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UMN - Rochester

Transcript: Fragments are combined into 'contigs' by overlapping their sequences Teaching philosophies and curriculum development Genomics Dominate Themes (>100): Building a Curriculum With Modeling Tertiary Themes (<30) What variables matter? Sample Computation charting a path from the present to the future quantitatively... Are there relationships? Can we make equations? Future Projects What we might have missed... 3. How to get (and use) help outside their expertise... Karl Schmitt February 8th, 2013 1. How to solve problems... An Example Comparing Computer Science & Aggregate STEM Expansion of Genomics work STEM and Non-STEM students have similar expectations of learning activities Directive: Open Forum University of Minnesota - Rochester To Analyze: Current / Future Work Instructor Survey Instructors were surveyed for their perceptions of student expectations Questions mirrored student survey Responses received from 115 tenure-track faculty, 77 graduate students, and 68 other instructors Analysis of faculty perceptions (in progress) Comparison of faculty perceptions and student expectations Refine Student Survey Tool Improvements to pilot survey will be made based on faculty and student feedback The refined survey can be customized and available for individual faculty use What are the two most important things a quantitative faculty member can teach health science students? Examples: Policy Lexical Analysis future health professional What about infection spread throughout a city? future health professionals know... Even More Complex Models... Mammals have millions of base-pairs The recently sequenced pine had 16 billion base-pairs Expectations of Learning Activity Components Expectations of Learning Assessment Components Health-care policies Basic Disease Spread--- SIR Model Expectations of Learning Assessment Components Individualized movement Tracking interactions & infections Social networks To find the orientation (forward or reversed) for each contig which satisfies the most sets of mate-pairs We can predict a weight from the current age & weight, using statistical models and data... Expectations of Technology Components What are students interested in? Complex Systems & Networks can be applied to almost any problem.... Network Research Seniors expect more Discussion, fewer Demonstrations, and less use of the Chalkboard/Whiteboard compared to other students Open Ended Responses from The Orientation Problem Collaborative work in development with Dr. Carrie Eaton @ Unity College, Maine Can we define "evolution based rules" for building a graph structure? this needs an iterative algorithm, but students can design it! How to get (and use) help outside their expertise... Expectations of Learning Activity Components Faculty Misconceptions Students had the opportunity to comment on their perceptions of faculty misconceptions. Dominant themes included constraints on student time, student effort, and student attitude toward classes. Other themes were faculty communication, effectiveness of pedagogy, course pace, and overall comprehension. “We don't want to be engaged. I am very frustrated that so many of my classes are so geared toward the exam, yes I want to learn the information but I could just read a book. I want to be engaged.” “That students prefer an excessive amount of ‘easy’ questions on exams in comparison to a shorter amount of more difficult questions. “ “That the students know exactly what the faculty member expects of them…every teacher has their own standards and expectations.” “… many instructors fail to realize that we are simultaneously taking 3-4 other courses that are just as difficult as this one. Devoting yourself entirely to a single class just isn't possible.” We can then treat each contig as a node in a network, and the count of mate-pairs as edge weights Agent-Based Models & Simulations Secondary Themes (~40): Students tend not to expect E-Textbooks and Social Media Fewer Freshmen expect PowerPoint compared to other students Computational Methods Required! How to solve problems... Starting Interdisciplinary What do you need out? What tools are already being used? How to approach (huge amounts of) data? Abstract Quality learning is most likely to occur when teacher and student are communicating clearly and have shared expectations. Frequently, faculty are unclear about student expectations and/or have difficulty assessing them early in a semester. Yet, student expectations are important for faculty to understand for shaping their classroom environments. Understanding these varied expectations is considered to be integral in forming a responsive teaching environment. To address this concern we have created and piloted an online tool to evaluate undergraduate student expectations of course components (technology, instructor, learning assessment and learning activities) at the beginning of a semester. During the pilot survey, data was collected from 25 different courses at

UMN Biostatistics

Transcript: Biostatistics @ University of Minnesota What is biostatistics? Academic programs Applicant pool, Fall 2015 Why Minnesota? Disease mapping: What does the distribution of asthma cases in the United States tell us about environmental risk factors for asthma? Personalized medicine: Can we target treatments at groups/individuals with specific risk factors? Statistical genetics: Which combinations of genes put you at highest risk for heart disease? Diagnostic testing: How effective are population screening programs for breast and prostate cancer? More information MS Leading experts in a wide variety of areas, with particular strength in spatial statistics, Bayesian analysis, clinical trials, and statistical genetics. Undergraduate students whose eventual goal is to obtain a PhD are encouraged to apply directly to our PhD program. 209 total applicants MS/MPH 90 applicants, 53 accepted (59%) Averages for accepted students 3.64 GPA 165/155/4 GRE Q/V/AW PhD 119 applicants, 30 accepted (25%) Averages for accepted students 3.84 GPA 166/162/4 GRE Q/V/AW The development and application of statistical methods for solving scientific problems in human biology, public health, and medicine. In recent surveys, UMN has ranked #5-7 out of >40 biostatistics programs in U.S. Mathematical/computing skills Interpersonal/communication skills Curiosity about science Offering the MPH, MS, and PhD Basic math background (same for all programs): Calculus (3 semesters, up to multivariable) Linear Algebra (1 semester) Highly recommended: Courses in probability and mathematical statistics Useful for PhD admission: Real analysis @umnbiostat Faculty on Twitter: @DrJWolfson @JSKoopmeiners @docvock 2 year program Coursework in applied (mostly) and theoretical (bio)statistics, plus public health Written Exam, Master’s Thesis and Presentation Graduates are prepared to work as statistical collaborators and consultants in public and private research institutions. Dynamic students Sally Olander, major coordinator: "The best thing about being a (bio)statistician is that you get to play in everyone's backyard." - J. Tukey Applying 2 year program Coursework in applied (mostly) and theoretical (bio)statistics, plus public health Master’s Thesis, Presentation, and Practicum Graduates are prepared to work as interdisciplinary practitioners of statistics in public health. A "few" faculty research interests: Bayesian analysis, cancer, cardiovascular disease, causal inference, clinical trials, computational biology, diagnostic testing, dynamic treatment regimes, HIV/AIDS, machine learning, medical imaging, pulmonary disease, spatial statistics, sports statistics, statistical computing, statistical genetics, survival analysis. 26 faculty, 65 staff, ~60 students (40 PhD, 25 MS/MPH) Collaborations with research units across campus and around the world. Involved in grants totaling over $150 million. PhD What do biostatisticians do? A highly ranked program A diverse student body spanning multiple cultures and countries. Division of Biostatistics, School of Public Health Minneapolis, Minnesota Pre-requisites What kinds of problems do biostatisticians tackle? 4-5 year program Courses in theoretical and applied (bio)statistics Written and Oral Exams PhD Thesis and Defense Graduates are prepared to work as independent researchers at universities, government institutions (eg. NIH, CDC) and private companies. About Biostatistics World-class faculty UMN Biostatistics MPH Develop new statistical methods. Collaborate with biomedical scientists to help plan, design, and analyze clinical and population studies. Act as consultants for government, industry, and legal proceedings. Teach and fulfill administrative duties. What kinds of skills do biostatisticians need? UMN students have won prestigious national and international awards for their research. Some Masters, most PhDs have at least one peer-reviewed scientific publication before graduation.


Transcript: #UMNProud #UMNProud Each year, the University of Minnesota awards more than 10,000 degrees, including bachelor’s, master’s, professional, and doctoral. UM has innovated a number of breakthrough ideas, including the black box flight recorder, anti-AIDS drug Ziagen and 26 different varieties of apples. It was also where the first open heart surgery and first transplants of a pancreas and human bone marrow took place. Be a part of Tradition Be a part of Tradition The University of Minnesota has been celebrating Homecoming annually since 1914. Traditions include a bonfire, coronation, pep fest, parade, and football game. 1963 1963 Homecoming 2016 2016 Homecoming 2019 2019 The Department of American Indian Studies Celebrates 50 years! #UMNProud We are proud to highlight our faculty, students, and alumni. Spotlight Spotlight Dr. David Wilkins, a leading treaty scholar, teaches and writes in the areas of comparative politics, federal Indian policy and law, and Native governance. He has written, co-authored, edited, and co-edited eleven books and numerous articles and essays grounded in soverignty. Faculty Faculty Summer Lara Fisheries & Wildlife, Dakota Language Sisseton Wahpeton Oyate Students Students Anthony Johnson Finance Red Lake Ojibwe Payton Counts Fisheries & Wildlife, Dakota Language Sisseton Wahpeton Oyate Lennixx-Rodney Lee Cultural Studies & Comparative Lit Dakota Vanessa GoodThunder American Indian Studies, Dakota Language and DirecTrack to Teaching Lower Sioux Aumnae 2016 Alumni Alumni Vanessa has completed her Masters' of Education and is opening a Dakota immersion school this June in Minnesota, where only five Dakota first-language speakers remain. Gov. Mark Dayton declared Dec.8 Vanessa Goodthunder Day in Minnesota. Student Life Student Life Academic There are over 150 different majors to choose from. Academic AccountingActingAerospace Engineering and MechanicsAfrican American and African StudiesAgricultural & Food Business ManagementAgricultural Communication and MarketingAgricultural EducationAgronomy MinorAmerican Indian StudiesAmerican StudiesAnimal ScienceAnthropologyApparel DesignApplied EconomicsApplied Psychology MinorArchitectureArtArt HistoryAsian American Studies MinorAsian Languages and LiteraturesAstrophysicsAustrian&Central European Studies MinorBachelor of Individualized StudiesBiblical StudiesBiochemistryBiologyBiology, Society, and EnvironmentBiomedical EngineeringBioproducts and Biosystems EngineeringBusiness and Marketing EducationBusiness Law MinorChemical EngineeringChemistryChicano-Latino StudiesChild PsychologyCivil EngineeringClassic & Near Eastern Archaeology MinorClassicsClimatology MinorCoaching MinorCommunication StudiesComparative U.S. Race & Ethnicity MinorComputer EngineeringComputer ScienceConstruction ManagementCorporate Environmental Management MinorCultural Studies & Comparative LitDanceDanish MinorDental HygieneDesign MinorDutch Studies MinorEarly ChildhoodEarth SciencesEcological Engineering MinorEcology, Evolution and BehaviorEconomicsElectrical EngineeringElementary Education FoundationsEnglishEntomology MinorEntrepreneurial ManagementEnvironmental EngineeringEnvironmental Geosciences MinorEnvironmental Sciences, Policy and MgmtFamily Social ScienceFamily Violence Prevention MinorFashion Studies MinorFinanceFinance & Risk Management InsuranceFinnish MinorFisheries, Wildlife, Conservation Bio.Food ScienceFood SystemsForest and Natural Resource ManagementFrench and Italian StudiesFrench StudiesGender, Women and Sexuality StudiesGenetics, Cell Biology, and DevelopmentGeoengineeringGeographic Information Science MinorGeographyGerman MinorGerman, Scandinavian, DutchGLBT Studies MinorGlobal StudiesGraphic DesignGreek MinorHealth Services ManagementHistoryHistory of Science, Tech., Med. MinorHorticulture MinorHousing and Community Development MinorHuman Resource DevelopmentHuman Resources and Industrial RelationsIndividually Designed InterdepartmentalIndustrial and Systems EngineeringInformation Technology InfrastructureInformation Technology MinorIntegrated Degree ProgramIntegrated Pest Management MinorInter-College ProgramInterior DesignInternational Agriculture MinorInternational BusinessItalian StudiesJewish StudiesJoint Military Science Leadership MinorJournalism and Mass CommunicationKinesiologyLandscape Design and PlanningLatin MinorLeadership MinorLinguisticsManagement Information SystemsManagement MinorManufacturing Operations ManagementMarine Biology MinorMarketingMass Communication MinorMaterials Science and EngineeringMathematicsMechanical EngineeringMedical Laboratory SciencesMedieval Studies MinorMicrobiologyMortuary ScienceMultidisciplinary StudiesMusicMusic EducationMusic TherapyNative American Env. Knowledge MinorNeuroscienceNorwegian MinorNursingNutritionOjibwe LanguageOutdoor Recreation and Education MinorPharmacology MinorPhilosophyPhysicsPhysiologyPlant and Microbial BiologyPlant SciencePolitical SciencePortuguese Studies It is important to stay


Transcript: The Orientation Problem Massive amounts of data exist: Individual Patients (GB's/TB's) & Comparable Patients (>>Peta-bytes) Is the patient similar? Should we use the same drugs? Modular Structure in Turkey Assessing Student Expectations Future Projects A man died several hours ago, how do we determine when? Networks and Genome Assembly Glimpses of the Present, Future and a path between them.... Network Research A Sample Model & Why Each fragment is sequenced from the ends making two "reads" and one "Mate-pair" Cohen, T.; , "Medical and information technologies converge," Engineering in Medicine and Biology Magazine, IEEE , May-June 2004, doi: 10.1109/MEMB.2004.1317983 Virtual Autopsies Karl Schmitt University of Maryland, College Park Filmed March 2, 1992 Fictional Year 2368 Finding an exact solution is NP-Hard Network Research Students vs. Faculty Perception Personalized Medicine Networks are frequently designed using attachment rules, then tested for equivalence to biological or empirical networks... What happens when we instead take ecological and evolutionary rules into account and use those to evolve our networks? Collaborate work in development with Dr. Carrie Eaton @ Unity College, Maine Real data sets are: Large Noisy Component Expectation vs. Value--Microbiology We have a patient on experimental drugs and want to know when the next dose can be safely given... how? Spring 2012 288 instructors across all disciplines at University of Maryland, College Park 'Growing' Networks using Evolution Dissipation MODELS A brief introduction General Research Goals: Student Survey Health, Science and Mathematics Genome Assembly -- Orientation Problem Contributing to Personalized Medicine Turning Data into Diagnoses Utilizing Networks TEDx 2011 Daniel Kraft-- "Medicine's Future, there's an App for that" Several additional algorithms remain to be explored for breaking apart genomic data More parameters and data validation can be incorporated into the ordering schemes in use Why Networks (or graphs)? Provide generic framework for relationships A lot of already established tools Already in wide-spread use for many biological investigations We can then treat each contig as a node in a network, and the count of mate-pairs as edge weights Specific Class Analysis Synchronization of Nonlinear dynamics We can predict a weight from the current age & weight, using statistical models and data... My Education Research 27 Instructors; 25 courses 816 undergraduate students enrolled in STEM courses Jamie Heywood TEDMed 2009 from Learning Assessment Expectations Portable, Personal Medicine Data from 200 level General Microbiology course 167 Students ~4-6 weeks into semester Questions & Discussion? Students... Thank You Fragments are combined into 'contigs' by overlapping their sequences How to Personalize? ASSESSMENT! Now: Off-The Shelf devices exist to self-monitor Populations are becoming more educated You can contribute: Better designed applications & devices Tailored health plans Medical knowledge & Relevance Instructor Survey Participant Summary Utilizing Networks Thermodynamic MODELS Previous Projects References & Acknowledgements Data from 6 Sophomore level courses ~150 Students in each department (CS/BIO/CHEM) Genome Sequencing --> A Network The orientation problem is to find a set of orientations (+/-) for each contig so that the most mate-pairs are satisfied Teaching Philosophies & Curriculum Development My Discipline Research Data -> Diagnosis “Student Expectations from CS and other STEM Courses” to appear April 2013 in Journal of Computing Sciences in College “A survey tool for assessing student expectations early in a semester” – Under revision for Journal of Microbiology & Biology Education “Expecting a Chasm: the gap between Student Expectations and Instructor’s Perceptions” – In preparation Data gathered while a Graduate Teaching Fellow through University of Maryland’s Center for Teaching Excellence (CTE) Teaching Cohort: Karl Schmitt, Abdel-Hameed Badawy, Elise Larsen, Katie Hrapczynski, Matthew Miller, Mara Dougherty, Artesha Taylor, Breanne Robertson, Andrew Andrew Assisting Investigators from CTE: Spencer Benson, Sabrina Kramer, Alexis Williams, Emily Grossnickle Statistical MODELS Table of Questions What Exists in 2013? Expected Course Components for 200-Level Courses Expansion of Genomics work (and Faculty Perceptions) Dissertation work. Publications are in preparation What Students Should be Prepared for... Find new collaborators with interesting problems! Any field that is interested in connections and relative relationships is a viable candidate.... General interest is algorithms development •“Complex Dynamics and Synchronization of Delayed-Feedback Nonlinear Oscillators”, Thomas E. Murphy, Adam B. Cohen, Bhargava Ravoori, Karl R. B. Schmitt, Anurag V. Setty, Francesco Sorrentino, Caitlin R.S. Williams, Edward Ott, and Rajarshi Roy. Philosophical

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