Varun Mithal, Vipin Kumarmore » « less
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null (Ed.)The number of published manufacturing science digital articles available from scientifc journals and the broader web have exponentially increased every year since the 1990s. To assimilate all of this knowledge by a novice engineer or an experienced researcher, requires signifcant synthesis of the existing knowledge space contained within published material, to fnd answers to basic and complex queries. Algorithmic approaches through machine learning and specifcally Natural Language Processing (NLP) on a domain specifc area such as manufacturing, is lacking. One of the signifcant challenges to analyzing manufacturing vocabulary is the lack of a named entity recognition model that enables algorithms to classify the manufacturing corpus of words under various manufacturing semantic categories. This work presents a supervised machine learning approach to categorize unstructured text from 500K+manufacturing science related scientifc abstracts and labelling them under various manufacturing topic categories. A neural network model using a bidirectional long-short term memory, plus a conditional random feld (BiLSTM+CRF) is trained to extract information from manufacturing science abstracts. Our classifer achieves an overall accuracy (f1-score) of 88%, which is quite near to the state-of-the-art performance. Two use case examples are presented that demonstrate the value of the developed NER model as a Technical Language Processing (TLP) workfow on manufacturing science documents. The long term goal is to extract valuable knowledge regarding the connections and relationships between key manufacturing concepts/entities available within millions of manufacturing documents into a structured labeled-property graph data structure that allow for programmatic query and retrieval.more » « less
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Abstract Motivation Best performing named entity recognition (NER) methods for biomedical literature are based on hand-crafted features or task-specific rules, which are costly to produce and difficult to generalize to other corpora. End-to-end neural networks achieve state-of-the-art performance without hand-crafted features and task-specific knowledge in non-biomedical NER tasks. However, in the biomedical domain, using the same architecture does not yield competitive performance compared with conventional machine learning models.
Results We propose a novel end-to-end deep learning approach for biomedical NER tasks that leverages the local contexts based on n-gram character and word embeddings via Convolutional Neural Network (CNN). We call this approach GRAM-CNN. To automatically label a word, this method uses the local information around a word. Therefore, the GRAM-CNN method does not require any specific knowledge or feature engineering and can be theoretically applied to a wide range of existing NER problems. The GRAM-CNN approach was evaluated on three well-known biomedical datasets containing different BioNER entities. It obtained an F1-score of 87.26% on the Biocreative II dataset, 87.26% on the NCBI dataset and 72.57% on the JNLPBA dataset. Those results put GRAM-CNN in the lead of the biological NER methods. To the best of our knowledge, we are the first to apply CNN based structures to BioNER problems.
Availability and implementation The GRAM-CNN source code, datasets and pre-trained model are available online at: https://github.com/valdersoul/GRAM-CNN.
Supplementary information Supplementary data are available at Bioinformatics online.
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Abstract Essential for society to function, the production and consumption of food, energy, and water (FEW) are deeply intertwined, leading to calls for a nexus approach to understand and manage the complex tradeoffs and cascading effects. What research exists to date on this FEW nexus? How have scholars conceptualized these interactions at the urban scale? What are some promising approaches? Where are the research gaps? To answer these questions, we conducted a quantitative review of the academic literature on the FEW nexus (1399 publications) over more than four decades (1973–2017), followed by in-depth analysis of the most influential papers using an evaluation matrix that examined four components: 1) modeling approach; 2) scale; 3) nexus ‘trigger’; and 4) governance and policy. Scholars in the fields of environmental science predominated, while social science domains were under-represented. Most papers used quantitative rather than qualitative approaches, especially integrated assessment and systems dynamics modeling although spatial scale was generally recognized, explicit consideration of multi-scalar interactions was limited. Issues of institutional structure, governance, equity, resource access, and behavior were also underdeveloped. Bibliometric analysis of this literature revealed six distinct research communities, including a nascent urban FEW community. We replicated the analysis for this urban group, finding it to be just emerging (80% of papers have been published since 2010) and dominated by scholars in industrial ecology. These scholars focus on quantifying FEW flows of the urban metabolism in isolation rather than as a nexus, largely ignoring the political and socio-economic factors shaping these flows. We propose the urban FEW metabolism as a boundary object to draw in diverse scholarly and practitioner communities. This will advance research on complex FEW systems in four key areas: (1) integration of heterogeneous models and approaches; (2) scalar linkages between urban consumption and trans-boundary resource flows; (3) how actors and institutions shape resource access, distribution and use; and (4) co-production of knowledge with stakeholders.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/frma.2020.600382
