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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 vagueness 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. 

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2. Generative imaging and image processing via generative encoder

   https://doi.org/10.3934/ipi.2021060  

   Ong, Yong Zheng ; Yang, Haizhao ( January 2022 , Inverse Problems & Imaging)

   This paper introduces a novel generative encoder (GE) framework for generative imaging and image processing tasks like image reconstruction, compression, denoising, inpainting, deblurring, and super-resolution. GE unifies the generative capacity of GANs and the stability of AEs in an optimization framework instead of stacking GANs and AEs into a single network or combining their loss functions as in existing literature. GE provides a novel approach to visualizing relationships between latent spaces and the data space. The GE framework is made up of a pre-training phase and a solving phase. In the former, a GAN with generator \begin{document}$ G $\end{document} capturing the data distribution of a given image set, and an AE network with encoder \begin{document}$ E $\end{document} that compresses images following the estimated distribution by \begin{document}$ G $\end{document} are trained separately, resulting in two latent representations of the data, denoted as the generative and encoding latent space respectively. In the solving phase, given noisy image \begin{document}$ x = \mathcal{P}(x^*) $\end{document}, where \begin{document}$ x^* $\end{document} is the target unknown image, \begin{document}$ \mathcal{P} $\end{document} is an operator adding an addictive, or multiplicative, or convolutional noise, or equivalently given such an image \begin{document}$ x $\end{document} in the compressed domain, i.e., given \begin{document}$ m = E(x) $\end{document}, the two latent spaces are unified via solving the optimization problem

   \begin{document}$ z^* = \underset{z}{\mathrm{argmin}} \|E(G(z))-m\|_2^2+\lambda\|z\|_2^2 $\end{document}

   and the image \begin{document}$ x^* $\end{document} is recovered in a generative way via \begin{document}$ \hat{x}: = G(z^*)\approx x^* $\end{document}, where \begin{document}$ \lambda>0 $\end{document} is a hyperparameter. The unification of the two spaces allows improved performance against corresponding GAN and AE networks while visualizing interesting properties in each latent space.

    

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3. Juror Scientific Reasoning Skills and Discussion of Scientific Evidence During Deliberation

   McCowan, K. ( March 2020 , Annual Conference of the American Psychology-Law Society.)

   Abstract We investigate the link between individual differences in science reasoning skills and mock jurors’ deliberation behavior; specifically, how much they talk about the scientific evidence presented in a complicated, ecologically valid case during deliberation. Consistent with our preregistered hypothesis, mock jurors strong in scientific reasoning discussed the scientific evidence more during deliberation than those with weaker science reasoning skills. Summary With increasing frequency, legal disputes involve complex scientific information (Faigman et al., 2014; Federal Judicial Center, 2011; National Research Council, 2009). Yet people often have trouble consuming scientific information effectively (McAuliff et al., 2009; National Science Board, 2014; Resnick et al., 2016). Individual differences in reasoning styles and skills can affect how people comprehend complex evidence (e.g., Hans, Kaye, Dann, Farley, Alberston, 2011; McAuliff & Kovera, 2008). Recently, scholars have highlighted the importance of studying group deliberation contexts as well as individual decision contexts (Salerno & Diamond, 2010; Kovera, 2017). If individual differences influence how jurors understand scientific evidence, it invites questions about how these individual differences may affect the way jurors discuss science during group deliberations. The purpose of the current study was to examine how individual differences in the way people process scientific information affects the extent to which jurors discuss scientific evidence during deliberations. Methods We preregistered the data collection plan, sample size, and hypotheses on the Open Science Framework. Jury-eligible community participants (303 jurors across 50 juries) from Phoenix, AZ (Mage=37.4, SD=16.9; 58.8% female; 51.5% White, 23.7% Latinx, 9.9% African-American, 4.3% Asian) were paid $55 for a 3-hour mock jury study. Participants completed a set of individual questionnaires related to science reasoning skills and attitudes toward science prior to watching a 45-minute mock armed-robbery trial. The trial included various pieces of evidence and testimony, including forensic experts testifying about mitochondrial DNA evidence (mtDNA; based on Hans et al. 2011 materials). Participants were then given 45 minutes to deliberate. The deliberations were video recorded and transcribed to text for analysis. We analyzed the deliberation content for discussions related to the scientific evidence presented during trial. We hypothesized that those with stronger scientific and numeric reasoning skills, higher need for cognition, and more positive views towards science would discuss scientific evidence more than their counterparts during deliberation. Measures We measured Attitudes Toward Science (ATS) with indices of scientific promise and scientific reservations (Hans et al., 2011; originally developed by the National Science Board, 2004; 2006). We used Drummond and Fischhoff’s (2015) Scientific Reasoning Scale (SRS) to measure scientific reasoning skills. Weller et al.’s (2012) Numeracy Scale (WNS) measured proficiency in reasoning with quantitative information. The NFC-Short Form (Cacioppo et al., 1984) measured need for cognition. Coding We identified verbal utterances related to the scientific evidence presented in court. For instance, references to DNA evidence in general (e.g. nuclear DNA being more conclusive than mtDNA), the database that was used to compare the DNA sample (e.g. the database size, how representative it was), exclusion rates (e.g. how many other people could not be excluded as a possible match), and the forensic DNA experts (e.g. how credible they were perceived). We used word count to operationalize the extent to which each juror discussed scientific information. First we calculated the total word count for each complete jury deliberation transcript. Based on the above coding scheme we determined the number of words each juror spent discussing scientific information. To compare across juries, we wanted to account for the differing length of deliberation; thus, we calculated each juror’s scientific deliberation word count as a proportion of their jury’s total word count. Results On average, jurors discussed the science for about 4% of their total deliberation (SD=4%, range 0-22%). We regressed proportion of the deliberation jurors spend discussing scientific information on the four individual difference measures (i.e., SRS, NFC, WNS, ATS). Using the adjusted R-squared, the measures significantly accounted for 5.5% of the variability in scientific information deliberation discussion, SE=0.04, F(4, 199)=3.93, p=0.004. When controlling for all other variables in the model, the Scientific Reasoning Scale was the only measure that remained significant, b=0.003, SE=0.001, t(203)=2.02, p=0.045. To analyze how much variability each measure accounted for, we performed a stepwise regression, with NFC entered at step 1, ATS entered at step 2, WNS entered at step 3, and SRS entered at step 4. At step 1, NFC accounted for 2.4% of the variability, F(1, 202)=5.95, p=0.02. At step 2, ATS did not significantly account for any additional variability. At step 3, WNS accounted for an additional 2.4% of variability, ΔF(1, 200)=5.02, p=0.03. Finally, at step 4, SRS significantly accounted for an additional 1.9% of variability in scientific information discussion, ΔF(1, 199)=4.06, p=0.045, total adjusted R-squared of 0.055. Discussion This study provides additional support for previous findings that scientific reasoning skills affect the way jurors comprehend and use scientific evidence. It expands on previous findings by suggesting that these individual differences also impact the way scientific evidence is discussed during juror deliberations. In addition, this study advances the literature by identifying Scientific Reasoning Skills as a potentially more robust explanatory individual differences variable than more well-studied constructs like Need for Cognition in jury research. Our next steps for this research, which we plan to present at AP-LS as part of this presentation, incudes further analysis of the deliberation content (e.g., not just the mention of, but the accuracy of the references to scientific evidence in discussion). We are currently coding this data with a software program called Noldus Observer XT, which will allow us to present more sophisticated results from this data during the presentation. Learning Objective: Participants will be able to describe how individual differences in scientific reasoning skills affect how much jurors discuss scientific evidence during deliberation. 

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4. LINKING EXPLOITS FROM THE DARK WEB TO KNOWN VULNERABILITIES FOR PROACTIVE CYBER THREAT INTELLIGENCE: AN ATTENTION-BASED DEEP STRUCTURED SEMANTIC MODEL1

   Samtani, S ; Chai, Y ; and Chen, H. ( June 2022 , MIS quarterly)

   Black hat hackers use malicious exploits to circumvent security controls and take advantage of system vulnerabilities worldwide, costing the global economy over $450 billion annually. While many organizations are increasingly turning to cyber threat intelligence (CTI) to help prioritize their vulnerabilities, extant CTI processes are often criticized as being reactive to known exploits. One promising data source that can help develop proactive CTI is the vast and ever-evolving Dark Web. In this study, we adopted the computational design science paradigm to design a novel deep learning (DL)-based exploit-vulnerability attention deep structured semantic model (EVA-DSSM) that includes bidirectional processing and attention mechanisms to automatically link exploits from the Dark Web to vulnerabilities. We also devised a novel device vulnerability severity metric (DVSM) that incorporates the exploit post date and vulnerability severity to help cybersecurity professionals with their device prioritization and risk management efforts. We rigorously evaluated the EVA-DSSM against state-of-the-art non-DL and DL-based methods for short text matching on 52,590 exploit-vulnerability linkages across four testbeds: web application, remote, local, and denial of service. Results of these evaluations indicate that the proposed EVA-DSSM achieves precision at 1 scores 20% - 41% higher than non-DL approaches and 4% - 10% higher than DL-based approaches. We demonstrated the EVA-DSSM’s and DVSM’s practical utility with two CTI case studies: openly accessible systems in the top eight U.S. hospitals and over 20,000 Supervisory Control and Data Acquisition (SCADA) systems worldwide. A complementary user evaluation of the case study results indicated that 45 cybersecurity professionals found the EVA-DSSM and DVSM results more useful for exploit-vulnerability linking and risk prioritization activities than those produced by prevailing approaches. Given the rising cost of cyberattacks, the EVA-DSSM and DVSM have important implications for analysts in security operations centers, incident response teams, and cybersecurity vendors. 

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5. Linking Exploits from the Dark Web to Known Vulnerabilities for Proactive Cyber Threat Intelligence: An Attention-based Deep Structured Semantic Model

   https://doi.org/10.25300/MISQ/2022/15392  

   Samtani, S ; Chai, Y ; and Chen, H ( June 2022 , MIS quarterly)

   Black hat hackers use malicious exploits to circumvent security controls and take advantage of system vulnerabilities worldwide, costing the global economy over $450 billion annually. While many organizations are increasingly turning to cyber threat intelligence (CTI) to help prioritize their vulnerabilities, extant CTI processes are often criticized as being reactive to known exploits. One promising data source that can help develop proactive CTI is the vast and ever-evolving Dark Web. In this study, we adopted the computational design science paradigm to design a novel deep learning (DL)-based exploit-vulnerability attention deep structured semantic model (EVA-DSSM) that includes bidirectional processing and attention mechanisms to automatically link exploits from the Dark Web to vulnerabilities. We also devised a novel device vulnerability severity metric (DVSM) that incorporates the exploit post date and vulnerability severity to help cybersecurity professionals with their device prioritization and risk management efforts. We rigorously evaluated the EVA-DSSM against state-of-the-art non-DL and DL-based methods for short text matching on 52,590 exploit-vulnerability linkages across four testbeds: web application, remote, local, and denial of service. Results of these evaluations indicate that the proposed EVA-DSSM achieves precision at 1 scores 20%-41% higher than non-DL approaches and 4%-10% higher than DL-based approaches. We demonstrated the EVA-DSSM's and DVSM's practical utility with two CTI case studies: openly accessible systems in the top eight U.S. hospitals and over 20,000 Supervisory Control and Data Acquisition (SCADA) systems worldwide. A complementary user evaluation of the case study results indicated that 45 cybersecurity professionals found the EVA-DSSM and DVSM results more useful for exploit-vulnerability linking and risk prioritization activities than those produced by prevailing approaches. Given the rising cost of cyberattacks, the EVA-DSSM and DVSM have important implications for analysts in security operations centers, incident response teams, and cybersecurity vendors. 

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