William H. Hsu

Huichen Yang, Carlos A. Aguirre, Maria F. De La Torre et al.

This paper describes a machine learning and data science pipeline for structured information extraction from documents, implemented as a suite of open-source tools and extensions to existing tools. It centers around a methodology for extracting procedural information in the form of recipes, stepwise procedures for creating an artifact (in this case synthesizing a nanomaterial), from published scientific literature. From our overall goal of producing recipes from free text, we derive the technical objectives of a system consisting of pipeline stages: document acquisition and filtering, payload extraction, recipe step extraction as a relationship extraction task, recipe assembly, and presentation through an information retrieval interface with question answering (QA) functionality. This system meets computational information and knowledge management (CIKM) requirements of metadata-driven payload extraction, named entity extraction, and relationship extraction from text. Functional contributions described in this paper include semi-supervised machine learning methods for PDF filtering and payload extraction tasks, followed by structured extraction and data transformation tasks beginning with section extraction, recipe steps as information tuples, and finally assembled recipes. Measurable objective criteria for extraction quality include precision and recall of recipe steps, ordering constraints, and QA accuracy, precision, and recall. Results, key novel contributions, and significant open problems derived from this work center around the attribution of these holistic quality measures to specific machine learning and inference stages of the pipeline, each with their performance measures. The desired recipes contain identified preconditions, material inputs, and operations, and constitute the overall output generated by our computational information and knowledge management (CIKM) system.

Huichen Yang, William H. Hsu

We present an approach for adapting convolutional neural networks for object recognition and classification to scientific literature layout detection (SLLD), a shared subtask of several information extraction problems. Scientific publications contain multiple types of information sought by researchers in various disciplines, organized into an abstract, bibliography, and sections documenting related work, experimental methods, and results; however, there is no effective way to extract this information due to their diverse layout. In this paper, we present a novel approach to developing an end-to-end learning framework to segment and classify major regions of a scientific document. We consider scientific document layout analysis as an object detection task over digital images, without any additional text features that need to be added into the network during the training process. Our technical objective is to implement transfer learning via fine-tuning of pre-trained networks and thereby demonstrate that this deep learning architecture is suitable for tasks that lack very large document corpora for training ab initio. As part of the experimental test bed for empirical evaluation of this approach, we created a merged multi-corpus data set for scientific publication layout detection tasks. Our results show good improvement with fine-tuning of a pre-trained base network using this merged data set, compared to the baseline convolutional neural network architecture.

Jianmei Luo, ChandraVyas Annakula, Aruna Sai Kannamareddy et al.

As the size $n$ of datasets become massive, many commonly-used clustering algorithms (for example, $k$-means or hierarchical agglomerative clustering (HAC) require prohibitive computational cost and memory. In this paper, we propose a solution to these clustering problems by extending threshold clustering (TC) to problems of instance selection. TC is a recently developed clustering algorithm designed to partition data into many small clusters in linearithmic time (on average). Our proposed clustering method is as follows. First, TC is performed and clusters are reduced into single "prototype" points. Then, TC is applied repeatedly on these prototype points until sufficient data reduction has been obtained. Finally, a more sophisticated clustering algorithm is applied to the reduced prototype points, thereby obtaining a clustering on all $n$ data points. This entire procedure for clustering is called iterative hybridized threshold clustering (IHTC). Through simulation results and by applying our methodology on several real datasets, we show that IHTC combined with $k$-means or HAC substantially reduces the run time and memory usage of the original clustering algorithms while still preserving their performance. Additionally, IHTC helps prevent singular data points from being overfit by clustering algorithms.