A Survey on Visual Approaches for Analyzing Scientific Literature and Patents

Exploring similarity patterns in a large scientific corpus

Similarity-based analysis is a common and intuitive tool for exploring large data sets. For instance, grouping data items by their level of similarity, regarding one or several chosen aspects, can reveal patterns and relations from the intrinsic structure of the data and thus provide important insights in the sense-making process. Existing analytical methods (such as clustering and dimensionality reduction) tend to target questions such as "Which objects are similar?"; but since they are not necessarily well-suited to answer questions such as "How does the result change if we change the similarity criteria?" or "How are the items linked together by the similarity relations?" they do not unlock the full potential of similarity-based analysis-and here we see a gap to fill. In this paper, we propose that the concept of similarity could be regarded as both: (1) a relation between items, and (2) a property in its own, with a specific distribution over the data set. Based on this approach, we developed an embedding-based computational pipeline together with a prototype visual analytics tool which allows the user to perform similarity-based exploration of a large set of scientific publications. To demonstrate the potential of our method, we present two different use cases, and we also discuss the strengths and limitations of our approach.

PUREsuggest: Citation-Based Literature Search and Visual Exploration with Keyword-Controlled Rankings

Citations allow quickly identifying related research. If multiple publications are selected as seeds, specific suggestions for related literature can be made based on the number of incoming and outgoing citation links to this selection. Interactively adding recommended publications to the selection refines the next suggestion and incrementally builds a relevant collection of publications. Following this approach, the paper presents a search and foraging approach, PUREsuggest, which combines citation-based suggestions with augmented visualizations of the citation network. The focus and novelty of the approach is, first, the transparency of how the rankings are explained visually and, second, that the process can be steered through user-defined keywords, which reflect topics of interests. The system can be used to build new literature collections, to update and assess existing ones, as well as to use the collected literature for identifying relevant experts in the field. We evaluated the recommendation approach through simulated sessions and performed a user study investigating search strategies and usage patterns supported by the interface.

Development of Predictive Statistical Model for Gaining Valuable Insights in Pharmaceutical Product Recalls

The rapid progress in artificial intelligence (AI) has revolutionized problem-solving across various domains. The global challenge of pharmaceutical product recalls imposes the development of effective tools to control and reduce shortage of pharmaceutical products and help avoid such recalls. This study employs AI, specifically machine learning (MI), to analyze critical factors influencing formulation, manufacturing, and formulation complexity which could offer promising avenue for optimizing drug development processes. Utilizing FDAZilla and SafeRX tools, an open database model was constructed, and predictive statistical models were developed using Multivariate Analysis and the Least Absolute Shrinkage and Selection Operator (LASSO) Approach. The study focuses on key descriptors such as delivery route, dosage form, dose, BCS classification, solid-state and physicochemical properties, release type, half-life, and manufacturing complexity. Through statistical analysis, a data simplification process identifies critical descriptors, assigning risk numbers and computing a cumulative risk number to assess product complexity and recall likelihood. Partial Least Square Regression and the LASSO approach established quantitative relationships between key descriptors and cumulative risk numbers. Results have identified key descriptors; BCS Class I, dose number, release profile, and drug half-life influencing product recall risk. The LASSO model further confirms these identified descriptors with 71% accuracy. In conclusion, the study presents a holistic AI and machine learning approach for evaluating and forecasting pharmaceutical product recalls, underscoring the importance of descriptors, formulation complexity, and manufacturing processes in mitigating risks associated with product quality.

VIStory: interactive storyboard for exploring visual information in scientific publications

Abstract

Many visual analytics have been developed for examining scientific publications comprising wealthy data such as authors and citations. The studies provide unprecedented insights on a variety of applications, e.g., literature review and collaboration analysis. However, visual information (e.g., figures) that is widely employed for storytelling and methods description are often neglected. We present VIStory, an interactive storyboard for exploring visual information in scientific publications. We harvest a new dataset of a large corpora of figures, using an automatic figure extraction method. Each figure contains various attributes such as dominant color and width/height ratio, together with faceted metadata of the publication including venues, authors, and keywords. To depict these information, we develop an intuitive interface consisting of three components: (1) Faceted View enables efficient query by publication metadata, benefiting from a nested table structure, (2) Storyboard View arranges paper rings—a well-designed glyph for depicting figure attributes, in a themeriver layout to reveal temporal trends, and (3) Endgame View presents a highlighted figure together with the publication metadata. We illustrate the applicability of VIStory with case studies on two datasets, i.e., 10-year IEEE VIS publications, and publications by a research team at CVPR, ICCV, and ECCV conferences. Quantitative and qualitative results from a formal user study demonstrate the efficiency of VIStory in exploring visual information in scientific publications.

Graphical abstract

Electronic supplementary material

The online version of this article (10.1007/s12650-020-00688-1) contains supplementary material, which is available to authorized users.

Scholar Plot: Design and Evaluation of an Information Interface for Faculty Research Performance

The ability to objectively assess academic performance is critical to rewarding academic merit, charting academic policy, and promoting science. Quintessential to performing these functions is first the ability to collect valid and current data through increasingly automated online interfaces. Moreover, it is crucial to remove disciplinary and other biases from these data, presenting them in ways that support insightful analysis at various levels. Existing systems are lacking in some of these respects. Here we present Scholar Plot (SP), an interface that harvests bibliographic and research funding data from online sources. SP addresses systematic biases in the collected data through nominal and normalized metrics. Eventually, SP combines synergistically these metrics in a plot form for expert appraisal, and an iconic form for broader consumption. SP's plot and iconic forms are scalable, representing equally well individual scholars and their academic units, thus contributing to consistent ranking practices across the university organizational structure. In order to appreciate the design principles underlying SP, in particular the informativeness of nominal vs. normalized metrics, we also present the results of an evaluation survey taken by senior faculty (n = 28) with significant promotion and tenure assessment experience.

Galex: Exploring the Evolution and Intersection of Disciplines

Revealing the evolution of science and the intersections among its sub-fields is extremely important to understand the characteristics of disciplines, discover new topics, and predict the future. The current work focuses on either building the skeleton of science, lacking interaction, detailed exploration and interpretation or on the lower topic level, missing high-level macro-perspective. To fill this gap, we design and implement Galaxy Evolution Explorer (Galex), a hierarchical visual analysis system, in combination with advanced text mining technologies, that could help analysts to comprehend the evolution and intersection of one discipline rapidly. We divide Galex into three progressively fine-grained levels: discipline, area, and institution levels. The combination of interactions enables analysts to explore an arbitrary piece of history and an arbitrary part of the knowledge space of one discipline. Using a flexible spotlight component, analysts could freely select and quickly understand an exploration region. A tree metaphor allows analysts to perceive the expansion, decline, and intersection of topics intuitively. A synchronous spotlight interaction aids in comparing research contents among institutions easily. Three cases demonstrate the effectiveness of our system.

Bridging Text Visualization and Mining: A Task-Driven Survey

Visual text analytics has recently emerged as one of the most prominent topics in both academic research and the commercial world. To provide an overview of the relevant techniques and analysis tasks, as well as the relationships between them, we comprehensively analyzed 263 visualization papers and 4,346 mining papers published between 1992-2017 in two fields: visualization and text mining. From the analysis, we derived around 300 concepts (visualization techniques, mining techniques, and analysis tasks) and built a taxonomy for each type of concept. The co-occurrence relationships between the concepts were also extracted. Our research can be used as a stepping-stone for other researchers to 1) understand a common set of concepts used in this research topic; 2) facilitate the exploration of the relationships between visualization techniques, mining techniques, and analysis tasks; 3) understand the current practice in developing visual text analytics tools; 4) seek potential research opportunities by narrowing the gulf between visualization and mining techniques based on the analysis tasks; and 5) analyze other interdisciplinary research areas in a similar way. We have also contributed a web-based visualization tool for analyzing and understanding research trends and opportunities in visual text analytics.

Visualization of Cultural Heritage Collection Data: State of the Art and Future Challenges

After decades of digitization, large cultural heritage collections have emerged on the web, which contain massive stocks of content from galleries, libraries, archives, and museums. This increase in digital cultural heritage data promises new modes of analysis and increased levels of access for academic scholars and casual users alike. Going beyond the standard representations of search-centric and grid-based interfaces, a multitude of approaches has recently started to enable visual access to cultural collections, and to explore them as complex and comprehensive information spaces by the means of interactive visualizations. In contrast to conventional web interfaces, we witness a widening spectrum of innovative visualization types specially designed for rich collections from the cultural heritage sector. This new class of information visualizations gives rise to a notable diversity of interaction and representation techniques while lending currency and urgency to a discussion about principles such as serendipity, generosity, and criticality in connection with visualization design. With this survey, we review information visualization approaches to digital cultural heritage collections and reflect on the state of the art in techniques and design choices. We contextualize our survey with humanist perspectives on the field and point out opportunities for future research.

SoS TextVis: An Extended Survey of Surveys on Text Visualization

Text visualization is a rapidly growing sub-field of information visualization and visual analytics. There are many approaches and techniques introduced every year to address a wide range of challenges and analysis tasks, enabling researchers from different disciplines to obtain leading-edge knowledge from digitized collections of text. This can be challenging particularly when the data is massive. Additionally, the sources of digital text have spread substantially in the last decades in various forms, such as web pages, blogs, twitter, email, electronic publications, and digitized books. In response to the explosion of text visualization research literature, the first text visualization survey article was published in 2010. Furthermore, there are a growing number of surveys that review existing techniques and classify them based on text research methodology. In this work, we aim to present the first Survey of Surveys (SoS) that review all of the surveys and state-of-the-art papers on text visualization techniques and provide an SoS classification. We study and compare the 14 surveys, and categorize them into five groups: (1) Document-centered, (2) user task analysis, (3) cross-disciplinary, (4) multi-faceted, and (5) satellite-themed. We provide survey recommendations for researchers in the field of text visualization. The result is a very unique, valuable starting point and overview of the current state-of-the-art in text visualization research literature.

ResumeVis

Massive public resume data emerging on the internet indicates individual-related characteristics in terms of profile and career experiences. Resume Analysis (RA) provides opportunities for many applications, such as recruitment trend predict, talent seeking and evaluation. Existing RA studies either largely rely on the knowledge of domain experts, or leverage classic statistical or data mining models to identify and filter explicit attributes based on pre-defined rules. However, they fail to discover the latent semantic information from semi-structured resume text, i.e., individual career progress trajectory and social-relations, which are otherwise vital to comprehensive understanding of people’s career evolving patterns. Besides, when dealing with large numbers of resumes, how to properly visualize such semantic information to reduce the information load and to support better human cognition is also challenging.

To tackle these issues, we propose a visual analytics system called ResumeVis to mine and visualize resume data. First, a text mining-based approach is presented to extract semantic information. Then, a set of visualizations are devised to represent the semantic information in multiple perspectives. Through interactive exploration on ResumeVis performed by domain experts, the following tasks can be accomplished: to trace individual career evolving trajectory; to mine latent social-relations among individuals; and to hold the full picture of massive resumes’ collective mobility. Case studies with over 2,500 government officer resumes demonstrate the effectiveness of our system.

VIS Author Profiles: Interactive Descriptions of Publication Records Combining Text and Visualization

Publication records and collaboration networks are important for assessing the expertise and experience of researchers. Existing digital libraries show the raw publication lists in author profiles, whereas visualization techniques focus on specific subproblems. Instead, we look at publication records from various perspectives mixing low-level publication data with high-level abstractions and background information. This work presents VIS Author Profiles, a novel approach to generate integrated textual and visual descriptions to highlight patterns in publication records. We leverage template-based natural language generation to summarize notable publication statistics, evolution of research topics, and collaboration relationships. Seamlessly integrated visualizations augment the textual description and are interactively connected with each other and the text. The underlying publication data and detailed explanations of the analysis are available on demand. We compare our approach to existing systems by taking into account information needs of users and demonstrate its usefulness in two realistic application examples.

Patent landscape of neglected tropical diseases: an analysis of worldwide patent families

BACKGROUND

"Neglected Tropical Diseases" (NTDs) affect millions of people in Africa, Asia and South America. The two primary ways of strategic interventions are "preventive chemotherapy and transmission control" (PCT), and "innovative and intensified disease management" (IDM). In the last 5 years, phenomenal progress has been achieved. However, it is crucial to intensify research effort into NTDs, because of the emerging drug resistance. According to the World Health Organization (WHO), the term NTDs covers 17 diseases, namely buruli ulcer, Chagas disease, dengue, dracunculiasis, echinococcosis, trematodiasis, human African trypanosomiasis, leishmaniasis, leprosy, lymphatic filariasis, onchocerciasis, rabies, schistosomiasis, soil-transmitted helminthes, taeniasis, trachoma, and yaws. The aim of this study is to map out research and development (R&D) landscape through patent analysis of these identified NTDs. To achieve this, analysis and evaluation have been conducted on patenting trends, current legal status of patent families, priority countries by earliest priority years and their assignee types, technological fields of patent families over time, and original and current patent assignees.

MAIN BODY

Patent families were extracted from Patseer, an international database of patents from over 100 patent issuing authorities worldwide. Evaluation of the patents was carried out using the combination of different search terms related to each identified NTD. In this paper, a total number of 12,350 patent families were analyzed. The main countries with sources of inventions were identified to be the United States (US) and China. The main technological fields covered by NTDs patent landscape are pharmaceuticals, biotechnology, organic fine chemistry, analysis of biological materials, basic materials chemistry, and medical technology. Governmental institutions and universities are the primary original assignees. Among the NTDs, leishmaniasis, dengue, and rabies received the highest number of patent families, while human African trypanosomiasis (sleeping sickness), taeniasis, and dracunciliasis received the least. The overall trend of patent families shows an increase between 1985 and 2008, and followed by at least 6 years of stagnation.

CONCLUSION

The filing pattern of patent families analyzed undoubtedly reveals slow progress on research and development of NTDs. Involving new players, such as non-governmental organizations may help to mitigate and reduce the burden of NTDs.