BIOE - Bioengineering
Bioengineering Seminar provides a broad introduction to the field, practice, and curriculum of Bioengineering. The major goals are for students to (1) meet the department faculty, (2) understand the curriculum and the 4-year goals, (3) understand and apply technologies central to the field through individual and group projects, (4) begin independent explorations into technologies in the field, and (5) practice teamwork, technical writing, and presentation. The course is designed for first-year Bioengineering majors.
Lectures and discussions of recent trends in bioengineering; topics typically include biological interaction with ultrasound and microwave radiation, modeling, instrumentation, biomaterials, biomechanics, biological heat and mass transfer, and medical imaging techniques.
Subject offerings related to Bioengineering intended to augment the Bioengineering curriculum. See class schedule or course information websites for topics and prerequisites. May be repeated to a maximum of 8 hours, if topics vary. Prerequisite: Restricted to majors only.
May be repeated.
This course provides exposure to Bioengineering careers through experiences in medicine, industry, and research. Students will observe professional practices to facilitate problem-based discoveries and technology design. Prerequisite: BIOE 120. Majors only.
Material, energy, charge, and momentum balances in biological problems. Steady-state and transient conservation equations for mass, energy, charge, and momentum will be derived and applied to mathematically analyze physiological systems using basic mathematical principles, physical laws, stoichiometry, and thermodynamic properties. Prerequisite: CHEM 104, MCB 150, and PHYS 211.
Principles of cell biology inherent in tissue engineering design. Lab experience in safely and skillfully manipulating cells of the four tissue types and performing various quantitative analyses on products produced by cells that have differentiated. Prerequisite: MCB 150, and credit or concurrent enrollment in BIOE 206.
Introduction to signals and linear systems with examples from biology and medicine. Linear systems and mathematical models of systems, including differential equations, convolution, Laplace transforms, Fourier series and transforms, and discrete representations. Class examples and coursework apply general techniques to problems in biological signal analysis, including circuits, enzyme kinematics, and physiological system analysis. Use of Matlab and Simulink software to understand more complex systems. Prerequisite: CS 101 or CS 124, PHYS 212, and credit or concurrent registration in MATH 285.
Molecular and cellular biology focusing on instrumentation and measurement techniques: gene expression, translation, and regulation; cellular energetics and enzyme kinetics; membrane transport and cell signaling; cytoskeleton and the cell cycle; cell biology fundamentals emphasizing modern imaging and measurement systems to quantify cellular function. Credit is not given for both BIOE 206 and MCB 252. Prerequisite: MCB 150.
Using analytical and computational tools from linear algebra, students will Solve large systems of linear equations, systems of linear ODEs, and linear PDEs; Analyze large, multivariable datasets to quantify relationships between variables; Decompose complex datasets into simpler representations; Introduce and solve common problems in classification, image processing, and machine learning; Develop a geometric understanding of high-dimensional spaces. Prerequisite: CS 101 or CS 124, and MATH 231.
Special project or reading activity. May be repeated in the same or separate terms to a maximum of 12 hours. Prerequisite: Approved written application to department as specified by department or instructor.
Subject offerings of new and developing areas of knowledge in bioengineering intended to augment the existing curriculum. See Class Schedule or departmental course information for topics and prerequisites. May be repeated to a maximum of 8 hours, if topics vary.
Description, quantification, and modeling of human physiological systems, based on systems fundamentals. Components, relationships, and homeostatic controls of neural, musculoskeletal, respiratory, cardiovascular, endocrine, digestion, and renal-filtration systems. Application of mathematical modeling and MATLAB simulation to further understanding of the systems and relate physiological consequences to changes in environment or component function. Prerequisite: BIOE 205 and one of MCB 252 or BIOE 206.
Experiments involving the modeling and measurement of animal and human physiology systems. Use of computer simulations to provide mathematical descriptions of physiology behavior. Calibration and validation of models through hands-on experiments. Focus on quantitative measurement of neural, cardiovascular, respiratory, muscular, and endocrine system functions. Prerequisite: Concurrent enrollment in BIOE 302 is allowed.
Experiments involving design of bioreactors and microfluidic systems, advanced cell culture, and quantitative analysis techniques such as polmerase chain reaction and atomic force microscopy. Laboratory techniques relating to current literature and state of the art in the field of bioengineering. Prerequisite: BIOE 202. Departmental approval required for non-majors.
Fundamental and applied statistics, including probability distributions, parameter estimation, descriptive statistics, hypothesis testing, and linear regression. Statistical methods in genomics including sequence analysis, gene expression data analysis, human genomic variation, regulatory genomics, and cancer genomics. Credit is not given towards graduation for both BIOE 310 and IE 300. Prerequisite: BIOE 210 or MATH 257. Students in the BS-BIOE must take BIOE 210 as the prerequisite.
Fundamentals of fluid dynamics and mass transport applied to analysis of biological systems. Quantitative understanding of microscopic to macroscopic phenomena in biological systems related to their sensing by imaging techniques. Molecular phenomena in both healthy tissue and disease using examples from cardiovascular problems and cancer using ultrasound, optical and MRI techniques. Credit is not given for both BIOE 360 and any of CHBE 421, CHBE 451, or TAM 335. Prerequisite: BIOE 201 and MATH 285.
Special project or reading activity. May be repeated up to 8 hours in a term to a maximum of 12 total hours. Prerequisite: Approved written application to department as specified by department or instructor.
Subject offerings of new and developing areas of knowledge in bioengineering intended to augment the existing curriculum. See Class Schedule or departmental course information for topics and prerequisites. May be repeated to a maximum of 8 hours, if topics vary.
This capstone design course is the culmination of the CS+BIOE curriculum. The course focuses on the design of computational technologies for needs in human health and in the life sciences. Students will perform market research, develop a prototype software, and explore entrepreneurship at the interface of bioengineering and computer science. Students will practice problem identification and the analysis of solutions for real world problems from the perspective of value added for end-users. Students will use principles of design, engineering analysis, and customer discovery. This course emphasizes effective teamwork and technical communication, and integrates content related to intellectual property, quality, human factors, FDA regulation, professionalism, and ethics. The overall goal of the course is to prepare students for careers using computational approaches in healthcare, biotechnology, life sciences, and pharmaceutical industries. 4 undergraduate hours. No graduate credit. Prerequisite: CS 374, BIOE 310, BIOE 206 or BIOE 302. Concurrent enrollment in CS 357 or CS 421. Restricted to CS + BIOE majors only.
Engineering aspects of the detection, acquisition, processing, and display of signals from living systems; biomedical sensors for measurements of biopotentials, ions and gases in aqueous solution, force, displacement, blood pressure, blood flow, heart sounds, respiration, and temperature; therapeutic and prosthetic devices; medical imaging instrumentation. Same as ECE 414. 3 undergraduate hours. 3 graduate hours. Prerequisite: BIOE 205, ECE 205 or ECE 210.
Laboratory to accompany BIOE 414. Use of sensors and medical instrumentation for static and dynamic biological inputs. Measurement of biomedical signals. Same as ECE 415. 2 undergraduate hours. 2 graduate hours. Prerequisite: Credit or concurrent registration in BIOE 414.
Systems engineering approach to modeling physiological systems to examine natural biological control systems, homeostasis, and control through external medical devices. Introduces open loop and closed loop feedback control; Laplace and Fourier analysis of system behavior; impulse and steady state responses; physiological modeling and system identification; and stability. Includes biological systems for endocrine function, muscle position, neuronal circuits, and cardiovascular function. Mathematical modeling, Matlab and Simulink simulation, and physiological measurements to relate control systems to maintenance of internal environment. 3 undergraduate hours. No graduate credit. Credit is not given for BIOE 420 if credit for AE 353, ECE 486, SE 320, or ME 340 has been earned. Prerequisite: BIOE 302, BIOE 303, BIOE 414, BIOE 415.
Introduction to the field of synthetic biology. Engineering applications of biomolecular systems and cellular capabilities for a variety of application biological background of gene regulation, experimental methods for circuit engineering, and mathematical basis for circuit modeling. Examples in biofuels, biomedicine, and other areas will be discussed. 3 undergraduate hours. 4 graduate hours. Prerequisite: BIOE 206 or MCB 252; and MATH 285.
Capstone bioengineering design activity to develop solutions to projects provided by academia, industry, or clinical settings, utilizing principles of design, engineering analysis, and functional operation of engineering systems. Concept-design, safety, human-factors, quality, and Six-Sigma considerations. Initial solution proposals meeting professional technical-writing and communication standards. Concluded in BIOE 436. 2 undergraduate hours. No graduate credit. Prerequisite: BIOE 414, BIOE 415, BIOE 302, and BIOE 303.
Continuation of BIOE 435. Design teams finalize concepts, evaluate alternatives, model and analyze solutions, build and test a final product, and present the results professionally to project sponsors. 2 undergraduate hours. No graduate credit. Prerequisite: BIOE 435.
The objective of this course is to provide the knowledge and hands-on experience required for both designing and building tools that are necessary to engineer biological systems at the molecular and cellular levels. This particular course will highlight diverse examples of applications in synthetic biology. It will deal with such topics as gene editing, epigenome engineering, regulation of gene expression and synthetic life. Projects will be assigned for small teams. Students will submit a report after completion of each project. Students will have the opportunity to independently design and execute a genetic engineering project and present their project to the class. 3 undergraduate hours. No graduate credit. Prerequisite: BIOE 202 and BIOE 206. For bioengineering undergraduate majors only.
Tissue engineering therapies for cell-based, material-based, and therapeutic-based solutions. Stem cells, immunology, and clinical applications. 3 undergraduate hours. 3 graduate hours. Prerequisite: MCB 150 and BIOE 206.
An elective course for undergraduate students who are interested in learning nanotechnology and its applications in biology and medicine. Key topics include: (1) cancer biology and clinical oncology, (2) fundamentals of nanoscience, (3) principles of nanoscale engineering, (4) major classes of nanoparticles and nanostructures, and (5) nanomedicine - technologies and applications 3 undergraduate hours. No graduate credit. Approved for Letter and S/U grading. Prerequisite: BIOE 206, CHEM 232.
The frontier of biomedical imaging is computed imaging where multi-dimensional images must be reconstructed from measured data that is otherwise not meaningful to human observers. In this course, computational image reconstruction techniques will be developed and employed across a broad range of radiographic, magnetic resonance, and nuclear imaging modalities. General imaging and detection principles common to all computational modalities will be covered in context of specific biomedical imaging scenarios. X-ray computed tomography will be covered in depth and in the context of the imaging science principles presented the co-requisites; this also includes practical concerns about computing resources and modern GPU-based computing. The physics of magnetic resonance imaging will be presented and related to specific mathematical issues of image reconstruction and under-sampled measurement space. Positron emission tomography (PET) will be covered and specific clinical issues discussed in terms of reconstruction algorithm and parameter choices. 3 undergraduate hours. 4 graduate hours. Prerequisite: BIOE 205, BIOE 210, ECE 380/BIOE 380. Concurrent enrollment in BIOE 485 and BIOE 580; or instructor approval.
Biomedical image data often come in extreme numbers: there is either so many of them that humans can't analyze them in reasonable time (e.g., three-dimensional light sheet microscopy data) or they are few, highly varied and of limited spatial and intensity resolutions (e.g., positron emission tomography scans). Furthermore, the extraction of image features and the characterization of modality-dependent background noise can be particularly challenging in typical biomedical scenarios. In this course, several applications of statistical learning to biomedical image data will be covered in depth from first principles. Analyses will be done in Python using the Scikit-learn package and all homework assignments comprise statistical analyses of biomedical image data in real decision scenarios. Histogram transforms and the fundamental properties of image texture will be introduced and revisited throughout the course. The extraction of both low- and high-order spatial features at multiple scales will be demonstrated and employed throughout the course. Support vector machines will be introduced and applied to image classification and interpretation tasks. The random forest algorithm will be introduced and used on a number of large- and small-data tasks. Multiple linear regression will be applied to neuroimaging data and some common methods of assessing model robustness shown. Cross-validation of image-derived decisions and some common methods of assessing model robustness will be shown. Feature selection and dimensionality will be discussed in terms of diagnostic task performance. The effects of inter-feature correlation upon prediction confidence will be discussed. Principal component analysis will be described and applied to various image processing tasks. Unsupervised clustering and cluster analysis of extracted image features will be introduced. Stochastic object models will be introduced and applied in various validation tasks. 3 undergraduate hours. 4 graduate hours. Prerequisite: BIOE 485 or permission of the instructor. Students are expected to be familiar with calculus, basic probability & sampling, vector spaces, matrix algebra and constrained optimization. Several NumPy objects and manipulations will be reviewed, and all necessary Sci-kit functions introduced; however, students are expected to have substantial experience with Python programming as the basics of such will not be covered.
Covers fundamental mathematical and computational methods needed to implement computational imaging and machine learning solutions. First, relevant aspects of probability theory, matrix decompositions, and vector calculus will be introduced. Subsequently, methods that underline approximate inference, such as stochastic sampling methods, are introduced. Finally, numerical optimization methods that represent core components of computed imaging and machine learning will be introduced. This will include numerical optimization-based formulations of inverse problems. An emphasis will be placed on first order deterministic and stochastic gradient-based methods. Second order optimization techniques including quasi-Newton and Hessian free methods will also be surveyed. The application of these methods to computed imaging and machine learning problems will be addressed in detail. 4 undergraduate hours. 4 graduate hours. Prerequisite: Restricted to senior undergraduate or graduate standing in an engineering degree program or consent of instructor.
Covers basic concepts, methodology and algorithms in deep learning and their applications to solve various biomedical imaging problems. Introduction to neural networks and their application to supervised and unsupervised learning problems formulated for biomedical imaging will be provided. Connections between general learning methodologies and specific challenges in the field of biomedical imaging, and design, implementation and evaluation of deep neural network-based solutions to imaging problems will be emphasized. Problems covered will include imaging system design and optimization, image recovery and reconstruction (built on the imaging physics and system course – BIOE 483), image processing (e.g., denoising, super-resolution and enhancement) and image analysis (e.g., same-contrast, multi-contrast and multimodal image registration, segmentation, classification and quality assessment). Biomedical application specific problems and solutions will be covered via hands-on problems and team-based projects. 3 undergraduate hours. 4 graduate hours. Prerequisite: MATH 241 or equivalent; BIOE 210, MATH 415 or equivalent; BIOE 310, ECE 310, STAT 410 or equivalent; BIOE 198, CS 101 or equivalent; BIOE 483; BIOE 485; or consent of the instructor.
Stem Cell Bioengineering will provide a foundation in the application of engineering approaches for the quantitative analysis of stem cell biology and the translation of stem cells into therapies. There will be 4 main sections of the course; (i) Stem Cell Basics, (ii) Stem Cell Genetics, (iii) Stem Cell Microenvironments, and (iv) Stem Cell Applications. The course will be targeted for first year graduate students and senior-level undergraduate students. The course will use a lecture and discussion format to effectively present relevant information. 3 undergraduate hours. 4 graduate hours. Prerequisite: BIOE 476.
Will introduce students to basic principles and practical applications of scientific computing as they relate to problems in machine learning and computed imaging. In this self-contained course, students will be introduced to a variety of important topics that underlie real-world machine learning and biomedical image computing tasks that are not typically comprised in a single course. The material will be presented in a practical way that will be accessible to engineering students who have a moderate level of experience in scientific computing but lack specific training in computer science. The emphasis will be on immediate applicability of scientific computing techniques as opposed to theoretical knowledge. The course will begin with an overview of good scientific coding practices in Python and introductions to canonical computing architectures. Subsequently, parallel computing concepts will be surveyed that address multi-core CPU and GPU-enabled systems. Distributed GPU computing on a cluster will also be covered. The salient aspects of TensorFlow and/or other relevant machine learning programming environments will be introduced and utilized in applications of machine learning. 3 undergraduate hours. 3 graduate hours. Prerequisite: Familiarity with the Python programming language. Restricted to students with senior undergraduate or graduate standing in an engineering major.
The application of machine learning (ML) to medical image data is an area of intense, well-funded research. Due to practical logistics, however, the ideas expounded in published research articles do not necessarily translate perfectly into clinical implementation. The purposeful design and assessment of machine learning experiments will be introduced and revisited throughout the course. The financial cost of training, data acquisition and expert labelling will be considered in the context of product delivery. Some relevant university, corporate and governmental regulatory policies will be presented by expert guest lecturers. Specific issues of clinical implementation and adoption of new technology will be covered. The ethics of using images influenced or analyzed by ML in patient care and/or medical research will be explored in depth. Topics include: diagnosis accuracy, mandated system upgrades, informed consent, patient privacy, researcher/vendor liability and the role and reliability of federal regulations in ethical application of ML to biomedical data. The policies and procedures of NIH study sections and internal review boards will be highlighted and some key issues related to intellectual property will be surveyed. 3 undergraduate hours. 4 graduate hours. Prerequisite: Restricted to students with senior undergraduate or graduate standing and familiarity with machine learning principles.
Special project or reading activity. 1 to 4 undergraduate hours. 1 to 4 graduate hours. May be repeated up to 8 hours in a term to a maximum of 12 total hours. Prerequisite: Approved written application to department as specified by department or instructor.
Subject offerings of new and developing areas of knowledge in bioengineering intended to augment the existing curriculum. See Class Schedule or departmental course information for topics and prerequisites. 1 to 4 undergraduate hours. 1 to 4 graduate hours. May be repeated if topics vary.
Limited in general to seniors in the curriculum in bioengineering. Any others must have the consent of the department chief advisor. Each student taking the course must register in a minimum of 5 hours either in one term or divided over two terms. 1 to 5 undergraduate hours. No graduate credit. May be repeated to a maximum of 10 hours between two semesters. Prerequisite: Senior Standing.
Lecture surveying a broad range of Bioengineering topics. 0 or 1 graduate hours. No professional credit. Approved for S/U grading only. May be repeated to a maximum of 2 hours.
Familiarization with reading and discussing academic journals in Bioengineering. Approved for S/U grading only.
Ethical questions and conduct, procedures, and professional standards in the practice of bioengineering. Authorship and mentoring, use of animal and human subjects, conflict of interest, ethical behavior in scientific research, intellectual property, and approval processes for drugs and biomedical devices. 2 graduate hours. No professional credit.
Mathematical concept relating to modeling of physiological and bio-molecular processes and the instrumentation used to measure those processes. Review of matrix methods, probability, linear systems, and integral transforms. Singular value decomposition, Bayesian decision making, and linear system solutions to ordinary differential equations. Application of concepts to biosensor design and evaluation, tracer kinetic modeling, and filtering and curve-fitting approaches to forward modeling problems. Prerequisite: MATH 285.
Mathematical and statistical models plus accompanying computational techniques central to many aspects of systems biology and bioengineering research. Theory of supervised and unsupervised learning; linear models; dimension reduction; Monte Carlo computation; analysis of gene expression data and genome sequence data; modeling of gene transcription network signaling pathways. Same as CSE 505. 4 graduate hours. No professional credit. Prerequisite: STAT 400.
Introduction to modern biotechnologies for studies on the Central Dogma of Biology (DNA, RNA, and Protein) as well as cellular organelles and cell imaging. In-depth review of traditional established methods and emerging ones, emphasizing high precision, high spatial/temporal resolution, high-throughput, molecular accuracy, sensitivity and real-time imaging. Techniques include single molecule sequencing, super resolution cell imaging, and gene therapeutic methods. Example applications of technology are included through relevant journal articles. 4 graduate hours. No professional credit. Prerequisite: MCB 250.
Instrumentation and underlying theory employed in bioengineering. Concepts in the design and operation of sensors, fundamentals of optics, basic control theory and systems, digital components, and fundamental principles of medical imaging techniques. Specific knowledge of one biomedical instrument or system will be emphasized including detailed mathematical analysis. Prerequisite: BIOE 504.
Mathematical modeling of the process of carcinogenesis as somatic cell evolution. Focus on current research topics in cancer biology using data from next-generation sequencing technologies. Overview of database resources and algorithmic and modeling methods relating to biological problems. 4 graduate hours. No professional credit. Prerequisite: BIOE 206, CS 101, MATH 285.
This is a core course for the pharmaceutical engineering concentration. Drug manufacturing often relies on principles of chemistry, pharmaceutics, and technology. This course will discuss in-depth understanding of compounds and materials to help designers predict and measure compound properties to define and characterize their constitutive behaviors. This course will provide students with an understanding of the principles, strategies, and materials used in the processes of controlled drug delivery systems. Gaining knowledge in ingredient interaction (thermodynamics vs. kinetics) and how the delivery requirements determine the ingredients and the corresponding processing is critical for the success of a pharmaceutical development. This course will first discuss the synthetic approaches to new drug discovery and repurposing followed by introducing the technology methodologies involved in translating a drug compound produced in the lab to an industrial process. It will also focus on topics at the interface between engineering and chemistry and biology covering fundamentals of drug delivery, including physiology, pharmacokinetics/pharmacodynamics, drug diffusion and permeation, and biomaterials used in drug delivery. Controlled release strategies for various administration routes will also discussed. 4 graduate hours. No professional credit. Prerequisite: Student should have completed courses in advanced math, including linear algebra and differential equations, as well as courses in chemistry and biological sciences. Open to all M.Eng. in Bioengineering students.
This is a core course for the pharmaceutical engineering concentration. This course will follow a combination of modular lecture and laboratory-based teaching (lab modules will require students to participate in conducting wet lab experiments followed by calculations). Drug manufacturing often relies on principles of chemistry, pharmaceutics, and technology. Most of the classical pharmaceutical engineering degree programs either do not extensively address newly defined design-based approaches or require long years of work experience to acquire integrated knowledge on pharm-science, relevant regulations and process technology. This knowledge gap on the interface of pharmacy and process technology has been identified independently by WHO and AAPS survey (Lawrence 2017; O'Connor 2016). The goal of this course is to help develop the desired skill sets covering the concepts to adapt technology principles to pharmaceutical and life sciences with topics ranging from process technology in the drug discovery, high throughput characterization and optimization of new chemical entities, solid-state engineering, and intelligent pharmaceutical manufacturing systems. The basic features of common unit operations used in the pharmaceutical industry will be reviewed, including batch reaction, solid-liquid separation, crystallization, drying, mixing, batch distillation and other separation systems. 4 graduate hours. No professional credit. Prerequisite: BIOE 531. Open to all M.Eng. in Bioengineering students.
Guest topics will vary, but will typically cover topics of current interest relevant to the bioengineering field. Lecture and discussion on topics relevant to the development, regulatory approval, marketing, and application of systems used in the fields of biomedical imaging, life science research, and pharmaceutical discovery. Emphasis upon case studies on topics that will include regulatory approval, intellectual property, strategy, and technology innovation. 1 graduate hour. No professional credit. Approved for S/U grading only. May be repeated up to 2 hours in separate terms. Prerequisite: For students enrolled in the M.Eng. in Bioengineering degree program.
With special focus on medical imaging, this course will introduce fundamental concepts related to the detection and analysis of biological analytes, biomedical images, and physiological parameters. Topics include signal-to-noise analysis, noise characterization, data aliasing, analog-to-digital conversion, common strategies for noise reduction, exogenous contrast agents and fundamentals of molecular imaging. The fundamental phenomena behind biological measurements such as DNA sequencing, fluorescence microscopy. MRI imaging, OCT imaging, and ultrasound imaging will be discussed along with the factors that influence noise and contrast from the standpoint of fundamental physics, instrumentation/hardware, and post-measurement data/signal processing. 4 graduate hours. No professional credit. Prerequisite: For students enrolled in the M.Eng in Bioengineering degree program.
With special focus on medical imaging, learn about advanced techniques relating to state-of-the-art bioinstrumentation technologies. Topics will broadly include fluorescence, genomic and proteomic diagnostics, biosensors, ultrasound imaging, microscopy and their uses relevant to physiological changes related to major human diseases. 4 graduate hours. No professional credit. Prerequisite: BIOE 571. For students enrolled in the M.Eng in Bioengineering degree program.
Introduction to fundamental principles of design, management, and improvement of business operations and product innovations. Strategies and techniques for managing processes, projects, process improvement and new product development. 4 graduate hours. No professional credit. Prerequisite: For students enrolled in the M.Eng in Bioengineering degree program.
Tools, concepts, and analytical frameworks that enhance the ability to define and analyze strategic problems stemming from innovation and technological change, and to identify sources of competitive advantage from both an industry and firm-level perspective. Introduction to financial decision making, including topics in valuation, project analysis and risk-return relationships. 4 graduate hours. No professional credit. Prerequisite: For students enrolled in the M.Eng. in Bioengineering degree program only.
Students in the Master of Engineering (M.Eng.) in Bioengineering program will demonstrate their proficiency through a capstone project, where students will work on a translational project to develop solutions for real world problems utilizing principles of design, engineering analysis, and functional operation of engineering systems. Depending on the student's flexibility and availability, capstone projects may include collaboration with other online M.Eng. students on a team-based project, analysis of case studies, or even a self-directed project that directly relates to a specific area of interest or on behalf of their employer. Project presentations and demonstrations may be required at the end of the program. 3 graduate hours. No professional credit. May be repeated for 6 hours in separate semesters. Students in the Master of Engineering program will be required to sign up for BIOE 575 in both the Fall and Spring semesters. Prerequisite: Proficiency in MATLAB and completion of or concurrent enrollment in core classes required for the Master of Engineering (M.Eng.) in Bioengineering program. Class only available to students in the M.Eng. in Bioengineering degree program.
Exposes students to a broad treatment of the mathematical and statistical principles of biomedical imaging. In addition to providing a foundation for understanding general principles of image formation and objective image quality assessment that are widely applicable, this material will be essential for the principled and successful application of artificial intelligence methods in biomedical imaging. This course will cover the mathematical concepts needed for the deterministic analysis of imaging systems. Linear operator theory will be employed to describe continuous-to-continuous, continuous-to-discrete, and discrete-to-discrete mappings from objects to images. In addition, imaging systems will be analyzed in a statistical framework where stochastic models for objects and images will be introduced. Methodologies for objective assessment of image quality (OAIQ) will be introduced, which will address classification tasks, receiver operator characteristic (ROC) analysis, and salient aspects estimation theory. An introduction to numerical observers for quantification of OAIQ will be provided. 4 graduate hours. No professional credit. Prerequisite: Concurrent enrollment in BIOE 485 and BIOE 483; or instructor approval. Restricted to students with graduate standing or consent of instructor.
Modular approach to pulse sequence programming in magnetic resonance imaging; descriptions of current pulse sequences; RF pulse design; data sampling considerations; k-space acquisition trajectories. Pulse sequence development simulator usage to program, simulate, and reconstruct images from student-designed acquisitions. Prerequisite: ECE 480.
This course will provide students with the practical knowledge of statistical analysis and computational modeling techniques relevant for applications in genomics and systems biology. The focus will be on the fundamental concepts and algorithms for gene finding, genome annotation, sequence alignment, phylogenetic reconstruction, gene expression and network analysis, Genome-Wide Association Studies (GWAS), etc. 4 graduate hours. No professional credit. Prerequisite: STAT 100, MCB 250, MATH 220, CS 101, or equivalent. Restricted to MEng Students only.
The course will provide students with important practical skills for handling genomic big data and analyzing the results of various types of high-throughput sequencing experiments. The focus will be on achieving proficiency in data management and processing based on popular file formats in genomic biology. 4 graduate hours. No professional credit. Prerequisite: STAT 100, MCB 250, CS 101, or equivalent. For students enrolled in the M.Eng in Bioengineering program or with consent of the M.Eng. program.
A generative model is a powerful way of learning any kind of data distribution using unsupervised learning and they have achieved tremendous success in recent years. In the context of biomedical imaging, generative models are being actively explored for many important and diverse applications that include image and video synthesis, representation learning and semi-supervised learning, domain adaptation, text to image synthesis, image compression, super-resolution, inpainting, saliency prediction, image enhancement, style transfer and texture synthesis, and image-to-image translation. Generative models also hold great potential for regularizing inverse problems that arise in biomedical image formation. This course will provide an introduction to the use of deep neural networks for generative modeling in the context of biomedical image science. An emphasis will be placed on variational autoencoders (VAEs) and generative adversarial networks (GANs), as these are currently two of the most commonly employed and efficient approaches. The use of generative models for exploring data-acquisition designs optimizing the performance of imaging systems will also be introduced. Practical details regarding the successful training and evaluation of deep generative models using biomedical image data will introduced throughout the course. This will be reinforced via homework assignments and a final project that require hands-on training of networks facilitated by allocations of GPU time. 4 graduate hours. No professional credit. Prerequisite: BIOE 486, BIOE 485, BIOE 483, BIOE 580 or consent of instructor.
This journal-club style course will expose students to the modern literature on biomedical imaging and machine learning. Students will be exposed to cutting edge topics in the rapidly evolving field of biomedical image computing. Additionally, the course will prepare students for the capstone project in the Biomedical Image Computing MS degree program that will take place in the third semester of the program. During this course, students will interact with potential project mentors and engage in detailed literature reviews related to potential projects. 1 graduate hour. No professional credit. Approved for S/U grading only. Prerequisite: Graduate student standing. Concurrent enrollment in BIOE 484 and BIOE 486 is required. Restricted to students in the Biomedical Image Computing M.S. degree program only.
In this course students will complete a project that utilizes machine learning methods and advanced computational tools to solve a problem related to bioimaging. The projects will utilize experimental bioimage data that is contributed by a project sponsor and/or available via open source databases. While these projects need not be publishable or perfectly novel, they will involve the systematic application and evaluation of machine learning and image computing methods. It is expected that, by solving actual problems posed by industry or clinical partners, students will gain marketable experience but, ideally, also will make inroads with their future employers. 4 graduate hours. No professional credit. Prerequisite: BIOE 588, BIOE 484, BIOE 486, BIOE 580. Concurrent enrollmment in BIOE 489 is required. Restricted to students enrolled in the Biomedical Image Computing MS degree program only.
Special project or reading activity. May be repeated. Prerequisite: Approved written application to department as specified by department or instructor.
Subject offerings of new and developing areas of knowledge in bioengineering intended to augment the existing curriculum. See Class Schedule or departmental course information for topics and prerequisites. 1 to 4 graduate hours. No professional credit. May be repeated in the same or separate terms if topics vary.
Bioengineering graduate thesis research. Approved for S/U grading only. May be repeated.