Syllabus
Contents
Syllabus#
MEM T680: Data Analysis and Machine Learning for Science and Manufacturing#
Instructor Information#
Name: Joshua C. Agar Office: XXX Email: jca92@drexel.edu Office Hours: XXX
Class Information#
Dates: Sep 19, 2022 - Dec 10, 2022 Times: Tuesday/Thursday 02:00 pm - 03:20 pm Class Room: Randell 238A
Course Description#
This course will demonstrate how to leverage computational of data analysis and machine learning in experimental science and manufacturing. This course will provide a survey of methodologies and tools which can be used to accelerate data analysis, data management, and visualization, on a pathway towards increased automated real-time analysis. The course is not meant to provide a detailed algorithmic understanding of methods, but instead provide the knowledge to be a practitioner of computation and machine learning methods.
Who this Course is Designed for?#
This course is meant to be accessible to all.
While machine learning requires a lot of mathematics this course will not require a deep understanding of mathematical methods.
It you have a deep understanding of mathematics I implore you to use it.
We look at machine learning as the assembly of simple mathematical functions.
Our goal will be for you to develop a practical mathematical intuition for machine learning.
The only prerequisite is that you know how to code and understand basic programing logic. This course will be taught it Python. If you know Python already thats great. If not, you can learn as you go. We have diverse experiences and backgrounds. This course is designed to extend the knowledge of people at all levels. Everyone, based on their background will get something different out of this course, and that is great!
Course Objectives#
After this course you should be able to:
Navigate the open source python ecosystem
Understand data structures and basics of databases
Hone your skills in automated data visualization
Basic understanding of supervised and unsupervised linear machine Learning
Exposure to a variety of deep learning topics
Classification and regression
Theory and optimization methods in deep learning
Segmentation techniques
Generative and Predictive models
Physics-informed and physics-constrained machine learning models
Course Schedule#
| Date | Lecture 1 Topic | Lecture 2 Topic | Homework |
|---|---|---|---|
| Week 1: 9/19 | Introduction to the course, Importance of Data Analysis | Modern Challenges in Scientific Data Analysis and Machine Learning | Homework 1: Building a Metadata Schema |
| Week 2: 9/26 | Setting up your computing environment, Introduction to Collaborations in Git | What you can do with machine learning? | Homework 2: Basics in Python |
| Week 3: 10/3 | Travel Makeup - One-on-One Meeting for Projects | Travel Makeup - One-on-One Meeting for Projects | Homework 3: Project Planning |
| Week 4: 10/10 | Introduction to Python: Variables, Operators, and Data Types | Introduction to Python: Flow Control, Loops, Functions,and Generators, | Homework 4: Building a Game of Craps |
| Week 5: 10/17 | Introduction to Python: Lambda Functions, Classes, *args and **kwargs, and Decorators | Numpy, Scipy, and Visualization | |
| Week 6: 10/24 | Databases and Scientific Data Management Systems | Introduction to Linear Supervised Learning | Homework 5: Data Management and Visualization |
| Week 7: 10/31 | Introduction to Linear Unsupervised Learning | Introduction to Deep Learning with Classifiers | |
| Week 8: 11/7 | Optimization Methods, Regularization, and Activation Functions | Neuron Types and Message Passing | Homework 6: TBD |
| Week 9: 11/14 | Regression from Images and Segmentation | Unsupervised Learning Autoencoders | Homework 7: TBD |
| Week 10: 11/21 | Physics Constrained and Physics Informed Neural Networks | **No Class Thanksgiving** | Homework 8: TBD |
| Week 11: 11/28 | Project Presentation | Project Presentation | |
| Week 12 | Final Exam |
Textbook, Computing, and Software#
Textbook: Open source software is evolving so fast that by the time a textbook is published it is nearly outdated. The best source of information comes from the software packages documentation.
Computing and Software: There are no specific computing requirements for this course. You likely could get by with a cell phone or a tablet, however, I would strongly recommend a computer with Linux, Windows, or MacOS. All software used will be open source. For some assignments we will require access to a Graphical processing unit (GPU). You will be required to purchase a subscription to Google Collaboratory for the deep learning section of the course. The cost of this is $10/month.
In-class Activities#
I cannot teach you how to code and solve problems using computational tools. Learning coding requires practice, practice, and more practice. The course is designed to provide sufficient practice with coding to increase your confidence in using computational tools. Programming takes a day to learn but a lifetime to master. To assist in learning we will have in class activities. We expect that you fully participate in these activities. These will be turned in and graded for credit.
Homework#
You will be assigned homework problems to increase your experience with independent problem solving. While it is allowed, and expected that you talk with your colleagues about the homework assignments it is expected that homework is completed independently. When completing homework it is acceptable to talk about code, or even look at each others code; however, it is not acceptable to share, or copy sections of code from one another.
Class Attendance and Participation#
It is essential to your success in this course that you attend each lecture and participate in the activities and discussions. Therefore, you are expected to attend each lecture and to show up on time. Should you need to miss a class for any reason, you are to contact the instructor in a timely manner. Reasons for missing lecture must be documentable and presented, if requested. You are responsible for any material covered, any work assigned, or any course changes made during the lecture. Prof. Agar will make reasonable efforts to provide missed material for approved absences. We will have in class activities. Missed in class activities will be required to be completed as homework within one week.
Exams#
We will have two exams, a midterm and a final. The exams will be in a mixed format. About 50% of the exam will be closed-book pen-and-paper style. The second half of the exam will be open resource - including the web - independent programing and problem solving.
Final Project#
This course will include a final project and presentation. The goal of this project is to apply the tools and concepts taught in this course to a problem that interests you. This project is intentionally open-ended. Example projects might include: building a data management workflow for a process in your company or research,developing an interactive dashboard and data visualization tool, or developing an automated analysis pipeline for a task of interest. To determine the topic for your project you will submit a one-page whitepaper and a logical diagram of your proposed project. See Final Project description page for more details.
Assignment Submission Format#
All assignments should be submitted in a professional digital format. In this course assignments will be submitted in a variety of formats (e.g., ipynb, github repositories, etc.). Submissions will only be accepted in the format specified in the assignment.
Regrade Policy#
If you are of the opinion you deserve more credit than provided to you after your homework was graded, provide a written document explaining why you are of the opinion you desire this credit within a week of receiving the graded assignment. You are welcome to discuss homework questions or concerns with Prof. Agar prior to submitting request for regrading. Grade modifications will only happen after a formal request is submitted.
Drexel University Attendance Policy#
Excused Absences due to University Sponsored Activities#
Many students participate in University-sponsored activities in which they represent the University or their academic college or department. Such activities may cause a student to be absent from class. In those instances, such absences qualify as “excused absences” which means that the absence, with proper prior arrangement, is not subject to penalty. Any missed coursework should be satisfied through agreement between the instructor and the student. Some examples of events that may qualify for excused absence include athletic competition, research or a presentation in which the student is an integral member of the presenting team, musical or performing arts events. To determine if an event qualifies as an excused absence, students are encouraged to discuss the activity with their instructor(s) and academic advisor prior to the absence.
Students seeking approval for an approved absence are responsible for notifying their instructor(s) at least two (2) weeks in advance of such absences. If the activity is at the beginning of the term or is the result of a particular level of achievement in an activity (i.e. qualifying for a post season tournament in athletics), students should notify their instructor(s) as soon as possible. Instructors are expected to make reasonable accommodations for these class absences including administration of make-up assignments and exams whenever possible. Please note, however, that the requirements of some courses or programs may preclude such accommodations. It is expected that students seeking an excused absence will work with their instructor(s) to develop a plan and timetable to make up the missed coursework.
Other Absences#
Unforeseen events or circumstances may occur that cause a student to be absent from class. These could include personal or family illness, bereavement, accident, or a catastrophic event such as fire. If such issues arise, students are encouraged to notify their instructors as soon as possible to explain their absence from class. In doing so, students should review the syllabi for their courses with particular attention given to the instructor’s statements on course attendance and/or absences. Jointly, the student and instructor will develop a plan, with a timetable, to make up missed coursework. Instructors are expected to make reasonable accommodations for these class absences including administration of make-up assignments and exams whenever possible.
If an instructor is concerned that a student is providing false information regarding the reasons for their absence from class, the matter should be referred to the Dean or Dean’s designee for additional inquiry. Providing false information regarding the reasons for a course absence may be a violation of the Student Code of Conduct and result in disciplinary action, as appropriate.
Religious Observances#
Students should review the Religious Observances Statement in the event they are seeking an excused absence for a religious observance
Extended Absences#
In the event of extended absence where several classes have been missed, students should explore options other than those described above, such as requesting an Incomplete grade (please reference the Incomplete Grades Policy) or withdrawal (please reference the Course Withdrawal Policy). It is strongly recommended that students consult with their academic advisor to determine the best course of action given the circumstances, academic progression, and goals.
In the event of an extended absence due to a chronic medical condition or disability, students are strongly advised to contact (1) the Office of Disability Resources to explore potential accommodations that may be available and (2) their academic advisor to explore possible academic options. A student’s academic advisor can review policies governing such options as withdrawal or incomplete grade and discuss the potential impact of electing these options.
Prof. Agar’s Attendance Policy#
Prof. Agar will approve absences associated with any physical or mental health requests, family emergency, religious request, or any other reasonable requests. Note that it is not a requirement that you disclose any specific details regarding your reason for requesting absenteeism. The requirement is that you specify, for instance, that the request is health or religion related. You should not feel the need to disclose the nature of your health issue or your religious affiliation. If absence is requested for an extended period of time a letter from a external professional representative (e.g., a doctor, a clergy member) might be requested. This letter should merely state the dates when you will be absence and the categorical reason for your absence (e.g., religious).
COVID-19#
We are in the midst of an unprecedented pandemic. We want to ensure the safety of our community. As a result, if you feel as if you are exhibiting COVID-19 symptoms, or had a possible exposure please refrain from coming to class. I will make sure to simulcast the lectures online as long as the request is made prior to the start of lecture. Upon request, we might switch from a mask-option to mask-required policy.
Homework#
The only way to learn coding is to solve problems! It is essential for students to complete all of the homework assignments. The purpose of homeworks will for you to practice the concepts covered in class. Completing all the homework problems is the best way to practice and prepare for quizzes and exams. \ If you need or desire an extension on any homework or lab for any reason, contact Prof. Agar in a timely fashion, as permitted by the need. There is no guarantee that you will receive an extension on any assignment, so plan your schedule carefully. Finally, you are encouraged to work with others on homeworks. Learning is a social activity! However, do not simply use others to do your work but rather use others to help work through and engage in the concepts. If you work with others on written homeworks, indicate on your assignment with whom you worked. \emph{Plagiarism is unacceptable} and will result in a zero grade for all persons involved, and will result in serious academic repercussions.
Homework should be submitted as a professional document, All homework should be submitted digitally. If you are of the opinion you deserve more credit than provided to you after your homework was graded, provide a written document explaining why you are of the opinion you desire this credit within a week of receiving the graded assignment. You are welcome to discuss homework questions or concerns with Prof. Agar prior to submitting request for regrading. Grade modifications will only happen after a formal request is submitted.
Exams#
There is a midterm and a final exam. You are expected to be present, seated, and ready to take the exam before the exam begins. The exam will have two parts. The first will be a closed book pen and paper style exam. The second part will be a problem solving exercise to be completed on a computer. You are required to follow the guidelines for the exams. Any violation of this policy is a violation of the university’s Academic Integrity Policy.
There will be no make-up exams. If an exam is missed because of an emergency please contact Prof. Agar to make arrangements. If there is a known scheduling conflict with an exam it is expected that you notify Prof. Agar at least 1 week prior to the exam, or when the scheduling conflict arises. \
The final exam is comprehensive and will be given during the University assigned exam time for the course. The exact time and location will be announced later in the semester. The final exam will only be given at the announced time. If a student has a conflict with another final exam, the student must contact their instructor at least two weeks in advance in order to have it resolved.
Grading Rubric#
| Topic | Percentage |
|---|---|
| Homework | 40 |
| Midterm | 15 |
| Final Presentation | 25 |
| Final Project | 20 |
Grading Scale#
| Score | Grade |
|---|---|
| A | 93-100 |
| A- | 90-92 |
| B+ | 87-90 |
| B+ | 87-90 |
| B | 83-86 |
| B- | 80-82 |
| C+ | 76-79 |
| C | 73-75 |
| C- | 70-73 |
| D | 60-69 |
| F | <60 |
Note, Prof. Agar has the discretion to curve the class grades. Curves will never be applied in a way that decreases your grades below what is specified in the grading scale.
Getting Help#
Be proactive about your success in the course! If you need help, there are many resources available to help you. Your first primary contact for help is the instructor. If you are struggling, attend office hours or send an email or teams message. Do not wait to bring issues, course related or otherwise, to the attention of the instructor. If you cannot attend office hours, send an email to the instructor to try to make other arrangements.
Accommodations for Learning Differences#
Prof. Agar welcomes individuals with learning differences and is committed to ensuring equal access so that all students can live, learn, and lead at Drexel. To request accommodations a current Accommodations Verification Letter (AVL) in the ClockWork database is required before accommodations can be made. These requests are received by Disability Resources (DR), who then issues the AVL to the appropriate contacts. For additional information, visit the Disability Resources website, or contact DR for more information by phone at 215.895.1401, or by email at disability@drexel.edu.
Students who are approved for accommodations at Drexel should share this letter and discuss their accommodations and learning needs with instructors as early in the semester as possible. Prof. Agar will do everything possible to accommodate students needs. If you feel that your accommodations are not being met please make sure to contact Prof. Agar.
Agar understands that there are inequities in access to testing required to get approved for accommodations. If you feel that you have learning difference that influence equity in your classroom performance please reach out to Prof. Agar. He will work with you to try and accommodate your learning differences.
Faith/Tradition Observance Policies#
Prof. Agar extends hospitality to all persons regardless of race, religion, ethnicity, sexual orientation, economic or social background.
Prof. Agar honors the free exercise of religion. People from a wide variety of religious traditions live and work at Drexel, and the demands of religious observance in some traditions may cause conflicts with classroom and work schedules.
Prof. Agar will exempt any person who requests an absence due to the demands of religious holiday observance. Of course, nothing exempts a student from meeting course requirements or completing assignments, so the student will have to negotiate with the instructor any make-up work.
Accommodations are to be dealt with on the basis of individual requests from students. Recall that religious holidays are numerous, and no holiday is privileged above another.
If you encounter a schedule conflict with your course work due to the demands of religious observance, here is what you should do:
Talk with your instructor and indicate that you will be absent from class due to observance of religious holidays.
Arrange with the instructor to complete assignments.
For any further questions please refer to Drexel’s Religious Accommodation Policy
Counseling Services#
College can be a time of uncertainty, inquiry, expansion, and adaptation for many students. Know that my office and conversations with me are a safe place. Personal information told to me in private will remain confidential. The only exception is sexual misconduct or if I feel that you are at risk of harming yourself or others. If this information is relayed to me I have an obligation to notify the dean of students. If an issues arises I promise to do my best to facilitate you getting the help you need to resolve your issues. I do not, however, have professional training in counseling or crisis management.
Students at Drexel have access to the Office of Counseling and Health Services.
Currently the following services are offered:
or more specific information about each of these options, please select from the menu on the left.
GROUP COUNSELING#
The Counseling Center offers a variety of groups each quarter. Some groups are time-limited with a specific focus, while others are broader and open-ended. Please see the group descriptions here for more information about groups currently offered at the Center. If you are interested in joining a group that is not currently being offered, please email counsel@drexel.edu.
INDIVIDUAL COUNSELING#
The personal concerns of Drexel students vary greatly, and our Counseling Center offers goal-focused individual counseling for support. Students initially meet with a therapist for an assessment to discuss their presenting concerns and to determine the type of services which will best meet their needs.
WELLNESS WORKSHOPS#
The Counseling Center offers several Emotional Wellbeing Workshops throughout the term that offer information, coping strategies, and tools to address common concerns faced by college students. We know that Drexel students are incredibly busy and can benefit from quick and useful tools for common presenting concerns. Workshops meet once a week for a series of 3-4 weeks for 50 minutes. Our Wellness Workshops are formatted so that you can expect a classroom-style learning environment, and you can share as much or as little as you want. Each workshop comes with a student workbook that allows you to practice new skills between sessions. Click here to see which Workshops are currently being offered.
If you are interested in attending any (or all!) of the workshops, schedule an Initial Consultation and tell your counselor. If you are already seeing a therapist at the Counseling Center, tell them you are interested in a workshop. You are free to do more than one workshop and to repeat them as often as you like! Check with the front desk for current scheduling and availability. When scheduled for an Emotional Wellbeing Workshop, you must come to each session on time, as the sessions build upon each other.
COUPLES COUNSELING#
Couples counseling is available for students and their partners if both are currently enrolled as full-time students at Drexel University. If your partner is not enrolled at Drexel, you may contact us for information on community referral resources. Couples of all genders and sexual orientations are welcome!
OUTREACH PROGRAMS#
The Counseling Center offers a variety of outreach to campus partners - including faculty and staff, student groups, and campus organizations - to promote wellness and resiliency, destigmatize mental health, and offer preventative interventions using a social justice lens. To schedule an outreach or for more information, please visit here.
CONSULTATION#
If you are concerned about a friend, student or family member; want advice about how to encourage someone you care about to get help; or you have general questions about our services; contact the Counseling Center at 215.895.1415 to request a consultation. We will have a counselor contact you to discuss further.
For faculty and staff who may wish to consult with a counselor, or who want to learn more about how and when to make a referral, please see our Faculty and Staff Resource section.
REFERRAL SERVICES#
Our Case Manager is available for students who would like assistance connecting with an off-campus mental health provider. The Counseling Center may make a recommendation for a student to be referred off-campus when a student may be better suited for specialized care and/or when the student’s needs fall outside the scope of the Center’s brief, goal-focused model. Our Case Manager also assists in navigating insurance and helping think through the type of care and provider you might be interested in working with in the community. The Case Manager will also be sure to follow up with you to see if you need any further assistance.
If you are currently in crisis, please contact our on-call counselor at 215.416.3337. If this is a psychological emergency and you need immediate attention, please dial 911, call Drexel Public Safety at 215.895.2222, or visit your nearest emergency room.
Gender and Sexual Identity#
People commonly use gender and sexual orientation as part of their identity. A person’s identity should not be assumed based on societal norms or constructs as they are not related to a person’s self-identity. Unfortunately, English uses gendered pronouns. A culture of pronoun sharing will be cultivated in my classroom. If you do not know someone’s pronouns, it is preferred to use identity-agnostic (they/them) pronouns until you hear from them directly. Prof. Agar will not tolerate any bias or discrimination based on a person’s likeness or identity.
Email Policy#
Drexel University has established email as a primary vehicle for official communication with students, faculty, and staff. All email communication in this course should be done using your @Drexel.edu email account. Due to federal laws, such as FERPA, emails coming from a non-drexel email may not receive a response. Please, title emails with MEM~T680: [Email Issue], where email issue is a summary title of the content of the email. This is to help ensure that your email is noticed and responded to.
Prof. get tons of junk mail, taking these steps will ensure that your emails are attended to.
Prof. Agar will do his best to respond to email requests within 24 hours.
If Prof. Agar has not responded in 24 please send him a reminder, email inboxes can become black holes.
Long and complicated technical issues related to the course are best addressed during office hours
Academic Integrity Policy#
Drexel University expects all members of its community to uphold the highest values of academic integrity. In upholding these values, the University is committed to investigating any allegation of violations of academic integrity against a student. Violations include, but are not limited to: plagiarism, cheating, fabrication, and academic misconduct.
Sanctions for violations of academic integrity are administered through the Office of Student Conduct and Community Standards in conjunction with the Office of the Provost and other University offices as deemed appropriate. It is generally the responsibility of the faculty member overseeing the academic activity to report the violation to the Office of Student Conduct and Community Standards and to determine the appropriate sanction. A student who believes they have been wrongly sanctioned has a right to an appeals process.
In addition to any other sanction, the University reserves the right in its sole discretion to withdraw an earned degree even though it has been granted should it be discovered at any time that the work upon which the degree was based, or the academic records in support of such degree, have been falsified. In that situation, the degree will be withdrawn promptly upon discovery of the falsification and the academic record will be updated to reflect the withdrawal of degree.
Student Code of Conduct#
Student Conduct & Care seeks to create and maintain a process that is transparent and equitable for Students and Student Organizations. The policies and process described on this website have, in some cases, been paraphrased to provide a general understanding. The full Code of Conduct (the Code) can be downloaded for review.
Conduct Creed Student Conduct & Care has established, in accordance with its mission, vision, and values, a code of high standards of behavior to include the following expectations for Students and Student Organizations to:
Accept responsibility when their choices or actions have negatively impacted themselves, others, or the community at large.
Engage in constant learning, practice self-reflection, and develop resilience to maintain academic, personal, and professional integrity.
Foster positive relationships with others.
Ensure the health, wellness, and safety of themselves and their communities.
Demonstrate mutual respect and equity within the bounds of the Code of Conduct.
Defining Drexel’s Culture of Inclusion#
At Drexel University, we are committed to fostering an inclusive and welcoming environment based on integrity, trust and respect. We view the diversity of our students, faculty, professional staff and partners as our strength. As such, we strive to create a culture where everyone can leverage their uniqueness to foster innovation because they feel a sense of belonging.
We define diversity as the differences that make us uniquely who we are. This includes both individual (personality, values, attitudes, etc.) and other dimensions of difference including ideological, intellectual, economic, gender, gender identity, ability, sexual orientation, religious, age, racial, cultural, ethnic, visible and invisible disabilities, veteran status, nationality, and all the diversity of our students, faculty, professional staff, alumni, and other partners.
To maximize the strength that our diversity brings, we center equity, inclusion and belonging, and incorporate an anti-racism approach to our strategic plan, organizational systems, policies, and structures.
Anti-racism#
The active process of identifying and ending racism by changing our organizational systems, policies and structures to redistribute power and resources more equitably among all individuals, both at the personal and systemic levels.
Belonging#
A sense of psychological safety that affords the ability for each member of the Drexel University community to be their authentic self without fear of judgement, where everyone can perform at their best because they feel accepted, respected, valued and heard.
Equity#
The process by which we aim to achieve fairness through reallocation of University resources and opportunities such that policies, structures, and their implementation work to eliminate historical, systemic disadvantage for the benefit of everyone. This requires providing varying levels of support both at the individual and systemic levels.
Inclusion#
We adopt Association of American Colleges and Universities’ definition of inclusion as: The active, intentional, and ongoing engagement with diversity—in the curriculum, in the cocurriculum, and in communities (intellectual, social, cultural, geographical) with which individuals might connect—in ways that increase awareness, content knowledge, cognitive sophistication, and empathic understanding of the complex ways individuals interact within systems and institutions.
Institutional Racism#
Institutional polices, processes and biased practices that favor white people over Black, Indigenous, and People of Color.
Racism#
Racial prejudice based on unfounded beliefs and irrational fear combined with institutional power. This can be at the individual level (conscious and subconscious beliefs and actions that promote racism), the interpersonal level (racist slurs or actions), and systemic level (in institutions).
Respect Policy#
Respect for My Students#
I will come prepared to help you understand the course material and prepare you for quizzes/exams.
Communication is key: I cannot help you if I do not know what is going on.
I am here to help you, this is your time, so let me know what I can do to help you succeed.
If there is something that you would like me to do differently, please, let me know. I am happy to work with you to make class the best it can be.
Respect my time:#
Be on time to class.
Pay attention when I am talking to you.
Come to class prepared by doing the work and going to office hours when you need help.
Respect each other:#
Do not be disruptive. If you need to take a call or text someone, take it outside.
Work with each other to find solutions. You learn more by helping each other.
Allow one another to make mistakes. This is an important part of the learning process.
Use respectful language when talking with one another.
Tips for Success#
Be proactive about your success in the course.
Do not procrastinate! Begin your assignments and studying early!
Attend every class.
Ask questions whether it is during class, recitation, office hours, or via email to your instructor.
Form a study group! Working together will help you and others better understand the course material as you can work through different difficulties and offer each other clarifications on concepts.
Do problems! Reading through your notes is not enough. Seek out new problems and work through them carefully. When you are done, check your answer. If you are wrong, examine carefully what misunderstanding occurred and how to avoid it in the future. If you were correct, examine if there was a faster way, check to see if your solution
flowedand was easy to read, and think over what concepts/computations were used and whattypeof problem the exercise was.Every time you approach a new concept, carefully think how it could be applied in your own field of study.
Carefully check your code when you use any computation device or program.