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Events for February 12, 2016
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Multi-scale integration and modularity in complex dynamical systems
Fri, Feb 12, 2016 @ 11:00 AM - 12:00 PM
Information Sciences Institute
Conferences, Lectures, & Seminars
Speaker: Artemy Kolchinsky, Santa Fe Institute
Talk Title: AI Seminar-Multi-scale integration and modularity in complex dynamical systems
Series: Artificial Intelligence Seminar
Abstract: I will discuss two novel approaches to studying distributed organization in complex dynamical systems. In the first [1], we define an information-theoretic measure of the strength of integration at multiple scales, where scale is defined according to an underlying distance metric. We show that our method generalizes several existing complexity measures and is tractable to compute. As demonstrated on human resting state fMRI time-series data, it also captures important aspects of integration in network- and spatially-embedded systems.
In the second approach [2], we address modularity, a pattern of organization in which a system is composed of weakly-coupled subsystems. We develop a technique to decompose dynamical systems based on the idea that modules constrain the spread of perturbations. The method captures variation of modular organization across different system states, time scales, and in response to different kinds of perturbations. It also offers a principled alternative to community detection applied to statistical-dependency networks (e.g. correlation matrices or "functional networks").
[1] A Kolchinsky, MP van den Heuvel, A Griffa, P Hagmann, LM Rocha, O Sporns and J Goñi, Multi-scale Integration and Predictability in Resting State Brain Activity, Frontiers Neuroinformatics, 2014. http://journal.frontiersin.org/article/10.3389/fninf.2014.00066/abstract
[2] A Kolchinsky, AJ Gates, and LM Rocha, Modularity and the spread of perturbations in complex dynamical systems, PRE, 2015. http://arxiv.org/abs/1509.04386
Biography: Artemy Kolchinsky received his PhD from the Center for Complex Systems and Networks, Dept of Informatics, Indiana University Bloomington in 2015. He is currently a postdoctoral fellow at the Santa Fe Institute, collaborating on projects involving optimal compression of dynamical systems as well as thermodynamic constraints on computation. He is broadly interested in novel methods for understanding multivariate dynamics in application to computational neuroscience, evolutionary biology, and other complex systems.
Host: Greg Ver Steeg
Webcast: http://webcasterms1.isi.edu/mediasite/Viewer/?peid=f413ecae075e40eaa3f6b51123178b791dLocation: Information Science Institute (ISI) - 11th Flr Conf Rm # 1135, Marina Del Rey
WebCast Link: http://webcasterms1.isi.edu/mediasite/Viewer/?peid=f413ecae075e40eaa3f6b51123178b791d
Audiences: Everyone Is Invited
Contact: Peter Zamar
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Facebook's Datacenter and Backbone Networks
Fri, Feb 12, 2016 @ 12:00 PM - 01:20 PM
Information Sciences Institute
Conferences, Lectures, & Seminars
Speaker: Dr. Rishi Sinha, Facebook
Talk Title: Facebook's Datacenter and Backbone Networks
Abstract: This talk will cover the design, operational, performance and capacity issues in global networking for large online services, using Facebook as a case study. We will describe Facebook's datacenter and backbone network architecture, explain the characteristics and unique demands of traffic generated in serving a billion daily users, detail the motivations for Facebook's decisions to adopt a next-generation fabric network architecture and to design its own network switches and accompanying operating system, and provide insights into the protocol and software engineering work that is applied to solving performance and capacity challenges in Facebook's network. Finally, we will point to open areas for research and commercialization.
Biography: Dr. Sinha is a performance capacity engineer at Facebook and leads several projects on server capacity planning, network capacity planning, efficiency, and data center logistics. Prior to joining Facebook at 2012, he worked at Brocade where he developed analysis tools for flow control bottlenecks in storage networks, and at Akamai where he worked on reliability of real-time streaming. He has extensive experience in packet flow analysis, experimentation and implementation of internet-scale systems and has four patents on networking related technologies. Dr. Sinha is a Trojan and completed his PhD at USC in 2006.
Host: Alefiya Hussain
Location: Mark Taper Hall Of Humanities (THH) - 210
Audiences: Everyone Is Invited
Contact: Alefiya Hussain
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W.V.T. Rusch Engineering Honors Program Colloquium
Fri, Feb 12, 2016 @ 01:00 PM - 01:50 PM
USC Viterbi School of Engineering, Viterbi School of Engineering Student Affairs
University Calendar
Join us for a presentation by Prof. George Bekey, from the University of Southern California, titled, "Ethical Issues Associated with Self-Driving Cars."
Location: Seeley G. Mudd Building (SGM) - 123
Audiences: Everyone Is Invited
Contact: Ramon Borunda/Academic Services
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Systems Cellular-Molecular Bioengineering Distinguished Speaker Series
Fri, Feb 12, 2016 @ 01:00 PM - 02:00 PM
Alfred E. Mann Department of Biomedical Engineering
Conferences, Lectures, & Seminars
Speaker: Elliot Botvinick, Associate Professor of Biomedical Engineering, UC Irvine
Talk Title: Feeling Pericellular Mechanical Heterogeneities
Abstract: While there is strong evidence for roles of bulk stromal stiffness in cell regulation, roles for the pericellular mechanical microenvironment are less clear, in large part due to the difficulty of measurement. My group implements automated Active Microrheology (aAMR), an optical tweezers technology, to probe extracellular stiffness and map it in the volume surrounding cells. Our aAMR applies sinusoidal optical forces onto microbeads embedded within natural extracellular matrices (ECMs), including those comprised of fibrin and type 1 collagen. As in the case of passive microrheology, aAMR reports the complex material response function of the ECM just surrounding each microbead. Different from passive methods, aAMR is valid for systems not in thermal equilibrium, as is typical for regions of the ECM near to contractile cells. Our aAMR microscope can probe many beads surrounding each cell to map the mechanical landscape, allowing us to seek correlations between local stiffness distributions and cell properties such as contractility, signaling, and differentiation. I will present specific examples for which the distribution of pericellular stiffness correlates with cell phenotype/state including: MT1-MMP deficient mesenchymal stem cells, human aortic smooth muscle cells with compromised contractility and fibrosarcoma cells cultured in type 1 collagen gels.
Biography: My research program has two areas of focus: mechanobiology and medical device development. My research group uses photonic tools to investigate roles for mechanical forces and physical properties in the regulation of tissues. We have expertise in the areas of photonics, laser ablation, imaging, tissue engineering and mechanobiology. Specifically, we develop instrumentation and devices for quantitative biophysical measurements towards the study of single molecule biophysics and cell-tissue physical interactions. In particular, we use optical tweezers to measure single receptor-ligand interactions and have discovered strong evidence for the role of ligand-endocytic forces in the activation of the Notch receptor. We also use optical tweezers/scissors to measure local continuum viscoelastic parameters in order to seek correlations between microenvironment mechanics and cell function. We have applied these tools to test mechanical hypotheses in the areas of cancer biology, microvascular morphogenesis, tissue engineering, stem cell biology and the transition of ductal carcinoma in situ into an invasive phenotype.
Host: Megan McCain
More Information: botvinick_flyer.pdf
Location: Corwin D. Denney Research Center (DRB) - 146
Audiences: Everyone Is Invited
Contact: Megan McCain
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Munushian Seminar - Rahul Sarpeshkar, Friday, February 12th at 2:00pm in EEB 132
Fri, Feb 12, 2016 @ 02:00 PM - 03:30 PM
Ming Hsieh Department of Electrical and Computer Engineering
Conferences, Lectures, & Seminars
Speaker: Rahul Sarpeshkar, Dartmouth College
Talk Title: Analog and Stochastic Computation in Living Cells and Supercomputing Chips
Abstract: Despite more than 15 years of research, synthetic circuits in living cells have been largely limited to a handful of digital logic gates and have not scaled. We show that one important reason for this failure to scale is an overemphasis on digital abstractions rather than on recognizing the true noisy, analog, and probabilistic nature of biological circuits. We show that synthetic and natural DNA, RNA, and protein circuits in cells must use analog, collective analog, probabilistic, and hybrid analog-digital computational approaches to function; otherwise, even relatively simple computations in cells will exceed energy, molecular-count, and cellular-resource budgets.
Analog circuits in electronics and molecular circuits in cell biology are also deeply connected: There are astounding similarities between the equations that describe noisy electronic flow in subthreshold transistors and the equations that describe noisy molecular flow in chemical reactions, both of which obey the laws of exponential thermodynamics. Based on these similarities, it is possible to take a principled approach to design circuits in living cells. For example, we have engineered logarithmic analog computation in living cells with less than three transcription factors, almost two orders of magnitude more efficient than prior digital approaches to create a "bio-molecular slide rule". In addition, highly computationally intensive noisy DNA-protein and protein-protein networks can be rapidly simulated in mixed-signal supercomputing chips that naturally capture their noisiness, dynamics, and non-modular interactions at lightning-fast speeds. Such an approach may enable large-scale design, analysis, simulation, and measurement of cells to be more precise and robust than it is today. To realize the promise of synthetic biology and systems biology for medicine, biotechnology, agriculture, and energy, we will need to go back to the future of computation and design and implement circuits via a collective analog approach like Nature does. We must also exploit and develop existing analog and mixed-signal electronic design tools for enabling biological design to scale.
Biography: Rahul Sarpeshkar is the Thomas E. Kurtz Professor and a Professor in the departments of Engineering, Microbiology & Immunology, Physics, and Physiology & Neurobiology at Dartmouth College. His research creates novel wet DNA-protein circuits in living cells and also advanced dry nanoelectronic circuits on silicon chips. His longstanding work on analog and biological computation and his most recent work have helped pioneer the field of analog synthetic biology. His work on a glucose fuel cell for medical implants was featured by Scientific American among 2012's 10 World Changing Ideas.
He holds over 36 awarded patents and has authored more than 127 publication, including one that was featured on the cover of Nature. His recent book, Ultra Low Power Bioelectronics: Fundamentals, Biomedical Applications, and Bio-inspired Systems revealed the deep connections between analog transistor circuits and biochemical circuits. His work has led to several first or best records in analog, bio-inspired, synthetic biology, medical device, ultra low power, and energy harvesting systems. His work has applications in implantable medical devices for the deaf, blind, and paralyzed and in biotechnology and medical applications that benefit from cellular engineering. He has received several awards including the NSF Career Award, the ONR Young Investigator Award, and the Packard Fellows Award. He received Bachelor's degrees in Electrical Engineering and Physics at MIT and PhD at CalTech. Before he joined Dartmouth's faculty, he was a tenured professor at MIT where he led the Analog Circuits and Biological Systems Group. Before he joined MIT, he was a member of the technical staff of Bell Labs' division of biological computation.
Host: EE-EP
Location: Hughes Aircraft Electrical Engineering Center (EEB) - 132
Audiences: Everyone Is Invited
Contact: Marilyn Poplawski
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NL Seminar-Recent Advances in Neural Machine Translation
Fri, Feb 12, 2016 @ 03:00 PM - 04:00 PM
Information Sciences Institute
Conferences, Lectures, & Seminars
Speaker: Thang Luong, Stanford University
Talk Title: Recent Advances in Neural Machine Translation
Series: Natural Language Seminar
Abstract: Neural Machine Translation (NMT) is a simple new architecture for getting machines to learn to translate. At its core, NMT is a single big recurrent neural network that is trained end-to-end with several advantages such as simplicity and generalization. Despite being relatively new, NMT has already been showing promising results in various translation tasks. In this talk, I will give an overview of NMT and highlight my recent work on (a) how to address the rare word problem in NMT, (b) how to improve the attention (alignment) mechanism, and (c) how to leverage data from other modalities to improve translation.
Biography: Thang Luong is currently a 5th-year PhD student in the Stanford NLP group under Prof. Chris Manning. In the past, he has published papers on various different NLP-related areas such as digital library, machine translation, speech recognition, parsing, psycholinguistics, and word embedding learning. Recently, his main interest shifts towards the area of deep learning using sequence to sequence models to tackle various NLP problems, especially neural machine translation. He has built state-of-the-art (academically) neural machine translation systems both at Google and at Stanford.
Host: Xing Shi and Kevin Knight
More Info: http://nlg.isi.edu/nl-seminar/
Location: Information Science Institute (ISI) - 6th Flr Conf Rm # 689, Marina Del Rey
Audiences: Everyone Is Invited
Contact: Peter Zamar
Event Link: http://nlg.isi.edu/nl-seminar/
