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1. Neural recall network: A neural network solution to low recall problem in regex-based qualitative coding

   https://doi.org/https://doi.org/10.5281/zenodo.6853047  

   Cai, Z. ; Marquart, C. ; Shaffer, D. ( January 2022 , Proceedings of the 15th International Conference on Educational Data Mining)

   Mitrovic, A. ; Bosch, N. (Ed.)

   Regular expression (regex) coding has advantages for text analysis. Humans are often able to quickly construct intelligible coding rules with high precision. That is, researchers can identify words and word patterns that correctly classify examples of a particular concept. And, it is often easy to identify false positives and improve the regex classifier so that the positive items are accurately captured. However, ensuring that a regex list is complete is a bigger challenge, because the concepts to be identified in data are often sparsely distributed, which makes it difficult to identify examples of \textit{false negatives}. For this reason, regex-based classifiers suffer by having low recall. That is, it often misses items that should be classified as positive. In this paper, we provide a neural network solution to this problem by identifying a \textit{negative reversion set}, in which false negative items occur much more frequently than in the data set as a whole. Thus, the regex classifier can be more quickly improved by adding missing regexes based on the false negatives found from the negative reversion set. This study used an existing data set collected from a simulation-based learning environment for which researchers had previously defined six codes and developed classifiers with validated regex lists. We randomly constructed incomplete (partial) regex lists and used neural network models to identify negative reversion sets in which the frequency of false negatives increased from a range of 3\\%-8\\% in the full data set to a range of 12\\%-52\\% in the negative reversion set. Based on this finding, we propose an interactive coding mechanism in which human-developed regex classifiers provide input for training machine learning algorithms and machine learning algorithms ``smartly" select highly suspected false negative items for human to more quickly develop regex classifiers. 

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2. Improving Crowdsourcing-Based Image Classification Through Expanded Input Elicitation and Machine Learning

   https://doi.org/10.3389/frai.2022.848056  

   Yasmin, Romena ; Hassan, Md Mahmudulla ; Grassel, Joshua T. ; Bhogaraju, Harika ; Escobedo, Adolfo R. ; Fuentes, Olac ( June 2022 , Frontiers in Artificial Intelligence)

   This work investigates how different forms of input elicitation obtained from crowdsourcing can be utilized to improve the quality of inferred labels for image classification tasks, where an image must be labeled as either positive or negative depending on the presence/absence of a specified object. Five types of input elicitation methods are tested: binary classification (positive or negative); the ( x, y )-coordinate of the position participants believe a target object is located; level of confidence in binary response (on a scale from 0 to 100%); what participants believe the majority of the other participants' binary classification is; and participant's perceived difficulty level of the task (on a discrete scale). We design two crowdsourcing studies to test the performance of a variety of input elicitation methods and utilize data from over 300 participants. Various existing voting and machine learning (ML) methods are applied to make the best use of these inputs. In an effort to assess their performance on classification tasks of varying difficulty, a systematic synthetic image generation process is developed. Each generated image combines items from the MPEG-7 Core Experiment CE-Shape-1 Test Set into a single image using multiple parameters (e.g., density, transparency, etc.) and may or may not contain a target object. The difficulty of these images is validated by the performance of an automated image classification method. Experiment results suggest that more accurate results can be achieved with smaller training datasets when both the crowdsourced binary classification labels and the average of the self-reported confidence values in these labels are used as features for the ML classifiers. Moreover, when a relatively larger properly annotated dataset is available, in some cases augmenting these ML algorithms with the results (i.e., probability of outcome) from an automated classifier can achieve even higher performance than what can be obtained by using any one of the individual classifiers. Lastly, supplementary analysis of the collected data demonstrates that other performance metrics of interest, namely reduced false-negative rates, can be prioritized through special modifications of the proposed aggregation methods. 

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3. Identifying transcription factor–DNA interactions using machine learning

   https://doi.org/10.1093/insilicoplants/diac014  

   Bang, Sohyun ; Galli, Mary ; Crisp, Peter A. ; Gallavotti, Andrea ; Schmitz, Robert J. ; Marshall-Colon, ed., Amy ( August 2022 , in silico Plants)

   Machine learning approaches have been applied to identify transcription factor (TF)–DNA interaction important for gene regulation and expression. However, due to the enormous search space of the genome, it is challenging to build models capable of surveying entire reference genomes, especially in species where models were not trained. In this study, we surveyed a variety of methods for classification of epigenomics data in an attempt to improve the detection for 12 members of the auxin response factor (ARF)-binding DNAs from maize and soybean as assessed by DNA Affinity Purification and sequencing (DAP-seq). We used the classification for prediction by minimizing the genome search space by only surveying unmethylated regions (UMRs). For identification of DAP-seq-binding events within the UMRs, we achieved 78.72 % accuracy rate across 12 members of ARFs of maize on average by encoding DNA with count vectorization for k-mer with a logistic regression classifier with up-sampling and feature selection. Importantly, feature selection helps to uncover known and potentially novel ARF-binding motifs. This demonstrates an independent method for identification of TF-binding sites. Finally, we tested the model built with maize DAP-seq data and applied it directly to the soybean genome and found high false-negative rates, which accounted for more than 40 % across the ARF TFs tested. The findings in this study suggest the potential use of various methods to predict TF–DNA interactions within and between species with varying degrees of success.

    

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4. What We Can Learn from Jury Note Taking: A Content Analysis

   Denne, E. ( March 2020 , Annual Conference of the American Psychology-Law Society.)

   Abstract: Jury notetaking can be controversial despite evidence suggesting benefits for recall and understanding. Research on note taking has historically focused on the deliberation process. Yet, little research explores the notes themselves. We developed a 10-item coding guide to explore what jurors take notes on (e.g., simple vs. complex evidence) and how they take notes (e.g., gist vs. specific representation). In general, jurors made gist representations of simple and complex information in their notes. This finding is consistent with Fuzzy Trace Theory (Reyna & Brainerd, 1995) and suggests notes may serve as a general memory aid, rather than verbatim representation. Summary: The practice of jury notetaking in the courtroom is often contested. Some states allow it (e.g., Nebraska: State v. Kipf, 1990), while others forbid it (e.g., Louisiana: La. Code of Crim. Proc., Art. 793). Some argue notes may serve as a memory aid, increase juror confidence during deliberation, and help jurors engage in the trial (Hannaford & Munsterman, 2001; Heuer & Penrod, 1988, 1994). Others argue notetaking may distract jurors from listening to evidence, that juror notes may be given undue weight, and that those who took notes may dictate the deliberation process (Dann, Hans, & Kaye, 2005). While research has evaluated the efficacy of juror notes on evidence comprehension, little work has explored the specific content of juror notes. In a similar project on which we build, Dann, Hans, and Kaye (2005) found jurors took on average 270 words of notes each with 85% including references to jury instructions in their notes. In the present study we use a content analysis approach to examine how jurors take notes about simple and complex evidence. We were particularly interested in how jurors captured gist and specific (verbatim) information in their notes as they have different implications for information recall during deliberation. According to Fuzzy Trace Theory (Reyna & Brainerd, 1995), people extract “gist” or qualitative meaning from information, and also exact, verbatim representations. Although both are important for helping people make well-informed judgments, gist-based understandings are purported to be even more important than verbatim understanding (Reyna, 2008; Reyna & Brainer, 2007). As such, it could be useful to examine how laypeople represent information in their notes during deliberation of evidence. Methods Prior to watching a 45-minute mock bank robbery trial, jurors were given a pen and notepad and instructed they were permitted to take notes. The evidence included testimony from the defendant, witnesses, and expert witnesses from prosecution and defense. Expert testimony described complex mitochondrial DNA (mtDNA) evidence. The present analysis consists of pilot data representing 2,733 lines of notes from 52 randomly-selected jurors across 41 mock juries. Our final sample for presentation at AP-LS will consist of all 391 juror notes in our dataset. Based on previous research exploring jury note taking as well as our specific interest in gist vs. specific encoding of information, we developed a coding guide to quantify juror note-taking behaviors. Four researchers independently coded a subset of notes. Coders achieved acceptable interrater reliability [(Cronbach’s Alpha = .80-.92) on all variables across 20% of cases]. Prior to AP-LS, we will link juror notes with how they discuss scientific and non-scientific evidence during jury deliberation. Coding Note length. Before coding for content, coders counted lines of text. Each notepad line with at minimum one complete word was coded as a line of text. Gist information vs. Specific information. Any line referencing evidence was coded as gist or specific. We coded gist information as information that did not contain any specific details but summarized the meaning of the evidence (e.g., “bad, not many people excluded”). Specific information was coded as such if it contained a verbatim descriptive (e.g.,“<1 of people could be excluded”). We further coded whether this information was related to non-scientific evidence or related to the scientific DNA evidence. Mentions of DNA Evidence vs. Other Evidence. We were specifically interested in whether jurors mentioned the DNA evidence and how they captured complex evidence. When DNA evidence was mention we coded the content of the DNA reference. Mentions of the characteristics of mtDNA vs nDNA, the DNA match process or who could be excluded, heteroplasmy, references to database size, and other references were coded. Reliability. When referencing DNA evidence, we were interested in whether jurors mentioned the evidence reliability. Any specific mention of reliability of DNA evidence was noted (e.g., “MT DNA is not as powerful, more prone to error”). Expert Qualification. Finally, we were interested in whether jurors noted an expert’s qualifications. All references were coded (e.g., “Forensic analyst”). Results On average, jurors took 53 lines of notes (range: 3-137 lines). Most (83%) mentioned jury instructions before moving on to case specific information. The majority of references to evidence were gist references (54%) focusing on non-scientific evidence and scientific expert testimony equally (50%). When jurors encoded information using specific references (46%), they referenced non-scientific evidence and expert testimony equally as well (50%). Thirty-three percent of lines were devoted to expert testimony with every juror including at least one line. References to the DNA evidence were usually focused on who could be excluded from the FBIs database (43%), followed by references to differences between mtDNA vs nDNA (30%), and mentions of the size of the database (11%). Less frequently, references to DNA evidence focused on heteroplasmy (5%). Of those references that did not fit into a coding category (11%), most focused on the DNA extraction process, general information about DNA, and the uniqueness of DNA. We further coded references to DNA reliability (15%) as well as references to specific statistical information (14%). Finally, 40% of jurors made reference to an expert’s qualifications. Conclusion Jury note content analysis can reveal important information about how jurors capture trial information (e.g., gist vs verbatim), what evidence they consider important, and what they consider relevant and irrelevant. In our case, it appeared jurors largely created gist representations of information that focused equally on non-scientific evidence and scientific expert testimony. This finding suggests note taking may serve not only to represent information verbatim, but also and perhaps mostly as a general memory aid summarizing the meaning of evidence. Further, jurors’ references to evidence tended to be equally focused on the non-scientific evidence and the scientifically complex DNA evidence. This observation suggests jurors may attend just as much to non-scientific evidence as they to do complex scientific evidence in cases involving complicated evidence – an observation that might inform future work on understanding how jurors interpret evidence in cases with complex information. Learning objective: Participants will be able to describe emerging evidence about how jurors take notes during trial. 

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5. Enhancing Image Classification Capabilities of Crowdsourcing-Based Methods through Expanded Input Elicitation

   Yasmin, Romena ; Grassel, Joshua T. ; Hassan, Md Mahmudulla ; Fuentes, Olac ; Escobedo, Adolfo R. ( November 2021 , Proceedings of the Ninth AAAI Conference on Human Computation and Crowdsourcing (HCOMP2021))

   Kamar, Ece ; Luther, Kurt (Ed.)

   This study investigates how different forms of input elicitation obtained from crowdsourcing can be utilized to improve the quality of inferred labels for image classification tasks, where an image must be labeled as either positive or negative depending on the presence/absence of a specified object. Three types of input elicitation methods are tested: binary classification (positive or negative); level of confidence in binary response (on a scale from 0-100%); and what participants believe the majority of the other participants’ binary classification is. We design a crowdsourcing experiment to test the performance of the proposed input elicitation methods and use data from over 200 participants. Various existing voting and machine learning (ML) methods are applied and others developed to make the best use of these inputs. In an effort to assess their performance on classification tasks of varying difficulty, a systematic synthetic image generation process is developed. Each generated image combines items from the MPEG-7 Core Experiment CE-Shape-1 Test Set into a single image using multiple parameters (e.g., density, transparency, etc.) and may or may not contain a target object. The difficulty of these images is validated by the performance of an automated image classification method. Experimental results suggest that more accurate classifications can be achieved when using the average of the self-reported confidence values as an additional attribute for ML algorithms relative to what is achieved with more traditional approaches. Additionally, they demonstrate that other performance metrics of interest, namely reduced false-negative rates, can be prioritized through special modifications of the proposed aggregation methods that leverage the variety of elicited inputs. 

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