Biomedical Informatics, PhD

Program Overview

---

Biomedical Informatics, PhD

Chairperson

Joel H. Saltz, Health Sciences Center Level 3, Room 3-043

Graduate Program Director

Ramana V Davuluri

Department Office

Department of Biomedical Informatics College of Engineering and Applied Sciences and School of Medicine Health Sciences Center Level 3, Room 3-043 Stony Brook University Stony Brook, NY Main number: 631-638-2590

Degrees Awarded

Ph.D. in Biomedical Informatics; M.S. in Biomedical Informatics; Advanced Graduate Certificate in Biomedical Informatics

Web Site

[Insert website URL]

Application

[Insert application URL]

The Department of Biomedical Informatics currently offers graduate work leading to the Doctor of Philosophy, Master of Science degree and Advanced Graduate Certificate in three areas of specialization, or Tracks:

1. Clinical Informatics - enhancing the quality and efficiency of clinical workflows;
2. Imaging Informatics - integrative analysis and management of biomedical images; and
3. Translational Bioinformatics - application of informatics methods to advance patient-related biomedical research, from Clinical Genomics to Population Health.

The new Stony Brook University Biomedical Informatics Program is a collaboration of the School of Medicine and in the College of Engineering and Applied Sciences. This interdisciplinary field studies and pursues the effective use of biomedical data, information, and knowledge for scientific inquiry, problem-solving, and decision-making, driven by efforts to improve human health.

We embed BMI Education in research and operations at the Stony Brook University Health Sciences Center, where quantitative sciences have emerged at the very core of efforts to understand, prevent, and treat disease. Further, our program emphasizes the ability of trainees to produce software artifacts and conduct computational experiments, along the same lines as the College of Engineering and Applied Sciences. The resulting refactoring of Informatics equips BMI trainees to play a new role in a Systems Biomedicine enterprise that spans from patient-centric information systems to the distributed analytics needed to contextualize emerging biomolecular Big Data resources.

Students will be instructed via a combination of classroom teaching, seminars, and/or structured projects. Graduates can expect careers in academia, research, healthcare, industry, or government.

Admission Requirements for Ph.D. in Biomedical Informatics

1. A bachelor's degree in Biomedical Informatics, or a related field such as computer science, another engineering discipline, physical science, chemistry, mathematics OR a bachelor's degree in biology, biochemistry, pharmacology, social science OR post-baccalaureate training equivalent to the above OR a bachelor's degree in humanities with coursework and projects in digital arts and media OR an MD Degree.
2. A grade point average of at least B or equivalent in all engineering, mathematics, and science courses.
3. Completion and submission of the Graduate Record Examination (GRE) General Test.
4. A Statement of Purpose describing the applicant's relevant past experience and immediate and long-term goals. Applicants should describe how the type of research that they expect to conduct while in the program relates to one of the department's research areas.
5. Three letters of recommendation.
6. Acceptance by both the Biomedical Informatics Graduate Program and the Graduate School.
7. In addition, students must meet all admissions requirements, fees, and deadlines of the Stony Brook University Graduate School.

Requests for exceptions to the stated admissions requirements must be submitted in writing and approved by the BMI Graduate Program Director and The Graduate School.

Facilities of the Biomedical Informatics Department and Graduate Program

The Biomedical Informatics Department has a strong foothold in computing and in biomedical sciences. Our Department was jointly established by the College of Engineering and Applied Sciences and the Stony Brook University School of Medicine.

BMI's three locations on campus offer students and faculty front seats in key centers of collaborative activity. Each BMI Department location features extensive learning and research suites with faculty and administrative offices, Postdoctoral trainee stations, classroom and meeting space, and student labs equipped with desktop computers, each with 1TB storage space, 16GB main memory, and a 4-core CPU. The Department's HSC Suites have opened in the Health Sciences Center HSC Level 3, and include the Chair's suite and administrative center. A second BMI location with office, meeting and student lab is under construction in the Old Computer Science Building on West Campus. The third BMI Department suite will be housed with the Cancer Center in the new Medical and Translational Research (MART) building being constructed adjacent to the new Stony Brook Children's Hospital. Virtual meeting solutions continue to keep all Department members together, and enable distance learning.

The Biomedical Informatics Department (BMI) has a cluster computing system dedicated to research, development, and education in high-performance computing, systems software, and applications. The cluster system consists of 10 compute nodes and 10 storage nodes. Each compute node has 2 10-core Intel Xeon CPUs, 2 NVIDIA K40 Tesla GPUs, one Intel Xeon Phi co-processor, 256GB main memory, a 512GB SSD, and 2 1TB hard-disks. Each of the storage nodes has 2 6-core CPUs, 64GB main memory and 95TB disk storage in RAID 5 configuration. All the nodes in the cluster are connected to each other via high-performance Infiniband Switches. The cluster system is housed in the Department of Computer Science. BMI also owns a small Virtual Machine server farm consisting of a Dell PowerEdge server with 4 8-core CPUs, 256 GB main memory, and 28TB disk storage. This server is used to host VMs for development and testing purposes.

In addition to BMI-owned servers and computers, researchers have access to XSEDE resources (through a scientific gateways grant. The XSEDE resources include Stampede which is a distributed-memory Dell Linux Cluster with over 6,400 nodes. Each node has 2 Intel Xeon E5 (Sandy Bridge) processors, 32GB memory, and an Intel Xeon Phi Coprocessor (MIC Architecture) with 8GB memory. The computation nodes are interconnected with Mellanox FDR InfiniBand technology. BMI's Student and meeting space has wifi and wired connections available to the SBU network. In recent years, the use of cloud computing has taken center stage in both translational biomedical informatics and bioinformatics, and students will also be introduced to those resources.

General Requirements for the Biomedical Informatics Graduate Program

Registration: Students must register for at least one graduate credit in the semester in which the diploma is awarded.

Language Requirement: There is no foreign language requirement.

Grade Point Average: To be certified for graduation, a cumulative graduate grade point average of 3.0 (out of 4.0) or better is required.

General Requirements for the Ph.D. in Biomedical Informatics

The Ph.D. program has been designed to provide students the flexibility to tailor their studies toward their individual research interests while maintaining a common foundational training. Each student's program of study will be defined by the student, the student's advisor, and the program director, while satisfying certain mandatory requirements of the program. The program of study has been designed to provide students with the fundamental knowledge of the domain and its tools, to provide depth in the key areas of, and tools used, in BMI, and to give them the flexibility to choose courses that meet their individual needs. A minimum of 24 credits beyond the M.S. degree is required for the Ph.D. degree. Students also select a track to focus on: Imaging Informatics, Clinical Informatics, or Translational Bioinformatics.

Required Courses

• 24 approved graduate course credits beyond the M.S. degree requirement.
• BMI 502 - Life Sciences for Biomedical Informatics 3 credits
• OR
• BMI 503 - Computer Science for Biomedical Informatics 3 credits
• A minimum of 9 graduate credits must be taken in the Biomedical Informatics Program (includes all BMI courses and all BMI-Approved Elective courses from other departments).

Transfer Credits

All requests for transfer of credits require the prior approval of the graduate program director, and all requests for transfer of credits beyond 12 graduate credits must also be approved by a majority vote of the primary Biomedical Informatics faculty. For a student who transferred from another comparable national BMI program and has already completed all course requirements and passed the preliminary written exam, the student can petition the Graduate School to be placed into advanced status (passing preliminary examination equivalent) with prior approval by a majority vote of the primary Biomedical Informatics faculty.

Preliminary Examination

Students will be required to pass a written preliminary examination. This examination is designed to broaden the multidisciplinary nature of the candidate student base. Biomedical Informatics attracts people working in many domains, often acquiring skills and interests that are not captured by the more conventional curricular track offered in those domains. Naturally, this is also an opportunity to verify the accuracy of the candidate's claims to quantitative skills as a route to a multidisciplinary curriculum. The examination will be offered at least once every year, usually in April. The preliminary examination will be developed by the student's advisor in consultation with the student's examination committee, and must then be approved by the graduate program director prior to being administered. The examination committee will consist of three Biomedical Informatics faculty members. Students will be encouraged to take the preliminary examination the first time it is offered after they begin academic residency. Each student can take the written preliminary examination two times before being disqualified as candidates to this Ph.D. program.

Qualifying Examination

This examination is designed to test the student's ability to utilize his or her background to carry out research in a chosen field of study, and to make clear written and oral presentations of research. As part of the qualifying examination, the student is required to submit a written dissertation proposal (15-page limit) and present it in a public oral examination conducted by the dissertation examining committee. The written dissertation proposal must be distributed to the committee members at least two weeks before the oral examination. The oral examination probes the doctoral student's ability and examines the progress, direction, and methodology of the dissertation research. The student will be examined on the dissertation topic and its objective, the problem formulation, research approach, and knowledge in related areas. A majority of the dissertation examining committee must approve the student's performance.

Teaching

Ph.D. students are required to take 3 credits of BMI 698 - Practicum in Teaching II or obtain approval of equivalent teaching experience from the Graduate Program Director as part of the degree requirement. BMI 698 is taken under a faculty advisor who is responsible for providing feedback and making a formal evaluation of the student's work. The form of this practicum may include making class presentations, teaching in recitation classes, or preparation and supervision of laboratory classes. All Teaching Assistants are required to take BMI 697 - Practicum in Teaching I prior to taking BMI 698. BMI 697 will provide students a background in learning theory, course design, learning styles, content delivery formats, teaching technology, advising, rubrics, and assessment.

Advancement to Candidacy

After passing the preliminary examination, a student will be advanced to candidacy for the Ph.D. degree when he/she has completed all formal coursework, passed the qualifying examination, and satisfied all other Ph.D. requirements except the dissertation. These requirements must be completed within one calendar year after passing the written qualifying examination. Advancement to candidacy must be at least one year before the beginning of the semester in which a student plans to defend his/her dissertation.

Dissertation

The student chooses a dissertation topic in consultation with his/her doctoral dissertation advisor as soon as possible. Dissertation research is an apprenticeship for the candidate, who, under the supervision of the dissertation advisor, independently carries out original work of significance. The dissertation examining committee should be established after the student passes the qualifying examination. The committee must include at least three members from the Department of Biomedical Informatics primary or secondary faculty, including the dissertation advisor, and at least one "outside" member from another program or from outside the University. This "outside" member may not be a member of the Biomedical Informatics program graduate faculty. The committee must be approved by the graduate program director upon recommendation by the dissertation advisor. The official recommendation for the appointment of the dissertation examining committee is made to the Dean of the Graduate School.

Dissertation Defense

Once the dissertation is complete, approval of the dissertation requires a formal oral defense. The formal defense is open to the public. A candidate must fill out the Doctoral Degree Defense Form (available on the Graduate School Web page) with dissertation abstract as well as other relevant details, and submit the Form to the graduate program director at least three weeks in advance of the proposed event. The Form is forwarded by the graduate program director to the dean of the Graduate School. Copies of the dissertation are to be distributed to the committee members at least two weeks before the dissertation defense; one copy is to be kept in the program office for examination by the faculty. The final approval of the dissertation must be by a majority vote of the dissertation examining committee.

Annual Review of Progress

The student's advisor must submit a written report to the graduate program director on the student's progress once per year documenting student progress and accomplishments (e.g., published papers or proceedings, presentations at conferences, fellowships, grants, awards, or other honors).

Time Limit/Residency Requirement

The time limit for a doctoral degree is seven years for a student who has a previous graduate degree or 24 credits of graduate study in such a degree program. For all other students, the time limit for a doctoral degree is seven years after completion of 24 graduate level credits at Stony Brook University.

Ph.D. Course Table with Track options

	"req" = required course for track "x" = elective course subject applies to track
Course #	Title	Imaging Informatics (II)	Clinical Informatics (CI)	Translational Bio-informatics (TBI)
BMI 501	Intro. To Biomedical Informatics	req	req	req
BMI 502	Life Sciences for Biomedical Informatics	req or 503	req or 503	req or 503
BMI 503	Computer Science for Biomedical Informatics	req or 502	req or 502	req or 502
BMI 511	Translational Bioinformatics			req
BMI 512	Clinical Informatics		req
BMI 513	Imaging Informatics	req
BMI 514	Imaging Informatics Analysis	req
BMI 517	Current Research in Signaling Pathways, Biochemistry, and Tissue Morphology of Disease	x	x	x
BMI 520	Data Analytics and Software Stacks	req	x	req
BMI 530	Software Development in Biomedical Informatics	req	x	req
BMI 540	Statistical Methods in Biomedical Informatics	req	req	req
BMI 550	Clinical Informatics Practice Patterns		req
BMI 551	Case Studies in Clinical Informatics		req
BMI 552	Quality Improvement Methods for Clinical Informatics		x
BMI 560	Personalized Medicine			x
BMI 590	Independent Study in Biomedical Informatics	x	x	x
BMI 591	Independent Reading in Biomedical Informatics	x	x	x
BMI 592	Maters/Pre-Candidate Seminar (FT students must register each semester prior to candidacy)	req	req	req
BMI 595	Special Topics in Biomedical Informatics	x	x	x
BMI 596	Special Problems in Biomedical Informatics	x	x	x
BMI 598	M.S. Capstone Project in Biomedical Informatics
BMI 599	M.S. Research and Thesis in Biomedical Informatics
BMI 620	Advanced Topics in Clinical Informatics		x
BMI 622	Advanced Topics in Translational Bioinformatics			x
BMI 625	Advanced Topics in Imaging Informatics	x
BMI 690	Independent Study in Biomedical Informatics	x	x	x
BMI 691	Independent Reading in Biomedical Informatics	x	x	x
BMI 692	BMI Candidate Seminar (FT students must register each semester after candidacy)	req	req	req
BMI 695	Special Topics in Biomedical Informatics	x	x	x
BMI 696	Special Problems in Biomedical Informatics	x	x	x
BMI 697	Teaching Practicum I	req	req	req
BMI 698	Teaching Practicum II	req	req	req
BMI 699	Dissertation Research-On Campus (up to 12 credits)	req or 700 or 701	req or 700 or 701	req or 700 or 701
BMI 700	Dissertation Research-Off campus, Domestic	req or 699 or 701	req or 699 or 701	req or 699 or 701
BMI 701	Dissertation Research-Off campus, International	req or 699 or 700	req or 699 or 700	req or 699 or 700
BMI 800	Full-Time Summer Research	x	x	x