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1. Author-Driven Computable Data and Ontology Production for Taxonomists

   https://doi.org/10.3897/biss.5.75741  

   Cui, Hong ; Ford, Bruce ; Starr, Julian ; Macklin, James ; Reznicek, Anton ; Giebink, Noah ; Longert, Dylan ; Léveillé-Bourret, Étienne ; Zhang, Limin ( September 2021 , Biodiversity Information Science and Standards)

   It takes great effort to manually or semi-automatically convert free-text phenotype narratives (e.g., morphological descriptions in taxonomic works) to a computable format before they can be used in large-scale analyses. We argue that neither a manual curation approach nor an information extraction approach based on machine learning is a sustainable solution to produce computable phenotypic data that are FAIR (Findable, Accessible, Interoperable, Reusable) (Wilkinson et al. 2016). This is because these approaches do not scale to all biodiversity, and they do not stop the publication of free-text phenotypes that would need post-publication curation. In addition, both manual and machine learning approaches face great challenges: the problem of inter-curator variation (curators interpret/convert a phenotype differently from each other) in manual curation, and keywords to ontology concept translation in automated information extraction, make it difficult for either approach to produce data that are truly FAIR. Our empirical studies show that inter-curator variation in translating phenotype characters to Entity-Quality statements (Mabee et al. 2007) is as high as 40% even within a single project. With this level of variation, curated data integrated from multiple curation projects may still not be FAIR. The key causes of this variation have been identified as semantic vaguenessmore »in original phenotype descriptions and difficulties in using standardized vocabularies (ontologies). We argue that the authors describing characters are the key to the solution. Given the right tools and appropriate attribution, the authors should be in charge of developing a project's semantics and ontology. This will speed up ontology development and improve the semantic clarity of the descriptions from the moment of publication. In this presentation, we will introduce the Platform for Author-Driven Computable Data and Ontology Production for Taxonomists, which consists of three components: a web-based, ontology-aware software application called 'Character Recorder,' which features a spreadsheet as the data entry platform and provides authors with the flexibility of using their preferred terminology in recording characters for a set of specimens (this application also facilitates semantic clarity and consistency across species descriptions); a set of services that produce RDF graph data, collects terms added by authors, detects potential conflicts between terms, dispatches conflicts to the third component and updates the ontology with resolutions; and an Android mobile application, 'Conflict Resolver,' which displays ontological conflicts and accepts solutions proposed by multiple experts. a web-based, ontology-aware software application called 'Character Recorder,' which features a spreadsheet as the data entry platform and provides authors with the flexibility of using their preferred terminology in recording characters for a set of specimens (this application also facilitates semantic clarity and consistency across species descriptions); a set of services that produce RDF graph data, collects terms added by authors, detects potential conflicts between terms, dispatches conflicts to the third component and updates the ontology with resolutions; and an Android mobile application, 'Conflict Resolver,' which displays ontological conflicts and accepts solutions proposed by multiple experts. Fig. 1 shows the system diagram of the platform. The presentation will consist of: a report on the findings from a recent survey of 90+ participants on the need for a tool like Character Recorder; a methods section that describes how we provide semantics to an existing vocabulary of quantitative characters through a set of properties that explain where and how a measurement (e.g., length of perigynium beak) is taken. We also report on how a custom color palette of RGB values obtained from real specimens or high-quality specimen images, can be used to help authors choose standardized color descriptions for plant specimens; and a software demonstration, where we show how Character Recorder and Conflict Resolver can work together to construct both human-readable descriptions and RDF graphs using morphological data derived from species in the plant genus Carex (sedges). The key difference of this system from other ontology-aware systems is that authors can directly add needed terms to the ontology as they wish and can update their data according to ontology updates. a report on the findings from a recent survey of 90+ participants on the need for a tool like Character Recorder; a methods section that describes how we provide semantics to an existing vocabulary of quantitative characters through a set of properties that explain where and how a measurement (e.g., length of perigynium beak) is taken. We also report on how a custom color palette of RGB values obtained from real specimens or high-quality specimen images, can be used to help authors choose standardized color descriptions for plant specimens; and a software demonstration, where we show how Character Recorder and Conflict Resolver can work together to construct both human-readable descriptions and RDF graphs using morphological data derived from species in the plant genus Carex (sedges). The key difference of this system from other ontology-aware systems is that authors can directly add needed terms to the ontology as they wish and can update their data according to ontology updates. The software modules currently incorporated in Character Recorder and Conflict Resolver have undergone formal usability studies. We are actively recruiting Carex experts to participate in a 3-day usability study of the entire system of the Platform for Author-Driven Computable Data and Ontology Production for Taxonomists. Participants will use the platform to record 100 characters about one Carex species. In addition to usability data, we will collect the terms that participants submit to the underlying ontology and the data related to conflict resolution. Such data allow us to examine the types and the quantities of logical conflicts that may result from the terms added by the users and to use Discrete Event Simulation models to understand if and how term additions and conflict resolutions converge. We look forward to a discussion on how the tools (Character Recorder is online at http://shark.sbs.arizona.edu/chrecorder/public) described in our presentation can contribute to producing and publishing FAIR data in taxonomic studies.« less
2. Trace2TAP: Synthesizing Trigger-Action Programs From Traces of Behavior

   https://doi.org/10.1145/3411838  

   Zhang, Lefan ; He, Weijia ; Morkved, Olivia ; Zhao, Valerie ; Littman, Michael L. ; Lu, Shan ; Ur, Blase ( September 2020 , Proceedings of the ACM on interactive mobile wearable and ubiquitous technologies)

   Two common approaches for automating IoT smart spaces are having users write rules using trigger-action programming (TAP) or training machine learning models based on observed actions. In this paper, we unite these approaches. We introduce and evaluate Trace2TAP, a novel method for automatically synthesizing TAP rules from traces (time-stamped logs of sensor readings and manual actuations of devices). We present a novel algorithm that uses symbolic reasoning and SAT-solving to synthesize TAP rules from traces. Compared to prior approaches, our algorithm synthesizes generalizable rules more comprehensively and fully handles nuances like out-of-order events. Trace2TAP also iteratively proposes modified TAP rules when users manually revert automations. We implemented our approach on Samsung SmartThings. Through formative deployments in ten offices, we developed a clustering/ranking system and visualization interface to intelligibly present the synthesized rules to users. We evaluated Trace2TAP through a field study in seven additional offices. Participants frequently selected rules ranked highly by our clustering/ranking system. Participants varied in their automation priorities, and they sometimes chose rules that would seem less desirable by traditional metrics like precision and recall. Trace2TAP supports these differing priorities by comprehensively synthesizing TAP rules and bringing humans into the loop during automation.
3. OpenFraming: Open-sourced Tool for Computational Framing Analysis of Multilingual Data

   https://doi.org/10.18653/v1/2021.emnlp-demo.28  

   Bhatia, Vibhu ; Akavoor, Vidya Prasad ; Paik, Sejin ; Guo, Lei ; Jalal, Mona ; Smith, Alyssa ; Tofu, David Assefa ; Halim, Edward Edberg ; Sun, Yimeng ; Betke, Margrit ; et al ( January 2021 , Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing: System Demonstrations, Online and Punta Cana, Dominican Republic)

   When journalists cover a news story, they can cover the story from multiple angles or perspectives. These perspectives are called “frames,” and usage of one frame or another may influence public perception and opinion of the issue at hand. We develop a web-based system for analyzing frames in multilingual text documents. We propose and guide users through a five-step end-to-end computational framing analysis framework grounded in media framing theory in communication research. Users can use the framework to analyze multilingual text data, starting from the exploration of frames in user’s corpora and through review of previous framing literature (step 1-3) to frame classification (step 4) and prediction (step 5). The framework combines unsupervised and supervised machine learning and leverages a state-of-the-art (SoTA) multilingual language model, which can significantly enhance frame prediction performance while requiring a considerably small sample of manual annotations. Through the interactive website, anyone can perform the proposed computational framing analysis, making advanced computational analysis available to researchers without a programming background and bridging the digital divide within the communication research discipline in particular and the academic community in general. The system is available online at http://www.openframing.org, via an API http://www.openframing.org:5000/docs/, or through our GitHub page https://github.com/vibss2397/openFraming.
4. Set Cover in Sub-linear Time

   Indyk, Piotr ; Mahabadi, Sepideh ; Rubinfeld, Ronitt ; Vakilian, Ali ; Yodpinyanee, Anak ( January 2018 , Annual ACM-SIAM Symposium on Discrete Algorithms)

   We study the classic set cover problem from the perspective of sub-linear algorithms. Given access to a collection of m sets over n elements in the query model, we show that sub-linear algorithms derived from existing techniques have almost tight query complexities. On one hand, first we show an adaptation of the streaming algorithm presented in [17] to the sub-linear query model, that returns an α-approximate cover using Õ(m(n/k)^1/(α–1) + nk) queries to the input, where k denotes the value of a minimum set cover. We then complement this upper bound by proving that for lower values of k, the required number of queries is , even for estimating the optimal cover size. Moreover, we prove that even checking whether a given collection of sets covers all the elements would require Ω(nk) queries. These two lower bounds provide strong evidence that the upper bound is almost tight for certain values of the parameter k. On the other hand, we show that this bound is not optimal for larger values of the parameter k, as there exists a (1 + ε)-approximation algorithm with Õ(mn/kε^2) queries. We show that this bound is essentially tight for sufficiently small constant ε, by establishing amore »lower bound of query complexity. Our lower-bound results follow by carefully designing two distributions of instances that are hard to distinguish. In particular, our first lower bound involves a probabilistic construction of a certain set system with a minimum set cover of size αk, with the key property that a small number of “almost uniformly distributed” modifications can reduce the minimum set cover size down to k. Thus, these modifications are not detectable unless a large number of queries are asked. We believe that our probabilistic construction technique might find applications to lower bounds for other combinatorial optimization problems.« less
5. A new 3/2-approximation algorithm for the b-edge cover problem

   https://doi.org/10.1137/1.9781611974690.ch6  

   Khan, Arif H. ; Pothen, Alex ( January 2016 , Proceedings of the Seventh SIAM Workshop on Combinatorial Scientific Computing)

   We describe a 3/2-approximation algorithm, \lse, for computing a b-edgecover of minimum weight in a graph with weights on the edges. The b-edgecover problem is a generalization of the better-known Edge Cover problem in graphs, where the objective is to choose a subset C of edges in the graph such that at least a specified number b(v) of edges in C are incident on each vertex v. In the weighted b-edgecover problem, we minimize the sum of the weights of the edges in C. We prove that the Locally Subdominant edge (LSE) algorithm computes the same b-edge cover as the one obtained by the Greedy algorithm for the problem. However, the Greedy algorithm requires edges to be sorted by their effective weights, and these weights need to be updated after each iteration. These requirements make the Greedy algorithm sequential and impractical for massive graphs. The LSE algorithm avoids the sorting step, and is amenable for parallelization. We implement the algorithm on a serial machine and compare its performance against a collection of approximation algorithms for the b-edge cover problem. Our results show that the algorithm is 3 to 5 times faster than the Greedy algorithm on a serial processor. Themore »approximate edge covers obtained by the LSE algorithm have weights greater by at most 17% of the optimal weight for problems where we could compute the latter. We also investigate the relationship between the b-edge cover and the b-matching problems, show that the latter has a faster implementation since edge weights are static in this algorithm, and obtain a heuristic solution for the former from the latter.« less