Graduate Courses

Term Schedule

Fall 2022

Number	Title	Instructor	Time
BCSC 433-1 Statistical Speech & Language Processing Daniel Gildea TR 11:05AM - 12:20PM
An introduction to statistical natural language processing and automatic speech recognition techniques. This course presents the theory and practice behind the recently developed language processing technologies that enable applications such as speech-driven dictation systems, document search engines (e.g., finding web pages) and automatic machine translation. Students taking this course at the 400 level will be required to complete additional readings and/or assignments. Location Hylan Building Room 101 (TR 11:05AM - 12:20PM)
BCSC 519-1 Statistics for Brain & Cognitive Sciences Tim Jaeger; Oviya Mohan; Yue Zhang MW 2:00PM - 3:15PM
This course discusses statistical concepts and procedures commonly used in brain and cognitive sciences research. It is a peer-led class, meaning that each student will take part in actively teaching some of the concepts. You will be evaluated on your participation in class and the effort in organizing your lessons. Major topics include: 1) linear models, 2) linear mixed effects models and 3) bayesian data analysis. If time permits, we will go over some more advanced topics in statistics, including MCMC, time series analysis, etc. Prerequisites for undergraduates: STAT 212 or equivalent; research experience from BCSC/NSCI 395 or BCSC 206/207; and programming experience in R, Python, or MATLAB. Interested undergraduates should contact Yue Zhang (yzh191@u.rochester.edu) and Oviya Mohan (omohan@u.rochester.edu). Location Meliora Room 301B (MW 2:00PM - 3:15PM)
BCSC 520-1 The Intelligent Eye Michele Rucci TR 3:25PM - 4:40PM
Provides an interdisciplinary view of modern research into how the human brain solves the problems involved in perception, including how we perceive the three-dimensional structure of the world, how we recognize objects and how visual information is used to control action in the world. Students read contemporary research and, through classroom discussion and critical essays, explore and analyze the questions and debates that define contemporary perceptual science. Location Meliora Room 269 (TR 3:25PM - 4:40PM)
BCSC 528-1 Special Topics in Vision Duje Tadin F 12:00PM - 2:30PM
Advanced graduate seminar on a chose problem in vision sciences. In previous years, topics have included motion perception, stereopsis, color vision and visuo-motor control. Readings for the course are drawn from the scientific literature in the topic being covered. Students are typically required to lead discussions on papers. Location Meliora Room 301B (F 12:00PM - 2:30PM)
BCSC 541-1 Neurons, Circuits, & Systems Farran Briggs TR 9:40AM - 10:55AM
This course takes a bottom-up approach to understanding the neurons and circuits of the sensory systems in the mammalian brain. Thematic topics will include: structural and functional diversity among sensory neuronal populations, common themes across sensory systems such as parallel information processing, coordination among feedforward/feedback circuits, and neuronal plasticity during development of functional domains. The final course module will focus on exploring the neuronal mechanisms of attention, again from a neuron- and circuit-centric perspective. Visual, auditory, and somatosensory systems will be discussed with most emphasis on the visual system as a model for understanding structure/function relationships. The course will also introduce students to modern methodological approaches in systems neuroscience aimed at measuring and manipulating the activity of large populations of neurons while also incorporating information about individual neuronal identity, structure, and circuit connectivity. Prerequisite: BCSC 240/NSCI 201 Location Meliora Room 205 (TR 9:40AM - 10:55AM)
BCSC 542-1 Neuropsychology Melinda Patterson MW 4:50PM - 6:05PM
Examines clinical neuropsychology, which bridges neurology, neuroscience, and clinical psychology. Covers history of clinical neuropsychology, principles of neuropsychological assessment, and the interpretation of cognition and behavior as they relate to brain dysfunction. Considers specific neurological syndromes including neurodegenerative, cerebrovascular, toxic, and memory disorders; epilepsy; head trauma; infectious processes; pediatric neuropsychology; psychiatric syndromes; and forensic neuropsychology. Patient presentations (videotape and in-person interviews) supplement lectures. Prerequisite: BCSC 110 or BCSC 240/NSCI 201 Location Meliora Room 203 (MW 4:50PM - 6:05PM)
BCSC 543-1 Neurochemical Foundations of Behavior Renee Miller MWF 10:25AM - 11:15AM
This class covers how the brain controls behavior, and what goes wrong in various diseases, from a neurochemistry perspective. We start by learning about the neurochemicals –neurotransmitters, peptides, growth factors, etc. and move on to their receptors and associated signaling pathways, including gene transcription and epigenetics. An emphasis is placed on primary research literature, experimentation/data analysis and application of knowledge to the interpretation of scientific data. Students will attend research seminars on campus or online and write brief summaries of their understanding. The course culminates in small group presentations about the neurochemistry of diseases of interest, and an individual research review paper on the same topic. Prerequisite: BCSC 240/NSCI 201. BIOL 250 is helpful but not required. Location Goergen Hall Room 109 (MWF 10:25AM - 11:15AM)
BCSC 547-1 Intro to Computational Neuroscience Ralf Haefner TR 12:30PM - 1:45PM
Computational neuroscience studies how the brain can be understood in terms of computations implemented by neural circuits, and in terms of using computational methods to analyze neural and behavioral data. This course for advanced undergraduates and graduate students starts with models of individuals neurons before moving on to networks of neurons and behavior. It provides both a classic signal processing, and a probabilistic perspective on how neurons support the brain’s computations. While primarily lecture-based, an important part of the course are exercises that typically consist on implementing (programming) a model discussed in the class and analyze its behavior. The course also provides the opportunity for a final project but this is not required. The material mostly considers the sensory system and perceptual decision-making. There are no formal prerequisites. However, programming experience and a minimal background in linear algebra (vectors and matrices) and analysis (basic ordinary differential equations) are essential. At the beginning, there will be a very brief introduction to the key biological concepts necessary for the course. In doubt, please email the instructor. Location Meliora Room 224 (TR 12:30PM - 1:45PM)
BCSC 570-1 Introduction to Augmented and Virtual Reality Mujdat Cetin MW 2:00PM - 3:15PM
This course provides a broad introduction to augmented and virtual reality (AR/VR) systems. The course involves lectures covering an overview of all aspects of the AR/VR domain, as well as individual work performed by each student aimed at providing more intensive training on various aspects of AR/VR. Topics covered in the lectures include history, conceptual origins, and design/evaluation principles of AR/VR technologies; overview of visual/auditory/haptic AR/VR interfaces and applications; visual perception; optics/platforms/sensors/displays; auditory perception and spatial audio; silicon hardware architecture and materials; graphics and computation; interfaces and user experience design; data processing and machine intelligence for AR/VR; introduction to AR/VR programming tools; societal implications and ethical aspects. At the end of the course, students will have gained familiarity with the techniques, languages, and cultures of fields integral to the convergent research theme of AR/VR. This course is co-instructed by Mujdat Cetin, Michele Rucci, Ross Maddox, Jannick Rolland, Yuhao Zhu, Andrew White, Chenliang Xu, and Zhen Bai. Location Goergen Hall Room 109 (MW 2:00PM - 3:15PM)
BCSC 572-1 Practicum in Augmented and Virtual Reality Mujdat Cetin TR 9:40AM - 10:55AM
This is the third course offered as part of the PhD training program on augmented and virtual reality (AR/VR). The goal of the course is to provide interdisciplinary collaborative project experience in AR/VR. The course involves small teams of students from multiple departments working together on semester-long projects on AR/VR with the guidance of one or more faculty involved in the PhD training program. The expected end products of this Practicum course are tangible artifacts that represent what the students have learned, discovered, or invented. Types of artifacts include research papers; patent applications; open-source software; as well as online tutorials and videos for undergraduates, K-12 students, or the general public. Prerequisites: ECE 410-1 or OPT 410-1 or BME 410-1 or BCSC 570-1 or NSCI 415-1 or CSC 413-1 or CVSC 534-1 Instructors: Lead - Mujdat Cetin; Zhen Bai, Jannick Rolland, Michele Rucci Location Computer Studies Room 426 (TR 9:40AM - 10:55AM)
BCSC 595-01 PhD Research Ralf Haefner –
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BCSC 595-02 PhD Research Manuel Gomez-Ramirez –
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BCSC 595-03 PhD Research Duje Tadin –
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BCSC 595-04 PhD Research Robert Jacobs –
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BCSC 595-05 PhD Research Michele Rucci –
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BCSC 595-06 PhD Research Adam Snyder –
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BCSC 595-07 PhD Research Martina Poletti –
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BCSC 595-08 PhD Research Gregory DeAngelis –
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BCSC 595-11 PhD Research Karl Rosengren –
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BCSC 595-12 PhD Research Elise Piazza –
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BCSC 595-13 PhD Research Dora Biro –
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BCSC 595-14 PhD Research Ian Fiebelkorn –
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BCSC 598-07 Supervised Teaching Assistant Ralf Haefner –
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BCSC 598-1 Supervised Teaching Assistant Melinda Patterson –
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BCSC 598-14 Supervised Teaching Assistant Farran Briggs –
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BCSC 598-2 Supervised Teaching Assistant Duje Tadin –
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BCSC 598-3 Supervised Teaching Assistant Chung-Lin Yang –
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BCSC 598-4 Supervised Teaching Assistant Gregory DeAngelis –
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BCSC 598-5 Supervised Teaching Assistant Dora Biro –
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BCSC 598-6 Supervised Teaching Assistant Robert Jacobs –
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BCSC 897-1 Master's Dissertation Ralf Haefner –
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BCSC 995-1 Cont of Doctoral Enrollment Tim Jaeger –
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BCSC 997-1 Doctoral Dissertation Michele Rucci –
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BCSC 997-2 Doctoral Dissertation Duje Tadin –
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BCSC 999-01 Doctoral Dissertation Ralf Haefner –
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BCSC 999-02 Doctoral Dissertation Manuel Gomez-Ramirez –
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BCSC 999-03 Doctoral Dissertation Duje Tadin –
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BCSC 999-04 Doctoral Dissertation Robert Jacobs –
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BCSC 999-05 Doctoral Dissertation Michele Rucci –
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BCSC 999-06 Doctoral Dissertation Adam Snyder –
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BCSC 999-07 Doctoral Dissertation Martina Poletti –
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BCSC 999-08 Doctoral Dissertation Gregory DeAngelis –
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BCSC 999-09 Doctoral Dissertation Rajeev Raizada –
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BCSC 999-10 Doctoral Dissertation Tim Jaeger –
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BCSC 999-11 Doctoral Dissertation Jude Mitchell –
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Number	Title	Instructor	Time
Monday
Monday and Wednesday
BCSC 519-1 Statistics for Brain & Cognitive Sciences Tim Jaeger; Oviya Mohan; Yue Zhang
This course discusses statistical concepts and procedures commonly used in brain and cognitive sciences research. It is a peer-led class, meaning that each student will take part in actively teaching some of the concepts. You will be evaluated on your participation in class and the effort in organizing your lessons. Major topics include: 1) linear models, 2) linear mixed effects models and 3) bayesian data analysis. If time permits, we will go over some more advanced topics in statistics, including MCMC, time series analysis, etc. Prerequisites for undergraduates: STAT 212 or equivalent; research experience from BCSC/NSCI 395 or BCSC 206/207; and programming experience in R, Python, or MATLAB. Interested undergraduates should contact Yue Zhang (yzh191@u.rochester.edu) and Oviya Mohan (omohan@u.rochester.edu).
BCSC 570-1 Introduction to Augmented and Virtual Reality Mujdat Cetin
This course provides a broad introduction to augmented and virtual reality (AR/VR) systems. The course involves lectures covering an overview of all aspects of the AR/VR domain, as well as individual work performed by each student aimed at providing more intensive training on various aspects of AR/VR. Topics covered in the lectures include history, conceptual origins, and design/evaluation principles of AR/VR technologies; overview of visual/auditory/haptic AR/VR interfaces and applications; visual perception; optics/platforms/sensors/displays; auditory perception and spatial audio; silicon hardware architecture and materials; graphics and computation; interfaces and user experience design; data processing and machine intelligence for AR/VR; introduction to AR/VR programming tools; societal implications and ethical aspects. At the end of the course, students will have gained familiarity with the techniques, languages, and cultures of fields integral to the convergent research theme of AR/VR. This course is co-instructed by Mujdat Cetin, Michele Rucci, Ross Maddox, Jannick Rolland, Yuhao Zhu, Andrew White, Chenliang Xu, and Zhen Bai.
BCSC 542-1 Neuropsychology Melinda Patterson
Examines clinical neuropsychology, which bridges neurology, neuroscience, and clinical psychology. Covers history of clinical neuropsychology, principles of neuropsychological assessment, and the interpretation of cognition and behavior as they relate to brain dysfunction. Considers specific neurological syndromes including neurodegenerative, cerebrovascular, toxic, and memory disorders; epilepsy; head trauma; infectious processes; pediatric neuropsychology; psychiatric syndromes; and forensic neuropsychology. Patient presentations (videotape and in-person interviews) supplement lectures. Prerequisite: BCSC 110 or BCSC 240/NSCI 201
Monday, Wednesday, and Friday
BCSC 543-1 Neurochemical Foundations of Behavior Renee Miller
This class covers how the brain controls behavior, and what goes wrong in various diseases, from a neurochemistry perspective. We start by learning about the neurochemicals –neurotransmitters, peptides, growth factors, etc. and move on to their receptors and associated signaling pathways, including gene transcription and epigenetics. An emphasis is placed on primary research literature, experimentation/data analysis and application of knowledge to the interpretation of scientific data. Students will attend research seminars on campus or online and write brief summaries of their understanding. The course culminates in small group presentations about the neurochemistry of diseases of interest, and an individual research review paper on the same topic. Prerequisite: BCSC 240/NSCI 201. BIOL 250 is helpful but not required.
Tuesday
Tuesday and Thursday
BCSC 541-1 Neurons, Circuits, & Systems Farran Briggs
This course takes a bottom-up approach to understanding the neurons and circuits of the sensory systems in the mammalian brain. Thematic topics will include: structural and functional diversity among sensory neuronal populations, common themes across sensory systems such as parallel information processing, coordination among feedforward/feedback circuits, and neuronal plasticity during development of functional domains. The final course module will focus on exploring the neuronal mechanisms of attention, again from a neuron- and circuit-centric perspective. Visual, auditory, and somatosensory systems will be discussed with most emphasis on the visual system as a model for understanding structure/function relationships. The course will also introduce students to modern methodological approaches in systems neuroscience aimed at measuring and manipulating the activity of large populations of neurons while also incorporating information about individual neuronal identity, structure, and circuit connectivity. Prerequisite: BCSC 240/NSCI 201
BCSC 572-1 Practicum in Augmented and Virtual Reality Mujdat Cetin
This is the third course offered as part of the PhD training program on augmented and virtual reality (AR/VR). The goal of the course is to provide interdisciplinary collaborative project experience in AR/VR. The course involves small teams of students from multiple departments working together on semester-long projects on AR/VR with the guidance of one or more faculty involved in the PhD training program. The expected end products of this Practicum course are tangible artifacts that represent what the students have learned, discovered, or invented. Types of artifacts include research papers; patent applications; open-source software; as well as online tutorials and videos for undergraduates, K-12 students, or the general public. Prerequisites: ECE 410-1 or OPT 410-1 or BME 410-1 or BCSC 570-1 or NSCI 415-1 or CSC 413-1 or CVSC 534-1 Instructors: Lead - Mujdat Cetin; Zhen Bai, Jannick Rolland, Michele Rucci
BCSC 433-1 Statistical Speech & Language Processing Daniel Gildea
An introduction to statistical natural language processing and automatic speech recognition techniques. This course presents the theory and practice behind the recently developed language processing technologies that enable applications such as speech-driven dictation systems, document search engines (e.g., finding web pages) and automatic machine translation. Students taking this course at the 400 level will be required to complete additional readings and/or assignments.
BCSC 547-1 Intro to Computational Neuroscience Ralf Haefner
Computational neuroscience studies how the brain can be understood in terms of computations implemented by neural circuits, and in terms of using computational methods to analyze neural and behavioral data. This course for advanced undergraduates and graduate students starts with models of individuals neurons before moving on to networks of neurons and behavior. It provides both a classic signal processing, and a probabilistic perspective on how neurons support the brain’s computations. While primarily lecture-based, an important part of the course are exercises that typically consist on implementing (programming) a model discussed in the class and analyze its behavior. The course also provides the opportunity for a final project but this is not required. The material mostly considers the sensory system and perceptual decision-making. There are no formal prerequisites. However, programming experience and a minimal background in linear algebra (vectors and matrices) and analysis (basic ordinary differential equations) are essential. At the beginning, there will be a very brief introduction to the key biological concepts necessary for the course. In doubt, please email the instructor.
BCSC 520-1 The Intelligent Eye Michele Rucci
Provides an interdisciplinary view of modern research into how the human brain solves the problems involved in perception, including how we perceive the three-dimensional structure of the world, how we recognize objects and how visual information is used to control action in the world. Students read contemporary research and, through classroom discussion and critical essays, explore and analyze the questions and debates that define contemporary perceptual science.
Wednesday
Wednesday and Friday
Thursday
Friday
BCSC 528-1 Special Topics in Vision Duje Tadin
Advanced graduate seminar on a chose problem in vision sciences. In previous years, topics have included motion perception, stereopsis, color vision and visuo-motor control. Readings for the course are drawn from the scientific literature in the topic being covered. Students are typically required to lead discussions on papers.