Incorporating prior information into association studies.

UnlabelledRecent technological developments in measuring genetic variation have ushered in an era of genome-wide association studies which have discovered many genes involved in human disease. Current methods to perform association studies collect genetic information and compare the frequency of variants in individuals with and without the disease. Standard approaches do not take into account any information on whether or not a given variant is likely to have an effect on the disease. We propose a novel method for computing an association statistic which takes into account prior information. Our method improves both power and resolution by 8% and 27%, respectively, over traditional methods for performing association studies when applied to simulations using the HapMap data. Advantages of our method are that it is as simple to apply to association studies as standard methods, the results of the method are interpretable as the method reports p-values, and the method is optimal in its use of prior information in regards to statistical power.AvailabilityThe method presented herein is available at http://masa.cs.ucla.edu

Partnering to Teach Orienteering: The UT Libraries\u27 and UT Outdoor Program\u27s Experience

Working with departments on campus to foster and support learning is a fundamental component of the University of Tennessee (UT) Libraries’ service philosophy. Academic libraries that have a broader view of the traditional liaison model and seek to develop unique and non-departmental relationships can raise their profile on campus (Dahl 2007, 3). An example of such a relationship, one that has provided a real life collaborative learning experience for students, is the partnership between the UT Libraries and the University of Tennessee Outdoor Progr am (UTOP) to teach orienteering

The Dark Energy Survey Data Management System

The Dark Energy Survey collaboration will study cosmic acceleration with a 5000 deg2 griZY survey in the southern sky over 525 nights from 2011-2016. The DES data management (DESDM) system will be used to process and archive these data and the resulting science ready data products. The DESDM system consists of an integrated archive, a processing framework, an ensemble of astronomy codes and a data access framework. We are developing the DESDM system for operation in the high performance computing (HPC) environments at NCSA and Fermilab. Operating the DESDM system in an HPC environment offers both speed and flexibility. We will employ it for our regular nightly processing needs, and for more compute-intensive tasks such as large scale image coaddition campaigns, extraction of weak lensing shear from the full survey dataset, and massive seasonal reprocessing of the DES data. Data products will be available to the Collaboration and later to the public through a virtual-observatory compatible web portal. Our approach leverages investments in publicly available HPC systems, greatly reducing hardware and maintenance costs to the project, which must deploy and maintain only the storage, database platforms and orchestration and web portal nodes that are specific to DESDM. In Fall 2007, we tested the current DESDM system on both simulated and real survey data. We used Teragrid to process 10 simulated DES nights (3TB of raw data), ingesting and calibrating approximately 250 million objects into the DES Archive database. We also used DESDM to process and calibrate over 50 nights of survey data acquired with the Mosaic2 camera. Comparison to truth tables in the case of the simulated data and internal crosschecks in the case of the real data indicate that astrometric and photometric data quality is excellent.Comment: To be published in the proceedings of the SPIE conference on Astronomical Instrumentation (held in Marseille in June 2008). This preprint is made available with the permission of SPIE. Further information together with preprint containing full quality images is available at http://desweb.cosmology.uiuc.edu/wik

From Human Days to Machine Seconds: Automatically Answering and Generating Machine Learning Final Exams

A final exam in machine learning at a top institution such as MIT, Harvard, or Cornell typically takes faculty days to write, and students hours to solve. We demonstrate that large language models pass machine learning finals at a human level, on finals available online after the models were trained, and automatically generate new human-quality final exam questions in seconds. Previous work has developed program synthesis and few-shot learning methods to solve university-level problem set questions in mathematics and STEM courses. In this work, we develop and compare methods that solve final exams, which differ from problem sets in several ways: the questions are longer, have multiple parts, are more complicated, and span a broader set of topics. We curate a dataset and benchmark of questions from machine learning final exams available online and code for answering these questions and generating new questions. We show how to generate new questions from other questions and course notes. For reproducibility and future research on this final exam benchmark, we use automatic checkers for multiple-choice, numeric, and questions with expression answers. We perform ablation studies comparing zero-shot learning with few-shot learning and chain-of-thought prompting using GPT-3, OPT, Codex, and ChatGPT across machine learning topics and find that few-shot learning methods perform best. We highlight the transformative potential of language models to streamline the writing and solution of large-scale assessments, significantly reducing the workload from human days to mere machine seconds. Our results suggest that rather than banning large language models such as ChatGPT in class, instructors should teach students to harness them by asking students meta-questions about correctness, completeness, and originality of the responses generated, encouraging critical thinking in academic studies.Comment: 9 page