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CS Department Colloquium Series

Detecting COVID-19 with Genomic Sequencing: From bench to vending machine

Date and Time
Tuesday, February 21, 2023 - 12:30pm to 1:30pm
Location
Computer Science Small Auditorium (Room 105)
Type
CS Department Colloquium Series
Speaker
Dr. Eleazar Eskin , from UCLA
Host
Ben Raphael

At UCLA we developed one of the only novel technologies for COVID-19 diagnostic testing that was deployed on a large scale.  The assay, which we named SwabSeq, performs genomic sequencing of pooled samples tagged with sample-specific molecular barcodes and then uses computational approaches to deconvolve the pooled samples into individual diagnoses, enabling the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction.   The efficiency of SwabSeq has enabled a small facility with a handful of staff to perform over 1,500,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR test with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.

 

Bio:  Dr. Eleazar Eskin is the founding Chair of the Department of Computational Medicine at UCLA.  He is also a Professor in the Computational Medicine, Computer Science and Human Genetics departments.  His research focuses on developing computational methods for the analysis of genetic variation and discovering the genetic basis of human disease.  He was a founding faculty of multiple academic programs at UCLA including the Bioinformatics Ph.D. Program, the Undergraduate Minor in Bioinformatics, the Bruins in Genomics Summer Research Program and the Computational Genomics Summer Institute.  He is a Fellow of the International Society of Computational Biology and a Alfred P Sloan Foundation Research Fellow. To learn more about Eleazar's work please visit: http://web.cs.ucla.edu/~eeskin/

 

To request accommodations for a disability, please contact Michael Estepp at mestepp@cs.princeton.edu at least one week prior to the event.

Enabling the Immersive Era of Computing

Date and Time
Wednesday, February 1, 2023 - 4:30pm to 5:30pm
Location
Computer Science Small Auditorium (Room 105)
Type
CS Department Colloquium Series
Speaker
Sarita Adve, from University of Illinois at Urbana-Champaign
Host
Kai Li & Sharad Malik

Sarita Adve
Computing is on the brink of a new immersive era. Recent innovations in virtual/augmented/mixed reality (extended reality or XR) show the potential for a new immersive modality of computing that will transform most human activities and change how we design, program, and use computers.  There is, however, an orders of magnitude gap between the power/performance/quality-of-experience (QoE) attributes of current and desirable immersive systems. Bridging this gap requires an ambitious systems research agenda that is end-to-end QoE driven, is based on hardware-software-algorithm co-design, and spans the end-user device, edge, and cloud. To enable this agenda, my group has built ILLIXR (Illinois eXtended Reality testbed), an open source XR system and testbed for end-to-end immersive systems research. I will describe ILLIXR and the research it has enabled across the computing stack. I will also discuss the industry supported ILLIXR consortium launched to democratize XR systems research, development, and benchmarking, and the Center for Immersive Computing at Illinois spanning immersive hardware to applications research and education.

Bio: Sarita Adve is the Richard T. Cheng Professor of Computer Science at the University of Illinois at Urbana-Champaign where she directs the Center for Immersive Computing. Her research interests span the system stack, ranging from hardware to applications. Her work on the data-race-free, Java, and C++ memory models forms the foundation for memory models used in most hardware and software systems today.  Recently, her group released ILLIXR (Illinois Extended Reality testbed), an open-source extended reality system and research testbed, and launched the ILLIXR consortium to democratize XR research, development, and benchmarking. She is also known for her work on heterogeneous systems and software-driven approaches for hardware resiliency. She is a member of the American Academy of Arts and Sciences, a fellow of the ACM and IEEE, and a recipient of the ACM/IEEE-CS Ken Kennedy award. As ACM SIGARCH chair, she co-founded the CARES movement, winner of the CRA distinguished service award, to address discrimination and harassment in Computer Science research events. She received her PhD from the University of Wisconsin-Madison and her B.Tech. from the Indian Institute of Technology, Bombay.

Co-sponsored by the Department of Computer Science and the Department of Electrical and Computer Engineering

Unpatched Vulnerabilities in Cellular Standards

Date and Time
Friday, November 11, 2022 - 4:30pm to 6:00pm
Location
Engineering Quadrangle B205
Type
CS Department Colloquium Series
Speaker
Host
Maria Apostolaki and Prateek Mittal

Yongdae Kim
In a couple of years, "study items" for the 6G security standard will be set. Security issues not included in these study items are unlikely to be standardized and patched even in 6G. Therefore, before these study items are set, the security research community needs to put in effort to find security vulnerabilities in cellular standards up to 5G. Furthermore, as a community, we need to find solutions to these vulnerabilities that are practical enough to be accepted by the standard bodies. In this talk, I will introduce unpatched design vulnerabilities and attacks in cellular standards up to 5G. I will also talk about potential defense mechanisms and reasons why they have not been accepted in 3GPP so far.

Bio: Yongdae Kim is a Professor in the Department of Electrical Engineering and the Graduate School of Information Security and a head of Police Science and Technology Research Center at KAIST. He received a PhD degree from the computer science department at the University of Southern California in 2002. Before joining KAIST in 2012, he was a professor in the Department of Computer Science and Engineering at the University of Minnesota - Twin Cities for 10 years. He served as a KAIST Chair Professor between 2013 and 2016 and a director of Cyber Security Research Center between 2018 and 2020.  He is currently serving as a steering committee member of ACM WISEC and served as a general chair for ACM CCS 2021, a program committee chair for ACM WISEC 2022, an associate editor for ACM TOPS and a steering committee member of NDSS. His main research interest is finding and fixing novel vulnerabilities for emerging technologies such as drones, self-driving cars, and cellular networks.


This seminar is partially supported with funds from the Korhammer Lecture Series

Sponsored by: Electrical and Computer Engineering, Computer Science, and the Center for Information Technology Policy

Learning Meets Gravity: Robots that Embrace Dynamics from Pixels

Date and Time
Monday, November 7, 2022 - 12:30pm to 1:30pm
Location
Computer Science Small Auditorium (Room 105)
Type
CS Department Colloquium Series
Host
Szymon Rusinkiewicz

Shuran Song
Despite the incredible capabilities (speed, repeatability) of our hardware, most robot manipulators today are deliberately programmed to avoid dynamics – moving slow enough so they can adhere to quasi-static assumptions about the world. In contrast, people frequently (and subconsciously) make use of dynamic phenomena to manipulate everyday objects – from unfurling blankets to tossing trash, to improve efficiency and physical reach range. These abilities are made possible by an intuition of physics, a cornerstone of intelligence. How do we impart the same on robots?

In this talk, I will discuss how we might enable robots to leverage dynamics for manipulation in unstructured environments. Modeling the complex dynamics of unseen objects from pixels is challenging. However, by tightly integrating perception and action, we show it is possible to relax the need for accurate dynamical models. Thereby, allowing robots to (i) learn dynamic skills for complex objects, (ii) adapt to new scenarios using visual feedback, and (iii) use their dynamic interactions to improve their understanding of the world. By changing the way we think about dynamics – from avoiding it to embracing it – we can simplify a number of classically challenging problems, leading to new robot capabilities.

Bio: Shuran Song is an Assistant Professor in the Department of Computer Science at Columbia University. Before that, she received her Ph.D. in Computer Science at Princeton University, BEng. at HKUST. Her research interests lie at the intersection of computer vision and robotics. Song’s research has been recognized through several awards including the Best Paper Awards at RSS’22 and T-RO’20, Best System Paper Awards at CoRL’21, RSS’19, and Amazon Robotics’18, and finalist at RSS’22, ICRA'20, CVPR'19, RSS’19, and IROS'18. She is also a recipient of the NSF Career Award, as well as research awards from Microsoft, Toyota Research, Google, Amazon, JP Morgan, and Sloan Foundation. To learn more about Shuran’s work please visit: https://www.cs.columbia.edu/~shurans/


To request accommodations for a disability, please contact Emily Lawrence at emilyl@cs.princeton.edu at least one week prior to the event.

 

The Power of Intelligent Language Models

Date and Time
Monday, November 21, 2022 - 12:30pm to 1:30pm
Location
Computer Science Small Auditorium (Room 105)
Type
CS Department Colloquium Series
Host
Elad Hazan

Adam Kalai
Recently, large language models have been trained on intelligent languages including natural languages, such as English, and programming languages, such as Python. We will examine several interesting applications of these models. First, they can be used to enumerate human stereotypes and discriminatory biases, suggesting that they must be used carefully. Second, they can be used to generate and solve their own programming puzzles, which can be used in a self-training pipeline to solve increasingly challenging algorithmic programming problems. Third, we illustrate how they can be used to simulate numerous human participants in classic behavioral economic and psychology experiments, such as the ultimatum game, risk aversion, garden path sentences, and the Milgram shock experiment. Finally, we discuss future directions in using these language models to understand intelligent animal communication in connection with ProjectCETI, which aims to understand the communication of sperm whales.

Bio: Adam Tauman Kalai is a Senior Principal Researcher at Microsoft Research New England. His research includes work on machine learning, artificial intelligence and algorithms.  He received his BA from Harvard and PhD from CMU. He has served as an Assistant Professor at Georgia Tech and the Toyota Technological Institute at Chicago. He has co-chaired AI and crowdsourcing conferences including the Conference on Learning Theory (COLT), the Conference on Human Computation and Crowdsourcing (HCOMP), and New England Machine Learning Day (NEML). His honors include an NSF CAREER award and an Alfred P. Sloan fellowship.


To request accommodations for a disability, please contact Emily Lawrence at emilyl@cs.princeton.edu at least one week prior to the event.

Large Language Models: Will they keep getting bigger? And, how will we use them if they do?

Date and Time
Thursday, November 17, 2022 - 12:30pm to 1:30pm
Location
Friend Center Convocation Room
Type
CS Department Colloquium Series
Host
Danqi Chen

Luke Zettlemoyer
The trend of building ever larger language models has dominated much research in NLP over the last few years. In this talk, I will discuss our recent efforts to (at least partially) answer two key questions in this area: Will we be able to keep scaling? And, how will we actually use the models, if we do? I will cover our recent efforts on learning new types of sparse mixtures of experts (MoEs) models. Unlike model-parallel algorithms for learning dense models, which are very difficult to further scale with existing hardware, our sparse approaches have significantly reduced cross-node communication costs and could possibly provide the next big leap in performance, although finding a version that scales well in practice remains an open challenge. I will also present our recent work on prompting language models that better controls for surface form variation, to improve performance of models that are so big we can only afford to do inference, with little to no task-specific fine tuning. Finally, time permitting, I will discuss work on new forms of supervision for language model training, including learning from the hypertext and multi-modal structure of web pages to provide new signals for both learning and prompting the model. Together, these methods present our best guesses for how to keep the scaling trend alive as we move forward to the next generation of NLP models. 

This talk describes work done at the University of Washington and Meta, primarily led by Armen Aghajanyan, Suchin Gururangan, Ari Holtzmann, Mike Lewis, Margaret Li, Sewon Min, and Peter West. 

Bio: Luke Zettlemoyer is a Professor in the Paul G. Allen School of Computer Science & Engineering at the University of Washington, and a Research Director at Meta. His research focuses on empirical methods for natural language semantics, and involves designing machine learning algorithms, introducing new tasks and datasets, and, most recently, studying how to best develop self-supervision signals for pre-training. His honors include being named an ACL Fellow as well as winning a PECASE award, an Allen Distinguished Investigator award, and multiple best paper awards. Luke received his PhD from MIT and was a postdoc at the University of Edinburgh.


To request accommodations for a disability, please contact Emily Lawrence at emilyl@cs.princeton.edu at least one week prior to the event.

This talk is co-sponsored by Computer Science and the Center for Statistics and Machine Learning.

This talk will be recorded and live streamed on Princeton University Media Central.  See link here.

Illuminating protein space with a programmable generative model

Date and Time
Thursday, November 10, 2022 - 12:30pm to 1:30pm
Location
Computer Science Small Auditorium (Room 105)
Type
CS Department Colloquium Series
Host
Ellen Zhong

John Ingraham
Three billion years of evolution have produced a tremendous diversity of protein molecules, but it is yet unknown how thoroughly evolution has sampled the space of possible protein folds and functions. Here, by introducing a new, scalable generative prior for proteins and protein complexes, we provide further evidence that earth's extant molecular biodiversity represents only a small fraction of what is possible for polypeptides. To enable this, we introduce customized neural networks that enable long-range reasoning, that respect the statistical structures of polymer ensembles, and that can efficiently realize 3D structures of proteins from predicted geometries. We show how this framework broadly enables protein design under auxiliary constraints, which can be any composition of semantics, substructure, symmetries, shape, and even natural language prompts.

Bio: John Ingraham is the Head of Machine Learning at Generate Biomedicines, Inc, where he leads a team of scientists and engineers developing new kinds of machine learning systems for protein design. He has spent most of his career developing structured statistical models of the rich diversity found in protein sequences and structures, including as a postdoc at MIT CSAIL with Tommi Jaakkola and Regina Barzilay working on some of the first generative models for structure-based sequence design and before that in his PhD with Debora Marks at Harvard Medical School developing deep learning and statistical-physics inspired models of deep evolutionary sequence variation and protein folding.


To request accommodations for a disability, please contact Emily Lawrence at emilyl@cs.princeton.edu at least one week prior to the event.

This talk will not be recorded or live streamed.

New Algorithms for Large-scale Species Tree Estimation

Date and Time
Monday, September 19, 2022 - 10:30am to 11:30am
Location
Computer Science Small Auditorium (Room 105)
Type
CS Department Colloquium Series
Host
Ben Raphael

Tandy Warnow
Constructing the Tree of Life (i.e., a species tree containing all of the extant species) is a Scientific Grand Challenge that is surprisingly difficult from a computational and statistical perspective.  One of the challenges is that different parts of the genome evolve down different trees, due to processes such as incomplete lineage sorting (ILS) and gene duplication and loss (GDL). In this talk, I will present new algorithms that can estimate species trees under both processes with high accuracy, even on very large datasets (thousands of species and genes).  Moreover, our new methods for species tree estimation addressing GDL do not require knowledge of orthology.  Some of this work is unpublished.

Bio: Tandy Warnow is the Grainger Distinguished Chair in Engineering in the Department of Computer Science at the University of Illinois at Urbana-Champaign. Tandy received her PhD in Mathematics at UC Berkeley under the direction of Gene Lawler, and her research focuses on reconstructing complex and large-scale evolutionary histories. She was awarded the David and Lucile Packard Foundation Award (1996), a Radcliffe Institute Fellowship (2003), and the John Simon Guggenheim Foundation Fellowship (2011). She was elected a Fellow of the Association for Computing Machinery (ACM) in 2015 and of the Association for the Advancement of Science (AAAS) in 2021.


To request accommodations for a disability, please contact Emily Lawrence at emilyl@cs.princeton.edu at least one week prior to the event.

This talk will not be recorded or live streamed.

Programmability, Scalability, and Security for Reconfigurable Computing in the Cloud

Date and Time
Monday, September 19, 2022 - 12:30pm to 1:30pm
Location
Computer Science Small Auditorium (Room 105)
Type
CS Department Colloquium Series
Host
Kai Li

Deming Chen
Reconfigurable Computing uses FPGAs (Field-Programmable Gate Arrays) as an alternative to microprocessors to enable high-performance and low-energy customized computing. It is becoming a mainstream technology as evident by Intel’s $16.7B acquisition of Altera in 2015 and AMD’s $49B acquisition of Xilinx in 2022. However, challenges remain in terms of FPGA programmability, scalability, and security before reconfigurable computing makes a transformative impact in the computing world, especially in the cloud. In this talk, Dr. Chen will present some new concepts and research results that demonstrate initial promises to overcome these challenges, including shared virtual memory system for computing with FPGAs, scalable high-level synthesis for FPGA programming, and trusted execution environment with accelerators. These results are developed within the AMD-Xilinx Center of Excellence and the Hybrid-Cloud Thrust of the IBM-Illinois Discovery Accelerator Institute at UIUC.  
 
Bio: Deming Chen is the Abel Bliss Professor of the Grainger College of Engineering at University of Illinois at Urbana-Champaign (UIUC). His current research interests include reconfigurable computing, hybrid cloud, system-level design methodologies, machine learning and acceleration, and hardware security. He has published more than 250 research papers, received ten Best Paper Awards and one ACM/SIGDA TCFPGA Hall-of-Fame Paper Award, and given more than 130 invited talks. He is an IEEE Fellow, an ACM Distinguished Speaker, and the Editor-in-Chief of ACM Transactions on Reconfigurable Technology and Systems (TRETS). He is the Director of the AMD-Xilinx Center of Excellence and the Hybrid-Cloud Thrust Co-Lead of the IBM-Illinois Discovery Accelerator Institute at UIUC. He has been involved in several startup companies, such as AutoESL and Inspirit IoT. He received his Ph.D. from the Computer Science Department of UCLA in 2005.


To request accommodations for a disability, please contact Emily Lawrence at emilyl@cs.princeton.edu at least one week prior to the event.

This talk will be recorded and live streamed on the Princeton University Media Central.  See link here.

Experiencing a New Internet Architecture

Date and Time
Thursday, May 26, 2022 - 2:00pm to 3:00pm
Location
Engineering Quadrangle B205
Type
CS Department Colloquium Series
Speaker
Host
Prateek Mittal & Jen Rexford

Andrian Perrig
Imagining a new Internet architecture enables us to explore new networking concepts without the constraints imposed by the current infrastructure. What are the benefits of a multi-path inter-domain routing protocol that finds dozens of paths? What about a data plane without inter-domain forwarding tables on border routers? What secure systems can we build if a router can derive a symmetric key for any host on the Internet within nanoseconds?

In this presentation, we invite you to join us on our 12-year long expedition of creating the SCION next-generation secure Internet architecture. SCION has already been deployed at several ISPs and domains, and has been in production use since 2017. On our journey, we have found that path-aware networking and multipath communication not only provide security benefits, but also enable higher efficiency for communication, increase network capacity, and can even provide opportunities for reducing the carbon footprint of communication.

Bio: Adrian Perrig is a Professor at the Department of Computer Science at ETH Zürich, Switzerland, where he leads the network security group. He is also a Distinguished Fellow at CyLab, and an Adjunct Professor of Electrical and Computer Engineering at Carnegie Mellon University. From 2002 to 2012, he was a Professor of Electrical and Computer Engineering, Engineering and Public Policy, and Computer Science (courtesy) at Carnegie Mellon University. From 2007 to 2012, he served as the technical director for Carnegie Mellon's Cybersecurity Laboratory (CyLab). He earned his MS and PhD degrees in Computer Science from Carnegie Mellon University, and spent three years during his PhD at the University of California at Berkeley. He received his BSc degree in Computer Engineering from EPFL. He is a recipient of the ACM SIGSAC Outstanding Innovation Award. Adrian is an ACM and IEEE Fellow. Adrian's research revolves around building secure systems -- in particular his group is working on the SCION secure Internet architecture.


This seminar is supported with funds from the Korhammer Lecture Series
Sponsored by the departments of Electrical & Computer Engineering and Computer Science

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