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1. Improving the Quality of the TUSZ Corpus

   Rahman, Safwanur Hamid ( December 2020 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, Iyad ; Selesnick, Ivan ; Picone, Joseph (Ed.)

   The Temple University Hospital Seizure Detection Corpus (TUSZ) [1] has been in distribution since April 2017. It is a subset of the TUH EEG Corpus (TUEG) [2] and the most frequently requested corpus from our 3,000+ subscribers. It was recently featured as the challenge task in the Neureka 2020 Epilepsy Challenge [3]. A summary of the development of the corpus is shown below in Table 1. The TUSZ Corpus is a fully annotated corpus, which means every seizure event that occurs within its files has been annotated. The data is selected from TUEG using a screening process that identifies files most likely to contain seizures [1]. Approximately 7% of the TUEG data contains a seizure event, so it is important we triage TUEG for high yield data. One hour of EEG data requires approximately one hour of human labor to complete annotation using the pipeline described below, so it is important from a financial standpoint that we accurately triage data. A summary of the labels being used to annotate the data is shown in Table 2. Certain standards are put into place to optimize the annotation process while not sacrificing consistency. Due to the nature of EEG recordings, some records start off with a segment of calibration. This portion of the EEG is instantly recognizable and transitions from what resembles lead artifact to a flat line on all the channels. For the sake of seizure annotation, the calibration is ignored, and no time is wasted on it. During the identification of seizure events, a hard “3 second rule” is used to determine whether two events should be combined into a single larger event. This greatly reduces the time that it takes to annotate a file with multiple events occurring in succession. In addition to the required minimum 3 second gap between seizures, part of our standard dictates that no seizure less than 3 seconds be annotated. Although there is no universally accepted definition for how long a seizure must be, we find that it is difficult to discern with confidence between burst suppression or other morphologically similar impressions when the event is only a couple seconds long. This is due to several reasons, the most notable being the lack of evolution which is oftentimes crucial for the determination of a seizure. After the EEG files have been triaged, a team of annotators at NEDC is provided with the files to begin data annotation. An example of an annotation is shown in Figure 1. A summary of the workflow for our annotation process is shown in Figure 2. Several passes are performed over the data to ensure the annotations are accurate. Each file undergoes three passes to ensure that no seizures were missed or misidentified. The first pass of TUSZ involves identifying which files contain seizures and annotating them using our annotation tool. The time it takes to fully annotate a file can vary drastically depending on the specific characteristics of each file; however, on average a file containing multiple seizures takes 7 minutes to fully annotate. This includes the time that it takes to read the patient report as well as traverse through the entire file. Once an event has been identified, the start and stop time for the seizure is stored in our annotation tool. This is done on a channel by channel basis resulting in an accurate representation of the seizure spreading across different parts of the brain. Files that do not contain any seizures take approximately 3 minutes to complete. Even though there is no annotation being made, the file is still carefully examined to make sure that nothing was overlooked. In addition to solely scrolling through a file from start to finish, a file is often examined through different lenses. Depending on the situation, low pass filters are used, as well as increasing the amplitude of certain channels. These techniques are never used in isolation and are meant to further increase our confidence that nothing was missed. Once each file in a given set has been looked at once, the annotators start the review process. The reviewer checks a file and comments any changes that they recommend. This takes about 3 minutes per seizure containing file, which is significantly less time than the first pass. After each file has been commented on, the third pass commences. This step takes about 5 minutes per seizure file and requires the reviewer to accept or reject the changes that the second reviewer suggested. Since tangible changes are made to the annotation using the annotation tool, this step takes a bit longer than the previous one. Assuming 18% of the files contain seizures, a set of 1,000 files takes roughly 127 work hours to annotate. Before an annotator contributes to the data interpretation pipeline, they are trained for several weeks on previous datasets. A new annotator is able to be trained using data that resembles what they would see under normal circumstances. An additional benefit of using released data to train is that it serves as a means of constantly checking our work. If a trainee stumbles across an event that was not previously annotated, it is promptly added, and the data release is updated. It takes about three months to train an annotator to a point where their annotations can be trusted. Even though we carefully screen potential annotators during the hiring process, only about 25% of the annotators we hire survive more than one year doing this work. To ensure that the annotators are consistent in their annotations, the team conducts an interrater agreement evaluation periodically to ensure that there is a consensus within the team. The annotation standards are discussed in Ochal et al. [4]. An extended discussion of interrater agreement can be found in Shah et al. [5]. The most recent release of TUSZ, v1.5.2, represents our efforts to review the quality of the annotations for two upcoming challenges we hosted: an internal deep learning challenge at IBM [6] and the Neureka 2020 Epilepsy Challenge [3]. One of the biggest changes that was made to the annotations was the imposition of a stricter standard for determining the start and stop time of a seizure. Although evolution is still included in the annotations, the start times were altered to start when the spike-wave pattern becomes distinct as opposed to merely when the signal starts to shift from background. This cuts down on background that was mislabeled as a seizure. For seizure end times, all post ictal slowing that was included was removed. The recent release of v1.5.2 did not include any additional data files. Two EEG files had been added because, originally, they were corrupted in v1.5.1 but were able to be retrieved and added for the latest release. The progression from v1.5.0 to v1.5.1 and later to v1.5.2, included the re-annotation of all of the EEG files in order to develop a confident dataset regarding seizure identification. Starting with v1.4.0, we have also developed a blind evaluation set that is withheld for use in competitions. The annotation team is currently working on the next release for TUSZ, v1.6.0, which is expected to occur in August 2020. It will include new data from 2016 to mid-2019. This release will contain 2,296 files from 2016 as well as several thousand files representing the remaining data through mid-2019. In addition to files that were obtained with our standard triaging process, a part of this release consists of EEG files that do not have associated patient reports. Since actual seizure events are in short supply, we are mining a large chunk of data for which we have EEG recordings but no reports. Some of this data contains interesting seizure events collected during long-term EEG sessions or data collected from patients with a history of frequent seizures. It is being mined to increase the number of files in the corpus that have at least one seizure event. We expect v1.6.0 to be released before IEEE SPMB 2020. The TUAR Corpus is an open-source database that is currently available for use by any registered member of our consortium. To register and receive access, please follow the instructions provided at this web page: https://www.isip.piconepress.com/projects/tuh_eeg/html/downloads.shtml. The data is located here: https://www.isip.piconepress.com/projects/tuh_eeg/downloads/tuh_eeg_artifact/v2.0.0/. 

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2. A Survey on Recent Trends and Open Issues in Energy Efficiency of 5G

   https://doi.org/10.3390/s19143126  

   Usama, Muhammad ; Erol-Kantarci, Melike ( July 2019 , Sensors)

   The rapidly increasing interest from various verticals for the upcoming 5th generation (5G) networks expect the network to support higher data rates and have an improved quality of service. This demand has been met so far by employing sophisticated transmission techniques including massive Multiple Input Multiple Output (MIMO), millimeter wave (mmWave) bands as well as bringing the computational power closer to the users via advanced baseband processing units at the base stations. Future evolution of the networks has also been assumed to open many new business horizons for the operators and the need of not only a resource efficient but also an energy efficient ecosystem has greatly been felt. The deployment of small cells has been envisioned as a promising answer for handling the massive heterogeneous traffic, but the adverse economic and environmental impacts cannot be neglected. Given that 10% of the world’s energy consumption is due to the Information and Communications Technology (ICT) industry, energy-efficiency has thus become one of the key performance indicators (KPI). Various avenues of optimization, game theory and machine learning have been investigated for enhancing power allocation for downlink and uplink channels, as well as other energy consumption/saving approaches. This paper surveys the recent works that address energy efficiency of the radio access as well as the core of wireless networks, and outlines related challenges and open issues. 

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3. Map-Assisted Millimeter Wave Localization for Accurate Position Location

   https://doi.org/10.1109/globecom38437.2019.9013365  

   Kanhere, Ojas ; Ju, Shihao ; Xing, Yunchou ; Rappaport, Theodore S. ( December 2019 , 2019 IEEE Global Communications Conference)

   null (Ed.)

   Accurate precise positioning at millimeter wave frequencies is possible due to the large available bandwidth that permits precise on-the-fly time of flight measurements using conventional air interface standards. In addition, narrow antenna beamwidths may be used to determine the angles of arrival and departure of the multipath components between the base station and mobile users. By combining accurate temporal and angular information of multipath components with a 3- D map of the environment (that may be built by each user or downloaded a-priori), robust localization is possible, even in non-line-of-sight environments. In this work, we develop an accurate 3-D ray tracer for an indoor office environment and demonstrate how the fusion of angle of departure and time of flight information in concert with a 3-D map of a typical large office environment provides a mean accuracy of 12.6 cm in line-of-sight and 16.3 cm in non-line-of-sight, over 100 receiver distances ranging from 1.5 m to 24.5 m using a single base station. We show how increasing the number of base stations improves the average non-line-of-sight position location accuracy to 5.5 cm at 21 locations with a maximum propagation distance of 24.5 m. Index Terms—localization; positioning; position location; navigation; mmWave; 5G; ray tracing; site-specific propagation; map-based 

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4. Evidence for exon shuffling is sensitive to model choice

   https://doi.org/10.1142/S0219720021400138  

   Cui, Xiaoyue ; Stolzer, Maureen ; Durand, Dannie ( December 2021 , Journal of Bioinformatics and Computational Biology)

   The exon shuffling theory posits that intronic recombination creates new domain combinations, facilitating the evolution of novel protein function. This theory predicts that introns will be preferentially situated near domain boundaries. Many studies have sought evidence for exon shuffling by testing the correspondence between introns and domain boundaries against chance intron positioning. Here, we present an empirical investigation of how the choice of null model influences significance. Although genome-wide studies have used a uniform null model, exclusively, more realistic null models have been proposed for single gene studies. We extended these models for genome-wide analyses and applied them to 21 metazoan and fungal genomes. Our results show that compared with the other two models, the uniform model does not recapitulate genuine exon lengths, dramatically underestimates the probability of chance agreement, and overestimates the significance of intron-domain correspondence by as much as 100 orders of magnitude. Model choice had much greater impact on the assessment of exon shuffling in fungal genomes than in metazoa, leading to different evolutionary conclusions in seven of the 16 fungal genomes tested. Genome-wide studies that use this overly permissive null model may exaggerate the importance of exon shuffling as a general mechanism of multidomain evolution. 

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5. Conflict-Driven Synthesis for Layout Engines

   https://doi.org/10.1145/3591246  

   Liu, Junrui ; Chen, Yanju ; Atkinson, Eric ; Feng, Yu ; Bodik, Rastislav ( June 2023 , Proceedings of the ACM on Programming Languages)

   Modern web browsers rely on layout engines to convert HTML documents to layout trees that specify color, size, and position. However, existing layout engines are notoriously difficult to maintain because of the complexity of web standards. This is especially true for incremental layout engines, which are designed to improve performance by updating only the parts of the layout tree that need to be changed. In this paper, we propose Medea, a new framework for automatically generating incremental layout engines. Medea separates the specification of the layout engine from its incremental implementation, and guarantees correctness through layout engine synthesis. The synthesis is driven by a new iterative algorithm based on detecting conflicts that prevent optimality of the incremental algorithm. We evaluated Medea on a fragment of HTML layout that includes challenging features such as margin collapse, floating layout, and absolute positioning. Medea successfully synthesized an incremental layout engine for this fragment. The synthesized layout engine is both correct and efficient. In particular, we demonstrated that it avoids real-world bugs that have been reported in the layout engines of Chrome, Firefox, and Safari. The incremental layout engine synthesized by Medea is up to 1.82× faster than a naive incremental baseline. We also demonstrated that our conflict-driven algorithm produces engines that are 2.74× faster than a baseline without conflict analysis. 

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