D. Caffarri – University and INFN Padova A. Alici – P. Antonioli INFN Bologna
April&2016&–INFN&enters&the&& HumanBrainProject...
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April 2016 – INFN enters the Human Brain Project leading the WaveScalES consorCum corCcal slow waves and impulse responses: matching experimental measures vs. large scale simulaCons Pier Stanislao Paolucci WaveScalES coordinator the APE lab INFN Roma January 2016 Pier Stanislao Paolucci INFN enters the Human Brain Project 1
Transcript of April&2016&–INFN&enters&the&& HumanBrainProject...
April 2016 – INFN enters the Human Brain Project
leading the WaveScalES consorCum corCcal slow waves and impulse responses:
matching experimental measures
vs. large scale simulaCons
Pier Stanislao Paolucci WaveScalES coordinator the APE lab -‐ INFN Roma
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 1
Brain Research: ScienCfic and TranslaConal
Europe, brain disorders and trauma cost: 798 billion € /year Increasing, due to the progressive populaNon aging Possible therapies from bePer understanding
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 2
Understanding the Brain, at different levels of abstracNon. Since ever, one of the greatest intellectual ambiNons. A quanNtaNve approach is emerging.
Novel experimental techniques permit a quanNtaNve exploraNon of the Brain Architecture
ComputaConal Neuroscience: an Emerging QuanCtaCve Discipline
Novel Brain Experimental Techniques, mulN-‐modal High SpaNal and Temporal DefiniNon
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 3
SimulaNons on Massive Parallel Computers, Robots, Neuromorphic pla\orms
TheoreNcal Models: Long-‐Range and Short Range Connectome (architecture of connecNons), Dynamic laws for Neuron Membrane PotenNal and Currents and SynapNc PlasNcity (learning), Consciousness Theories
ComputaConal Neuroscience: a kingdom for physics
The Human Brain Project -‐ Intro
q Planned European fund. 500 MEuro, Oct 2013 – 2023 q Original ConsorNum: 112 research insNtutes q Ramp up phase: Oct 2013 – March 2016
q Spring 2015 (also in response to criNcism during first-‐years ramp-‐up phase): q CompeNNve call for new scienNfic proposals/partners (evaluaNon by external
reviewers) q INFN leads the WaveScalES proposal, 4 proposals selected among 57 submiPed
q HBP Commitment: before 2018 define transformaNon into legal enNty q NaNonal Stakeholders board – will be proporNonal to naNonal investments q NaConal /Regional Partnering Projects q ScienNfic Board (presently, 13 + 10 members)
q Periodic (bi-‐annual) plan revision, new compeNNve calls, addiNonal partners
q First HBP operaNonal phase, April 2016-‐March 2018 q WaveScalES starts April 2016, 1 MEuro/year, if good results, unNl 2023 q 5 senior INFN research posiNons funded by WaveScalES q Discussion of next “WaveScalES HBP budget” in 2018
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 4
Slow Waves and PerturbaCons
q During deep-‐sleep and anesthesia the cortex moves in a low-‐complexity mode: q CollecNve oscillaNons, ~ @ 1Hz, between two states:
q Down state: neurons nearly silent (firing @ few Hz) q Up state: neurons acNve (firing @ tens of Hz) for a few hundreds ms, then inhibiNon switch the system to the down-‐state
q Local oscillaNon phase -‐> slow-‐waves moving on the corNcal surface (planar, spirals, …)
q PerturbaNve approach: q Localized spaNo-‐temporal impulse q Measure the impulse response q QuanNficaNon of consciousness potenNal and damages in disease/trauma, forecast of emergence from coma
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 5
References: About the proposal of measurable observables about consciousness and integraCon/differenCaCon and macro/scale connecCvity q Casali et al., (2013) “A TheoreNcally Based Index of Consciousness Independent of Sensory Processing and Behavior” Science TranslaNonal
Medicine q G. Deco, G. Tononi, et al., (2015) “Rethinking segregaNon and integraNon: contribuNons of whole-‐brain modelling” Nature Reviews Neuroscience About Consciousness: example of system of axiomes / postulates focusing on a balance of integraCon and differenCaCon q G. Tononi (2015) “Integrated InformaNon Theory” Scholarpedia q G. Tononi and C. Koch (2015) “Consciousness: here, there and everywhere” Philos. Trans. q SupporCng mathemaCcal framework
q Balduzzi, Tononi (2009) “Integrated InformaNon in Discrete Dynamical Systems: MoNvaNon and TheoreNcal Framework” PLoS ComputaNonal Biology
q Balduzzi, Tononi (2009) “Qualia: The Geometry of Integrated InformaNon” About meso-‐scale corCcal connecCvity models q Schnepel P, et al. (2015) “Physiology and impact of horizontal connecNons in rat neocortex” Cerebral Cortex q T.C. Potjans and M. Diesmann (2014) “The Cell-‐Type Specific CorNcal Microcircuit: RelaNng Structure and AcNvity in a Full-‐Scale Spiking Network
Model”, Cerebral Cortex About pioneering large scale modeling experiments of the thalamo-‐corCcal system q Modha, S. D., & al., (2011) “CogniNve CompuNng”, CommunicaNons of the ACM, q E. M. Izhikevich, G. M. Edelman, (2008) “Large-‐scale model of mammalian thalamocorNcal systems” PNAS About Slow Waves q Destexhe, A., & Contreras, D. (2011).” The Fine Structure of Slow-‐Wave Sleep OscillaNons: from Single Neurons to Large Networks.” Sleep and
Anesthesia q Timofeev, I., & ChauvePe, S. (2011). ”ThalamocorNcal OscillaNons: Local Control of EEG Slow Waves.” Current Topics in Medicinal Chemistry, About DPSNN, the large scale neural simulator developed by the APE lab of INFN in cooperaCon with ISS q P.S. Paolucci, et al., (2015) “Dynamic Many-‐process ApplicaNons on Many-‐Nle Embedded Systems and HPC Clusters: the EURETILE programming
environment and execuNon pla\orms”, Journal of Systems Architecture q P.S. Paolucci, et al. (2015) “Impact of exponenNal long range and Gaussian short range lateral connecNvity on the distributed simulaNon of neural
networks including up to 30 billion synapses “ arXiv:1512.05264 q P.S. Paolucci, et al.. (2013) “Distributed simulaNon of polychronous and plasNc spiking neural networks: strong and weak scaling of a
representaNve mini-‐applicaNon benchmark executed on a small-‐scale commodity cluster”. arXiv:1310.8478 q M. Masa, P. Del Giudice (2000) “Efficient Event-‐Driven SimulaNon of Large Networks of Spiking Neurons and Dynamical Synapses. Neural
ComputaNon”
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 6
WaveScalES in HBP -‐ Summary
q Experimental WaveScalES partners (will) measure brain Slow Waves during deep-‐sleep and anaesthesia, and during the transiNon to consciousness, including: q non invasive techniques on human: high-‐def. electro-‐encephalographic response to trans-‐cranial magneNc sNmulaNons
q electro-‐physiological response to in-‐vitro/in-‐vivo opto-‐pharmacologic sNmulaNon of murine models
q INFN in WaveScalES – mainly in collab. with ISS Roma q large scale parallel/distributed simulaNon of Slow Waves and perturbaNon responses
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 7
WaveScalES measures: from the human
bedside downto the murine slice.
TMS/EEG to assess the changes in corNcal connecNvity and complexity in physiological and pathological condiNons;
IntracorNcal single-‐pulse electrical sNmulaNons (SPES) and stereo-‐EEG recordings in combinaNon with scalp hd-‐EEG to link slow-‐wave dynamics to overall network connecNvity and complexity.
Electrical / opNcal sNmulaNons / recordings in brain (slices) to study the effects of (opto)-‐pharmacological manipulaNons on bistability, connecNvity and complexity.
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 8
WaveScalES: Research Tasks Understand mulNscale brain exploiNng Slow-‐Wave AcNvity (SWA) as a RosePa stone. Five Tasks: 1. Slow-‐wave acNvity changes
during sleep/anesthesia (leader: ISS Roma: Masa, Del Giudice)
2. Slow-‐wave and complexity: from the micro-‐scale to the bedside (leader: UniMi: Massimini)
3. Slow-‐wave acNvity in murine transgenic models of neurological disease
4. ModulaNon of slow-‐wave acNvity with opto-‐pharmacology
5. Slow wave simulaNon pla\orms (leader: INFN)
INFN (with ISS): Large-‐scale spiking simulaNons (hundreds of billions synapses) distributed over (tens of) thousands of MPI processes, including columnar, areal and inter-‐areal connecNvity models. ComputaNonal objecNves: match, explain and predict experimental observaNons. Improve simulators / HPC interconnects
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 9
Pier Stanislao Paolucci – parallel compuCng CV
q Since 1984, member of APE massive parallel comp. lab, INFN Roma led by Nicola Cabibbo, Giorgio Parisi
q Inventor/developer of parallelizaNon algorithms, parallel hardware architectures, system sovware tools, applied to: q QCD, mulNdim. FFT, meteorology (cubed-‐sphere), syntheNc aperture
radar, oil exploraNon, acousNc arrays, digital signal processing, mulN-‐processor systems-‐on-‐chip, …, large scale neural networks
q 2010-‐2015 Coordinator, European FP7 Project EURETILE, 5M€ q 2006-‐2009 Coordinator, European FP6 Project SHAPES, 9M€ q 2000-‐2010 Chief Technical Officer, Atmel Roma design center (NASDAQ:
ATML), 4 year tech. tranf. detachment, then part-‐Nme researcher unNl 2010, then back to INFN (full-‐Nme researcher) q US patent 6,766,439, US patent 7,437,540 q 2000-‐2006 Coordinator, Eureka Project DIAM,
q 1997-‐2000 Principal InvesNgator, ESPRIT European proj. mAgic-‐FPU
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 10
WaveScalES partners/key-‐persons
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project
Pier Stanislao Paolucci
Piero Vicini
Maria Victoria Sanchez-Vives
Julia Weinert
Marcello Massimini
Mario Rosanova
Pau Gorostiza
Miquel Bosch
Maurizio Mattia
Paolo Del Giudice
1) INFN, Istituto Nazionale di Fisica Nucleare, APE Parallel Computing Lab, Roma, Italy
2) Consorci Institut d´Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain – Murine electro-physiology
3) Università degli Studi di Milano, Italy – Measures in humans
4) Fundació Institut de Bioenginyeria de Catalunya, Spain – optopharmacological perturbations
5) Istituto Superiore di Sanità, Italy – theoretical models
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Development of Distributed PlasCc Spiking Neural Net Simulator in INFN-‐
q INFN coordinated EURETILE(2010 -‐ 2015) FP7 project q InvesNgaNon of future generaNons of distributed/parallel computers q Focus on sovware/hardware scalability on many core systems q Start of DPSNN-‐STDP code development as a source of requirements
and architectural inspiraNon for extreme parallel compuNng q The brain consumes < 50 W computaNons. A high abstracNon simulator of
its computaNons would require >> 50 MW on present generaNon HPC q INFN third party of ISS Roma in CORTICONIC (2013 – 2016) FP7 project
q IdenNfy computaNonal principles of the cerebral cortex q First comparison with in-‐vivo/in-‐vitro experimental results q DPSNN improved for CORTICONIC simulaNons (support of more
realisNc biological models) imporNng models from ISS Perseo scalar simulator
q DPSNN simulator key benchmark in EXANEST (2016-‐2018) FET Project (INFN, Piero Vicini) – good overlap and development potenNal for APE lab
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 12
Strong Scaling of our simulator, measured up to 1024 cores, 20 Gsynapses
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 13
P.S. Paolucci, et. al (2015) arXiv:1512.05264
(very small scale example of) neural net simulaCon
q 200 inhibitory neurons q 800 excitatory neurons q Time resoluNon: 1ms
q (horizontal axis) q Each dot in the rastergram
represents an individual spike q The evoluNon of the membrane
potenNal of individual neurons is simulated
q The evoluNon of individual synapNc strength is computed (not shown in the picture)
q individual synapNc delays are taken into account
q Individual connecNons and neural types can be programmed January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 14
Examples of recent experimental development: White Ma\er Long Range Connectome
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 15
Year 1909 -‐ Brodmann CorNcal Areas Defined
Image: John A Beal CC-‐BY license. 2005 Louisiana State Univ.
Ȼ(2009) Mark Dow
Year 2015 – White maPer mapping, DTI -‐ fiber tractography
Experimental techniques… an ample room for INFN contribuCons
A few examples of novel (last ten years) techniques that are transforming brain research in a quanNtaNve discipline:
q Connectome by DTI-‐Fiber tractography: measure of the (probability of) long-‐range connecNons among brain areas (white maPer…)
q opto-‐geneNc/opto-‐pharmacology: real-‐Nme visualizaNon of neuro-‐synapNc acNvity and short-‐range connecNon (probability)
q High definiNon Electro Encephalography and MulN-‐unit Electrode Arrays: hundreds of electro-‐physiological acquisiNon/sNmulaNon channels
q FuncNonal MagneNc Resonance Imaging (areas vs. tasks correlaNon) q Measure of synapNc STDP (Spiking Time Dependent PlasNcity): understanding
Nme-‐dependent causal/anN-‐causal learning and temporal arrow q ComputaNonally efficient models of neural acNvity/spiking (20 arithmeNc
operaNons / (neuron * simulated ms); Parallel/distributed compuNng q QuanNtaNve Complexity/Consciousness Indexes/Theories
q …ample room for improvement, e.g. number of acquisiNon channels, spaNal /temporal resoluNon, (and capacity to manage large teams of researchers
q Possible INFN contribuNon on experimental methods January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 16
INFN APE lab
Team (10 people): q (staff, Roma 1):
q Piero Vicini, Pier Stanislao Paolucci, Alessandro Lonardo q (art. 36, Roma 2):
q Roberto Ammendola q (Temporary posiNons, mainly funded by European Projects, Roma 1)
q Andrea Biagioni, OPorino Frezza, Francesca Lo Cicero, Michele MarNnelli, Elena Pastorelli, Francesco Simula
q Long term brain research would benefit from a long term perspecCve for research personnel. Investment in know-‐how (personnel) should be secured
q Created in 1984 by Nicola Cabibbo & Giorgio Parisi q Since then research & development of parallelizaNon algorithms, system
sovware and hardware architectures for numerical simulaNons /digital signal processing / HPC
q Several technological / industrial spin-‐off
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Conclusions
q Brain: emergence of a quanNtaNve discipline, scienNfic and translaNonal impact q Novel experimental methodologies, MulN-‐scale Theories, ComputaNonal
Neuroscience q WaveScalES in Human Brain Project
q Combines experiments, theory and simulaNons q Several opportuniCes for INFN to be explored…also about the experimental
measures/treatment techniques q Long term brain research in INFN will benefit from a long term perspecCve.
Investment in know-‐how (INFN research personnel) should be secured. Adequate computaConal resources needed. Investment (from overhead, in kind and support of naConal projects) will be key to play a key role in the HBP naConal stakeholders board.
q Opportunity for Regional/NaConal HBP Partnering Projects q Strong collaboraNon with ISS (Del Giudice, Masa), Brain SimulaNon a key
benchmark also in EXANEST FET Project (INFN, Vicini) future interconnects/storage, strategic overlap exists
q DidacNc/employment opportunity: complex system numerical/theoreNcal physics
January 2016 -‐ Pier Stanislao Paolucci INFN enters the Human Brain Project 18
