A qualitative assessment of QCA: method stretching in large-N studies and temporality

Qualitative Comparative Analysis (QCA) is a descriptive research method that can provide causal explanations for an outcome of interest. Despite extensive quantitative assessments of the method, my objective is to contribute to the scholarly discussion with insights constructed through a qualitative lens. Researchers using the QCA approach have less ability to incorporate and nuance information on set membership as the number of cases grows. While recognizing the suggested ways to overcome such challenges, I argue that since setting criteria for membership, calibrating, and categorizing are crucial QCA aspects that require in-depth knowledge, QCA is unfit for larger-N studies. Additionally, I also discuss that while the method is able to identify various parts of a causal configuration—the ‘what’—it falls short to shed light on the ‘how’ and ‘why,’ especially when temporality matters. Researchers can complement it with other methods, such as process tracing and case studies, to fill in these missing explanatory pieces or clarify contradictions—which begs the question of why they would also choose to use QCA.

Applying Set Membership Strategy in State of Charge Estimation for Lithium-ion Battery

As state of charge is one important variable to monitor the later battery management system, and as traditional Kalman filter can be used to estimate the state of charge for Lithium-ion battery on basis of probability distribution on external noise. To relax this strict assumption on external noise, set membership strategy is proposed to achieve our goal in case of unknown but bounded noise. External noise with unknown but bounded is more realistic than white noise. After equivalent circuit model is used to describe the Lithium-ion battery charging and discharging properties, one state space equation is constructed to regard state of charge as its state variable. Based on state space model about state of charge, two kinds of set membership strategies are put forth to achieve the state estimation, which corresponds to state of charge estimation. Due to external noise is bounded, i.e. external noise is in a set, we construct interval and ellipsoid estimation for state estimation respectively in case of external noise is assumed in an interval or ellipsoid. Then midpoint of interval or center of the ellipsoid are chosen as the final value for state of charge estimation. Finally, one simulation example confirms our theoretical results.

Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes

SARS-CoV-2 genomic sequencing efforts have scaled dramatically to address the current global pandemic and aid public health. However, autonomous genome annotation of SARS-CoV-2 genes, proteins, and domains is not readily accomplished by existing methods and results in missing or incorrect sequences. To overcome this limitation, we developed a novel semi-supervised pipeline for automated gene, protein, and functional domain annotation of SARS-CoV-2 genomes that differentiates itself by not relying on the use of a single reference genome and by overcoming atypical genomic traits that challenge traditional bioinformatic methods. We analyzed an initial corpus of 66,000 SARS-CoV-2 genome sequences collected from labs across the world using our method and identified the comprehensive set of known proteins with 98.5% set membership accuracy and 99.1% accuracy in length prediction, compared to proteome references, including Replicase polyprotein 1ab (with its transcriptional slippage site). Compared to other published tools, such as Prokka (base) and VAPiD, we yielded a 6.4- and 1.8-fold increase in protein annotations. Our method generated 13,000,000 gene, protein, and domain sequences—some conserved across time and geography and others representing emerging variants. We observed 3362 non-redundant sequences per protein on average within this corpus and described key D614G and N501Y variants spatiotemporally in the initial genome corpus. For spike glycoprotein domains, we achieved greater than 97.9% sequence identity to references and characterized receptor binding domain variants. We further demonstrated the robustness and extensibility of our method on an additional 4000 variant diverse genomes containing all named variants of concern and interest as of August 2021. In this cohort, we successfully identified all keystone spike glycoprotein mutations in our predicted protein sequences with greater than 99% accuracy as well as demonstrating high accuracy of the protein and domain annotations. This work comprehensively presents the molecular targets to refine biomedical interventions for SARS-CoV-2 with a scalable, high-accuracy method to analyze newly sequenced infections as they arise.

Narrowband Interference Cancellation using Set-membership Adaptive Predictor for GPS Receiver

The global positioning system (GPS) provides accurate positioning and timing information that is useful in various civil and military applications. The adaptive filtering predictor for GPS jamming suppression applications is proposed. This research uses the gLab-G software to substitute for the hardware receiver to record the GPS signal waveform. The normalized least-mean-square (NLMS) and set-membership NLMS (SM-NLMS) filtering methods are employed for continuous wave interference suppression. Simulation results reveal that our proposed methods can provide the better performances when the interference-to-noise ratios (INR) are varied from 20 to 50 dB. The anti-jamming performances are evaluated via extensive simulation by computing mean squared prediction error (MSPE) and signal-to-noise ratio (SNR) improvements.