Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search™

Motivation: With the tremendous growth in scientific literature, it is necessary to improve upon the standard pattern matching style of the available search engines. Semantic NLP may be the solution to this problem. Cognition Search (CSIR) is a natural language technology. It is best used by asking a simple question that might be answered in textual data being queried, such as MEDLINE. CSIR has a large English dictionary and semantic database. Cognition’s semantic map enables the search process to be based on meaning rather than statistical word pattern matching and, therefore, returns more complete and relevant results. The Cognition Search engine uses downward reasoning and synonymy which also improves recall. It improves precision through phrase parsing and word sense disambiguation.
Result: Here we have carried out several projects to "teach" the CSIR lexicon medical, biochemical and molecular biological language and acronyms from curated web-based free sources. Vocabulary from the Alliance for Cell Signaling (AfCS), the Human Genome Nomenclature Consortium (HGNC), the United Medical Language System (UMLS) Meta-thesaurus, and The International Union of Pure and Applied Chemistry (IUPAC) was introduced into the CSIR dictionary and curated. The resulting system was used to interpret MEDLINE abstracts. Meaning-based search of MEDLINE abstracts yields high precision (estimated at >90%), and high recall (estimated at >90%), where synonym information has been encoded. The present implementation can be found at http://MEDLINE.cognition.com. 
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Favorite Teams and Athletes Data Brief

ABOUT THIS STUDY The annual Los Angeles Public Opinion Survey conducted by StudyLA involved 20-minute telephone sessions and online surveys with more than 2,000 adults (1,200 phone and 800 online) living in Los Angeles County. Respondents were asked about qualityof-life perceptions, personal economic wellbeing, economic concerns, overall life satisfaction, and various civic issues. The margin of error is ±3.0% for the entire sample. ABOUT THIS REPORT The following data brief contains responses to the survey questions on Los Angeles’ favorite teams and athletes and is divided into two sections: (1) toplines for all respondents, and (2) answers crossed by all major respondent demographics. QUESTION(S) INCLUDED IN THIS REPORT Which is your favorite professional team with LA in its name? Lakers | Clippers | Dodgers | Angels | Galaxy | Kings | Sparks | Rams | Chargers | LAFC (2020) Of the following players, who is your favorite athlete that plays for a team with LA in its name? LeBron James | Kawhi Leonard | Cody Bellinger | Mike Trout | Zlatan Ibrahimovic | Anze Kopitar | Candace Parker | Aaron Donald | Phillip Rivers | Carlso Vela | Otherhttps://digitalcommons.lmu.edu/studyla-databriefs/1001/thumbnail.jp

25 Years After Prop 187 Report

ABOUT THIS REPORT This report provides a comparative look at the demographics of California and Los Angeles County electorate, voters, and residents from 1994 (“Then”) to the present (“Now”) to understand the impact of California Proposition 187 (1994). Data from the U.S. Census Bureau and the California Secretary of State are analyzed to study trends in the makeup of California and Los Angeles County. The proposition’s impact is captured through political representation, voter registration, and total population data examined as well as demographic shifts in the makeup of both the electorate and the voters by political affiliation and by race and ethnicity. For more information about these results, please contact Brianne Gilbert, Associate Director, at [email protected]://digitalcommons.lmu.edu/studyla-reports/1002/thumbnail.jp

Structural Studies on Dy to 119 GPa and Applications to Lanthanide Systematics

Abstract The Rare Earth elements (REE) are known to undergo crystallographic as well as electronic structure changes with applied pressure. On increasing pressure, the trivalent lanthanides follow the sequence hcp Sm-type dhcp fcc dfcc. In this report we present room-temperature high-pressure x-ray diffraction data for Dy as well as our observations on the post-dfcc phases and concomitant volume changes in the heavy REE

COVID-19 Public Opinion Survey Data Brief

ABOUT THIS STUDY The COVID-19 Survey conducted by StudyLA involved 15-minute telephone sessions and online surveys with 2,000 adults living in Los Angeles County (1,000 in the city of Los Angeles and 1,000 in the rest of LA County). The survey was conducted in both English and Spanish from March 23rd to April 8th, and respondents were asked a range of questions concerning the COVID-19 pandemic. ABOUT THIS REPORT Survey results are presented in two sections: (1) toplines, or total responses for each question, and (2) crosstabs, or all questions crossed by major demographics. The margin of error for the final sample of 2,000 respondents is ±2%.https://digitalcommons.lmu.edu/studyla-databriefs/1003/thumbnail.jp

MOSEL: Inference Serving Using Dynamic Modality Selection

Rapid advancements over the years have helped machine learning models reach previously hard-to-achieve goals, sometimes even exceeding human capabilities. However, to attain the desired accuracy, the model sizes and in turn their computational requirements have increased drastically. Thus, serving predictions from these models to meet any target latency and cost requirements of applications remains a key challenge, despite recent work in building inference-serving systems as well as algorithmic approaches that dynamically adapt models based on inputs. In this paper, we introduce a form of dynamism, modality selection, where we adaptively choose modalities from inference inputs while maintaining the model quality. We introduce MOSEL, an automated inference serving system for multi-modal ML models that carefully picks input modalities per request based on user-defined performance and accuracy requirements. MOSEL exploits modality configurations extensively, improving system throughput by 3.6$\times$ with an accuracy guarantee and shortening job completion times by 11$\times$

LA Votes: Vote Center Experience Data Brief – Final

The 2020 Presidential Primary Election Exit Poll asked LA County voters for whom and for what they voted and their overall voting experience at their respective vote centers. The following data brief reports on questions related to the vote center experience as well as knowledge about the switch from polling places for 3,596 respondents. See Addendum for questions crossed by the time the respondent voted.https://digitalcommons.lmu.edu/studyla-databriefs/1005/thumbnail.jp

HTA: A Scalable High-Throughput Accelerator for Irregular HPC Workloads

We propose a new architecture called HTA for high throughput irregular HPC applications with little data reuse. HTA reduces the contention within the memory system with the help of a partitioned memory controller that is amenable for 2.5D implementation using Silicon Photonics. In terms of scalability, HTA supports 4 × higher number of compute units compared to the state-of-the-art GPU systems. Our simulation-based evaluation on a representative set of HPC benchmarks shows that the proposed design reduces the queuing latency by 10% to 30%, and improves the variability in memory access latency by 10% to 60%. Our results show that the HTA improves the L1 miss penalty by 2.3 × to 5 × over GPUs. When compared to a multi-GPU system with the same number of compute units, our simulation results show that the HTA can provide up to 2 × speedup

Scaling Observation Error for Optimal Assimilation of CCI SST Data into a Regional HYCOM EnOI System

South Africa currently possesses no operational ocean forecasting system for the purpose of predicting ocean state variables including temperature,salinity and velocity. Substantial initial efforts towards this goal have been made and resulted in a system using a regional Hybrid Coordinate Ocean Model (HYCOM) along with the Ensemble Optimal Interpolation (EnOI)assimilation scheme. Assimilating only sea surface temperature (SST) observations from the Operational Sea Surface Temperature and Sea Ice Analysis (OSTIA) product into the system resulted in a degraded forecast. Aiming to address this, Climate Change Initiative (CCI) SSTs are assimilated into the system in an effort to improve the forecast skill. Observation errors in the assimilated product are used in the EnOI to determine whether more confidence should be placed in the model or observations in producing the analysis, but overconfidence in observations can shock the model and result in failure. To tweak the impact of the assimilation, a scaling factor is applied in the assimilation code. A scaling factor of 25 was found to produce a favourable result with lowest mean root mean square error (RMSE;1.098C) between the model and observations over time. Postulating the error to be overconfident, a floor value is introduced in order to set a minimum value for the observation error thereby reducing confidence in the observations. These experiments fared less favourably with a floor value of 0.5 and a scaling factor of 15 producing the best mean RMSE (1.118C)

Designing a Magnetic Measurement Data Acquisition and Control System with Reuse in Mind: A Rotating Coil System Example

Accelerator magnet test facilities frequently need to measure different magnets on differently equipped test stands and with different instrumentation. Designing a modular and highly reusable system that combines flexibility built-in at the architectural level as well as on the component level addresses this need. Specification of the backbone of the system, with the interfaces and dataflow for software components and core hardware modules, serves as a basis for building such a system. The design process and implementation of an extensible magnetic measurement data acquisition and control system are described, including techniques for maximizing the reuse of software. The discussion is supported by showing the application of this methodology to constructing two dissimilar systems for rotating coil measurements, both based on the same architecture and sharing core hardware modules and many software components. The first system is for production testing 10 m long cryo-assemblies containing two MQXFA quadrupole magnets for the high-luminosity upgrade of the Large Hadron Collider and the second for testing IQC conventional quadrupole magnets in support of the accelerator system at Fermilab