34 research outputs found
Collective analog bioelectronic computation
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references (p. 677-710).In this thesis, I present two examples of fast-and-highly-parallel analog computation inspired by architectures in biology. The first example, an RF cochlea, maps the partial differential equations that describe fluid-membrane-hair-cell wave propagation in the biological cochlea to an equivalent inductor-capacitor-transistor integrated circuit. It allows ultra-broadband spectrum analysis of RF signals to be performed in a rapid low-power fashion, thus enabling applications for universal or software radio. The second example exploits detailed similarities between the equations that describe chemical-reaction dynamics and the equations that describe subthreshold current flow in transistors to create fast-and-highly-parallel integrated-circuit models of protein-protein and gene-protein networks inside a cell. Due to a natural mapping between the Poisson statistics of molecular flows in a chemical reaction and Poisson statistics of electronic current flow in a transistor, stochastic effects are automatically incorporated into the circuit architecture, allowing highly computationally intensive stochastic simulations of large-scale biochemical reaction networks to be performed rapidly. I show that the exponentially tapered transmission-line architecture of the mammalian cochlea performs constant-fractional-bandwidth spectrum analysis with O(N) expenditure of both analysis time and hardware, where N is the number of analyzed frequency bins. This is the best known performance of any spectrum-analysis architecture, including the constant-resolution Fast Fourier Transform (FFT), which scales as O(N logN), or a constant-fractional-bandwidth filterbank, which scales as O (N2).(cont.) The RF cochlea uses this bio-inspired architecture to perform real-time, on-chip spectrum analysis at radio frequencies. I demonstrate two cochlea chips, implemented in standard 0.13m CMOS technology, that decompose the RF spectrum from 600MHz to 8GHz into 50 log-spaced channels, consume < 300mW of power, and possess 70dB of dynamic range. The real-time spectrum analysis capabilities of my chips make them uniquely suitable for ultra-broadband universal or software radio receivers of the future. I show that the protein-protein and gene-protein chips that I have built are particularly suitable for simulation, parameter discovery and sensitivity analysis of interaction networks in cell biology, such as signaling, metabolic, and gene regulation pathways. Importantly, the chips carry out massively parallel computations, resulting in simulation times that are independent of model complexity, i.e., O(1). They also automatically model stochastic effects, which are of importance in many biological systems, but are numerically stiff and simulate slowly on digital computers. Currently, non-fundamental data-acquisition limitations show that my proof-of-concept chips simulate small-scale biochemical reaction networks at least 100 times faster than modern desktop machines. It should be possible to get 103 to 106 simulation speedups of genome-scale and organ-scale intracellular and extracellular biochemical reaction networks with improved versions of my chips. Such chips could be important both as analysis tools in systems biology and design tools in synthetic biology.by Soumyajit Mandal.Ph.D
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Examing the evidence for a pitch centre in human auditory cortex: a multi method approach
This PhD used a combination of psychophysical, functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) methods to evaluate the evidence for a pitch centre within auditory cortex according to the four pitch criteria: 1) pitch selectivity, 2) pitch constancy, 3) covariation with pitch salience, and 4) accounting for confounding factors, that were described in an article by Hall and Plack (2009). An fMRI study re-examined pitch criteria 1, 3 and 4 using stimuli and a subtractive study design informed by Penagos et al. (2004), but extended this work by addressing some of their limitations. Results indicated that the representation of pitch compared to noise is widely distributed across auditory cortex, while the evidence for an effect of pitch salience was questionable given that the weak pitch salience condition was not significantly different from matched noise at a group level. These findings raise concerns regarding fMRIâs sensitivity to pitch salience effects in the context of high individual variability. An ERP âadaptationâ study evaluated pitch criteria 1, 2 and 4 using pitch and timbre stimulus parameters that had been previously matched for discriminability, and sequences either varied in pitch, timbre or both across listeners. Findings from both sensor and source-based analyses suggested that pitch responses may be influenced by timbre (i.e., non-invariant); although further research is required. Thus, evidence failed to support the notion of pitch constancy at the level of the auditory cortex. Further studies using psychophysical listening paradigms continued this work, and again seemed to confirm a lack of evidence for pitch constancy. Reaction times and accuracy data demonstrated that timbre changes (non-target stimulus) interfered with listenerâs ability to discriminate pitch (target stimulus), and vice versa. Overall, these convergent results suggest that there is no modular representation of pitch (pitch centre), but rather pitch processing sites are distributed throughout multiple areas of primary and non-primary auditory cortex and are seemingly non-invariant to other stimulus parameters related to its perception (e.g., timbre). Under this assumption, the spatio-temporal model of pitch perception may best describe the neural mechanism underpinning pitch perception. Several recommendations are made to address challenges to interpretation identified throughout this PhD, which are likely to guide further research in this area
Neural plasticity and the limits of scientific knowledge
Western science claims to provide unique, objective information about the world. This
is supported by the observation that peoples across cultures will agree upon a common
description of the physical world. Further, the use of scientific instruments and
mathematics is claimed to enable the objectification of science.
In this work, carried out by reviewing the scientific literature, the above claims are
disputed systematically by evaluating the definition of physical reality and the scientific
method, showing that empiricism relies ultimately upon the human senses for the
evaluation of scientific theories and that measuring instruments cannot replace the
human sensory system.
Nativist and constructivist theories of human sensory development are reviewed, and it
is shown that nativist claims of core conceptual knowledge cannot be supported by the
findings in the literature, which shows that perception does not simply arise from a
process of maturation. Instead, sensory function requires a long process of learning
through interactions with the environment.
To more rigorously define physical reality and systematically evaluate the stability of
perception, and thus the basis of empiricism, the development of the method of
dimension analysis is reviewed. It is shown that this methodology, relied upon for the
mathematical analysis of physical quantities, is itself based upon empiricism, and that
all of physical reality can be described in terms of the three fundamental dimensions of
mass, length and time.
Hereafter the sensory modalities that inform us about these three dimensions are
systematically evaluated. The following careful analysis of neuronal plasticity in these
modalities shows that all the relevant senses acquire from the environment the capacity
to apprehend physical reality. It is concluded that physical reality is acquired rather than
given innately, and leads to the position that science cannot provide unique results.
Rather, those it can provide are sufficient for a particular environmental setting
The neurobiology of cortical music representations
Music is undeniable one of humanityâs defining traits, as it has been documented since the earliest
days of mankind, is present in all knowcultures and perceivable by all humans nearly alike.
Intrigued by its omnipresence, researchers of all disciplines started the investigation of musicâs
mystical relationship and tremendous significance to humankind already several hundred
years ago. Since comparably recently, the immense advancement of neuroscientific methods
also enabled the examination of cognitive processes related to the processing of music. Within
this neuroscience ofmusic, the vast majority of research work focused on how music, as an auditory
stimulus, reaches the brain and howit is initially processed, aswell as on the tremendous
effects it has on and can evoke through the human brain. However, intermediate steps, that is
how the human brain achieves a transformation of incoming signals to a seemingly specialized
and abstract representation of music have received less attention. Aiming to address this gap,
the here presented thesis targeted these transformations, their possibly underlying processes
and how both could potentially be explained through computational models. To this end, four
projects were conducted. The first two comprised the creation and implementation of two
open source toolboxes to first, tackle problems inherent to auditory neuroscience, thus also affecting
neuroscientific music research and second, provide the basis for further advancements
through standardization and automation. More precisely, this entailed deteriorated hearing
thresholds and abilities in MRI settings and the aggravated localization and parcellation of the
human auditory cortex as the core structure involved in auditory processing. The third project
focused on the humanâs brain apparent tuning to music by investigating functional and organizational
principles of the auditory cortex and network with regard to the processing of different
auditory categories of comparable social importance, more precisely if the perception of music
evokes a is distinct and specialized pattern. In order to provide an in depth characterization
of the respective patterns, both the segregation and integration of auditory cortex regions was
examined. In the fourth and final project, a highly multimodal approach that included fMRI,
EEG, behavior and models of varying complexity was utilized to evaluate how the aforementioned
music representations are generated along the cortical hierarchy of auditory processing
and how they are influenced by bottom-up and top-down processes. The results of project 1
and 2 demonstrated the necessity for the further advancement of MRI settings and definition
of working models of the auditory cortex, as hearing thresholds and abilities seem to vary as
a function of the used data acquisition protocol and the localization and parcellation of the
human auditory cortex diverges drastically based on the approach it is based one. Project 3
revealed that the human brain apparently is indeed tuned for music by means of a specialized
representation, as it evoked a bilateral network with a right hemispheric weight that was not
observed for the other included categories. The result of this specialized and hierarchical recruitment
of anterior and posterior auditory cortex regions was an abstract music component
ix
x SUMMARY
that is situated in anterior regions of the superior temporal gyrus and preferably encodes music,
regardless of sung or instrumental. The outcomes of project 4 indicated that even though
the entire auditory cortex, again with a right hemispheric weight, is involved in the complex
processing of music in particular, anterior regions yielded an abstract representation that varied
excessively over time and could not sufficiently explained by any of the tested models. The
specialized and abstract properties of this representation was furthermore underlined by the
predictive ability of the tested models, as models that were either based on high level features
such as behavioral representations and concepts or complex acoustic features always outperformed
models based on single or simpler acoustic features. Additionally, factors know to influence
auditory and thus music processing, like musical training apparently did not alter the
observed representations. Together, the results of the projects suggest that the specialized and
stable cortical representation of music is the outcome of sophisticated transformations of incoming
sound signals along the cortical hierarchy of auditory processing that generate a music
component in anterior regions of the superior temporal gyrus by means of top-down processes
that interact with acoustic features, guiding their processing.Musik ist unbestreitbarer Weise eine der definierenden Eigenschaften des Menschen. Dokumentiert
seit den fruÌhesten Tagen der Menschheit und in allen bekannten Kulturen vorhanden,
ist sie von allenMenschen nahezu gleichwahrnehmbar. Fasziniert von ihrerOmniprÀsenz
haben Wissenschaftler aller Disziplinen vor einigen hundert Jahren begonnen die mystische
Beziehung zwischen Musik und Mensch, sowie ihre enorme Bedeutung fuÌr selbigen zu untersuchen.
Seit einem vergleichsweise kurzem Zeitraum ist es durch den immensen Fortschritt
neurowissenschafticher Methoden auch möglich die kognitiven Prozesse, welche an der Verarbeitung
von Musik beteiligt, sind zu untersuchen. Innerhalb dieser Neurowissenschaft der
Musik hat sich ein GroĂteil der Forschungsarbeit darauf konzentriert wie Musik, als auditorischer
Stimulus, das menschliche Gehirn erreicht und wie sie initial verarbeitet wird, als auch
welche kolossallen Effekte sie auf selbiges hat und auch dadurch bewirken kann. Jedoch haben
die Zwischenschritte, also wie das menschliche Gehirn eintreffende Signale in eine scheinbar
spezialisierte und abstrakte ReprÀsentation vonMusik umwandelt, vergleichsweise wenig Aufmerksamkeit
erhalten. Um die dadurch entstandene LuÌcke zu adressieren, hat die hier vorliegende
Dissertation diese Prozesse und wie selbige durch Modelle erklÀrt werden können in
vier Projekten untersucht. Die ersten beiden Projekte beinhalteten die Herstellung und Implementierung
von zwei Toolboxen um erstens, inhÀrente Probleme der auditorischen Neurowissenschaft,
daher auch neurowissenschaftlicher Untersuchungen von Musik, zu verbessern
und zweitens, eine Basis fuÌr weitere Fortschritte durch Standardisierung und Automatisierung
zu schaffen. Im genaueren umfasste dies die stark beeintrÀchtigten Hörschwellen und
âfĂ€higkeiten in MRT-Untersuchungen und die erschwerte Lokalisation und Parzellierung des
menschlichen auditorischen Kortex als Kernstruktur auditiver Verarbeitung. Das dritte Projekt
befasste sich mit der augenscheinlichen Spezialisierung von Musik im menschlichen Gehirn
durch die Untersuchung funktionaler und organisatorischer Prinzipien des auditorischen
Kortex und Netzwerks bezuÌglich der Verarbeitung verschiedener auditorischer Kategorien vergleichbarer
sozialer Bedeutung, im genaueren ob die Wahrnehmung von Musik ein distinktes
und spezialisiertes neuronalenMuster hervorruft. Umeine ausfuÌhrliche Charakterisierung
der entsprechenden neuronalen Muster zu ermöglichen wurde die Segregation und Integration
der Regionen des auditorischen Kortex untersucht. Im vierten und letzten Projekt wurde
ein hochmultimodaler Ansatz,welcher fMRT, EEG, Verhalten undModelle verschiedener KomplexitÀt
beinhaltete, genutzt, umzu evaluieren, wie die zuvor genannten ReprÀsentationen von
Musik entlang der kortikalen Hierarchie der auditorischen Verarbeitung generiert und wie sie
möglicherweise durch Bottom-up- und Top-down-AnsÀtze beeinflusst werden. Die Ergebnisse
von Projekt 1 und 2 demonstrierten die Notwendigkeit fuÌr weitere Verbesserungen von MRTUntersuchungen
und die Definition eines Funktionsmodells des auditorischen Kortex, daHörxi
xii ZUSAMMENFASSUNG
schwellen und âfĂ€higkeiten stark in AbhĂ€ngigkeit der verwendeten Datenerwerbsprotokolle
variierten und die Lokalisation, sowie Parzellierung des menschlichen auditorischen Kortex
basierend auf den zugrundeliegenden AnsÀtzen drastisch divergiert. Projekt 3 zeigte, dass das
menschliche Gehirn tatsÀchlich eine spezialisierte ReprÀsentation vonMusik enthÀlt, da selbige
als einzige auditorische Kategorie ein bilaterales Netzwerk mit rechtshemisphÀrischer Gewichtung
evozierte. Aus diesemNetzwerk, welches die Rekrutierung anteriorer und posteriorer
Teile des auditorischen Kortex beinhaltete, resultierte eine scheinbar abstrakte ReprÀsentation
von Musik in anterioren Regionen des Gyrus temporalis superior, welche prÀferiert Musik enkodiert,
ungeachtet ob gesungen oder instrumental. Die Resultate von Projekt 4 deuten darauf
hin, dass der gesamte auditorische Kortex, erneut mit rechtshemisphÀrischer Gewichtung, an
der komplexen Verarbeitung vonMusik beteiligt ist, besonders aber anteriore Regionen, die bereits
genannten abstrakte ReprĂ€sentation hervorrufen, welche sich exzessiv uÌber die Zeitdauer
derWahrnehmung verÀndert und nicht hinreichend durch eines der getestetenModelle erklÀrt
werden kann. Die spezialisierten und abstrakten Eigenschaften dieser ReprÀsentationen wurden
weiterhin durch die prÀdiktiven FÀhigkeiten der getestetenModelle unterstrichen, daModelle,
welche entweder auf höheren Eigenschaften wie VerhaltensreprÀsentationen und mentalen
Konzepten oder komplexen akustischen Eigenschaften basierten, stets Modelle, welche
auf niederen Attributen wie simplen akustischen Eigenschaften basierten, uÌbertrafen. ZusĂ€tzlich
konnte kein Effekt von Faktoren, wie z.B. musikalisches Training, welche bekanntermaĂen
auditorische und daherMusikverarbeitung beeinflussen, nachgewiesen werden.
Zusammengefasst deuten die Ergebnisse der Projekte darauf, hin dass die spezialisierte und
stabile kortikale ReprÀsentation vonMusik ein Resultat komplexer Prozesse ist, welche eintreffende
Signale entlang der kortikalen Hierarchie auditorischer Verarbeitung in eine abstrakte
ReprÀsentation vonMusik innerhalb anteriorer Regionen des Gyrus temporalis superior durch
Top-Down-Prozesse, welche mit akustischen Eigenschaften interagieren und deren Verarbeitung
steuern, umwandeln
Investigating the build-up of precedence effect using reflection masking
The auditory processing level involved in the buildâup of precedence [Freyman et al., J. Acoust. Soc. Am. 90, 874â884 (1991)] has been investigated here by employing reflection masked threshold (RMT) techniques. Given that RMT techniques are generally assumed to address lower levels of the auditory signal processing, such an approach represents a bottomâup approach to the buildup of precedence. Three conditioner configurations measuring a possible buildup of reflection suppression were compared to the baseline RMT for four reflection delays ranging from 2.5â15 ms. No buildup of reflection suppression was observed for any of the conditioner configurations. Buildup of template (decrease in RMT for two of the conditioners), on the other hand, was found to be delay dependent. For five of six listeners, with reflection delay=2.5 and 15 ms, RMT decreased relative to the baseline. For 5â and 10âms delay, no change in threshold was observed. It is concluded that the lowâlevel auditory processing involved in RMT is not sufficient to realize a buildup of reflection suppression. This confirms suggestions that higher level processing is involved in PE buildup. The observed enhancement of reflection detection (RMT) may contribute to active suppression at higher processing levels
29th Annual Computational Neuroscience Meeting: CNS*2020
Meeting abstracts
This publication was funded by OCNS. The Supplement Editors declare that they have no competing interests.
Virtual | 18-22 July 202
25th Annual Computational Neuroscience Meeting: CNS-2016
Abstracts of the 25th Annual Computational Neuroscience
Meeting: CNS-2016
Seogwipo City, Jeju-do, South Korea. 2â7 July 201