Clustering of neural activity: A design principle for population codes

We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement

Optimal Encoding in Stochastic Latent-Variable Models.

In this work we explore encoding strategies learned by statistical models of sensory coding in noisy spiking networks. Early stages of sensory communication in neural systems can be viewed as encoding channels in the information-theoretic sense. However, neural populations face constraints not commonly considered in communications theory. Using restricted Boltzmann machines as a model of sensory encoding, we find that networks with sufficient capacity learn to balance precision and noise-robustness in order to adaptively communicate stimuli with varying information content. Mirroring variability suppression observed in sensory systems, informative stimuli are encoded with high precision, at the cost of more variable responses to frequent, hence less informative stimuli. Curiously, we also find that statistical criticality in the neural population code emerges at model sizes where the input statistics are well captured. These phenomena have well-defined thermodynamic interpretations, and we discuss their connection to prevailing theories of coding and statistical criticality in neural populations

From statistical mechanics to machine learning: effective models for neural activity

In the retina, the activity of ganglion cells, which feed information through the optic nerve to the rest of the brain, is all that our brain will ever know about the visual world. The interactions between many neurons are essential to processing visual information and a growing body of evidence suggests that the activity of populations of retinal ganglion cells cannot be understood from knowledge of the individual cells alone. Modelling the probability of which cells in a population will fire or remain silent at any moment in time is a difficult problem because of the exponentially many possible states that can arise, many of which we will never even observe in finite recordings of retinal activity. To model this activity, maximum entropy models have been proposed which provide probabilistic descriptions over all possible states but can be fitted using relatively few well-sampled statistics. Maximum entropy models have the appealing property of being the least biased explanation of the available information, in the sense that they maximise the information theoretic entropy. We investigate this use of maximum entropy models and examine the population sizes and constraints that they require in order to learn nontrivial insights from finite data. Going beyond maximum entropy models, we investigate autoencoders, which provide computationally efficient means of simplifying the activity of retinal ganglion cells

Critical bistability and large-scale synchrony in human brain dynamics

Neurophysiological dynamics of the brain, overt behaviours, and private experiences of the mind are co-emergent and co-evolving phenomena. An adult human brain contains ~100 billion neurons that are hierarchically organized into intricate networks of functional units comprised of interconnected neurons. It has been hypothesized that neurons within a functional unit communicate with each other or neurons from other units via synchronized activity. At any moment, cascades of synchronized activity from millions of neurons propagate through networks of all sizes, and the levels of synchronization wax and wane. How to understand cognitive functions or diseases from such rich dynamics poses a great challenge. The brain criticality hypothesis proposes that the brain, like many complex systems, optimize its performance by operating near a critical point of phase transition between disorder and order, which suggests complex brain dynamics be effectively studied by combining computational and empirical approaches. Hence, the brain criticality framework requires both classic reductionist and reconstructionist approaches. Reconstructionism in the current context refers to addressing the “Wholeness” of macro-level emergence due to fundamental mechanisms such as synchrony between neurons in the brain. This thesis includes five studies and aims to advance theory, empirical evidence, and methodology in the research of neuronal criticality and large-scale synchrony in the human brain. Study I: The classic criticality theory is based on the hypothesis that the brain operates near a continuous, second order phase transition between order and disorder in resource-conserving systems. This idea, however, cannot explain why the brain, a non-conserving system, often shows bistability, a hallmark of first order, discontinuous phase transition. We used computational modeling and found that bistability may occur exclusively within the critical regime so that the first-order phase transition emerged progressively with increasing local resource demands. We observed that in human resting-state brain activity, moderate α-band (11 Hz) bistability during rest predicts cognitive performance, but excessive resting-state bistability in fast (> 80 Hz) oscillations characterizes epileptogenic zones in patients’ brain. These findings expand the framework of brain criticality and show that near-critical neuronal dynamics involve both first- and second-order phase transitions in a frequency-, neuroanatomy-, and state-dependent manner. Study II: Long-range synchrony between cortical oscillations below ~100 Hz is pervasive in brain networks, whereas oscillations and broad-band activities above ~100 Hz have been considered to be strictly local phenomena. We showed with human intracerebral recordings that high-frequency oscillations (HFOs, 100−400 Hz) may be synchronized between brain regions separated by several centimeters. We discovered subject-specific frequency peaks of HFO synchrony and found the group-level HFO synchrony to exhibit laminar-specific connectivity and robust community structures. Importantly, the HFO synchrony was both transiently enhanced and suppressed in separate sub-bands during tasks. These findings showed that HFO synchrony constitutes a functionally significant form of neuronal spike-timing relationships in brain activity and thus a new mesoscopic indication of neuronal communication per se. Studies III: Signal linear mixing in magneto- (MEG) and electro-encephalography (EEG) artificially introduces linear correlations between sources and confounds the separability of cortical current estimates. This linear mixing effect in turn introduces false positives into synchrony estimates between MEG/EEG sources. Several connectivity metrics have been proposed to supress the linear mixing effects. We show that, although these metrics can remove false positives caused by instantaneous mixing effects, all of them discover false positive ghost interactions (SIs). We also presented major difficulties and technical concerns in mapping brain functional connectivity when using the most popular pairwise correlational metrics. Study IV and V: We developed a novel approach as a solution to the SIs problem. Our approach is to bundle observed raw edges, i.e., true interactions or SIs, into hyperedges by raw edges’ adjacency in signal mixing. We showed that this bundling approach yields hyperedges with optimal separability between true interactions while suffers little loss in the true positive rate. This bundling approach thus significantly decreases the noise in connectivity graphs by minimizing the false-positive to true-positive ratio. Furthermore, we demonstrated the advantage of hyperedge bundling in visualizing connectivity graphs derived from MEG experimental data. Hence, the hyperedges represent well the true cortical interactions that are detectable and dissociable in MEG/EEG sources. Taken together, these studies have advanced theory, empirical evidence, and methodology in the research of neuronal criticality and large-scale synchrony in the human brain. Study I provided modeling and empirical evidence for linking bistable criticality and the classic criticality hypothesis into a unified framework. Study II was the first to reveal HFO phase synchrony in large-scale neocortical networks, which was a fundamental discovery of long-range neuronal interactions on fast time-scale per se. Study III raised awareness of the ghost interaction (SI) problem for a critical view on reliable interpretation of MEG/EEG connectivity, and for the development of novel approaches to address the SI problem. Study IV offered a practical solution to the SI problem and opened a new avenue for mapping reliable MEG/EEG connectivity. Study V described the technical details of the hyperedge bundling approach, shared the source code and specified the simulation parameters used in Study IV.Ihmisaivojen neurofysiologinen dynamiikka, ihmisen käyttäytyminen, sekä yksityiset mielen kokemukset syntyvät ja kehittyvät rinnakkaisina ilmiöinä. Ihmisen aivot koostuvat ~100 miljardista hierarkisesti järjestäytyneestä hermosolusta, jotka toisiinsa kytkeytyneinä muodostavat monimutkaisen verkoston toiminnallisia yksiköitä. Hermosolujen aktiivisuuden synkronoitumisen on esitetty mahdollistavan neuronien välisen kommunikoinnin toiminnallisten yksiköiden sisällä sekä niiden välillä. Hetkenä minä hyvänsä, synkronoidun aktiivisuuden kaskadit etenevät aivojen erikokoisissa verkostoissa jatkuvasti heikentyen ja voimistuen. Kognitiivisten funktioiden ja erilaisten aivosairauksien ymmärtäminen tulkitsemalla aivojen rikasta dynamiikkaa on suuri haaste. Kriittiset aivot -hypoteesi ehdottaa aivojen, kuten monien muidenkin kompleksisten systeemien, optimoivan suorituskykyään operoimalla lähellä kriittistä pistettä järjestyksen ja epäjärjestyksen välissä, puoltaen sitä, että aivojen kompleksisia dynamiikoita voitaisiin tutkia yhdistämällä laskennallisia ja empiirisiä lähestymistapoja. Aivojen kriittisyyden viitekehys edellyttää perinteistä reduktionismia ja rekonstruktionismia. Erityisesti, rekonstruktionismi tähtää kuvaamaan aivojen makrotason “yhteneväisyyden” syntymistä perustavanlaatuisten mekaniikoiden, kuten aivojen toiminnallisten yksiköiden välisen synkronian avulla. Tämä väitöskirja sisältää viisi tutkimusta, jotka edistävät teoriaa, empiirisiä todisteita ja metodologiaa aivojen kriittisyyden ja laajamittaisen synkronian tutkimuksessa. Tutkimus I tarjosi mallinnuksia ja empiirisiä todisteita bistabiilin kriittisyyden ja klassisen kriittisyyden hypoteesien yhdistämiseksi yhdeksi viitekehykseksi. Tutkimus II oli ensimmäinen laatuaan paljastaen korkeataajuisten oskillaatioiden (high-frequency oscillation, HFO) vaihesynkronian laajamittaisissa neokortikaalisissa verkostoissa, mikä oli perustavanlaatuinen löytö pitkän matkan neuronaalisista vuorovaikutuksista nopeilla aikaskaaloilla. Tutkimus III lisäsi tietoisuutta aave-vuorovaikutuksien (spurious interactions, SI) ongelmasta MEG/EEG kytkeytyvyyden luotettavassa tulkinnassa sekä uudenlaisten menetelmien kehityksessä SI-ongelman ratkaisemiseksi. Tutkimus IV tarjosi käytännöllisen “hyperedge bundling” -ratkaisun SI-ongelmaan ja avasi uudenlaisen tien luotettavaan MEG/EEG kytkeytyvyyden kartoittamiseen. Tutkimus V kuvasi teknisiä yksityiskohtia hyperedge bundling -menetelmästä, jakoi menetelmän lähdekoodin ja täsmensi tutkimuksessa IV käytettyjä simulaatioparametreja. Yhdessä nämä tutkimukset ovat edistäneet teoriaa, empiirisiä todisteita ja metodologiaa neuronaalisen kriittisyyden sekä laajamittaisen synkronian hyödyntämisessä ihmisaivojen tutkimuksessa

Laboratory Directed Research and Development Program FY 2004 Annual Report

The Oak Ridge National Laboratory (ORNL) Laboratory Directed Research and Development (LDRD) Program reports its status to the U.S. Department of Energy (DOE) in March of each year. The program operates under the authority of DOE Order 413.2A, 'Laboratory Directed Research and Development' (January 8, 2001), which establishes DOE's requirements for the program while providing the Laboratory Director broad flexibility for program implementation. LDRD funds are obtained through a charge to all Laboratory programs. This report describes all ORNL LDRD research activities supported during FY 2004 and includes final reports for completed projects and shorter progress reports for projects that were active, but not completed, during this period. The FY 2004 ORNL LDRD Self-Assessment (ORNL/PPA-2005/2) provides financial data about the FY 2004 projects and an internal evaluation of the program's management process. ORNL is a DOE multiprogram science, technology, and energy laboratory with distinctive capabilities in materials science and engineering, neutron science and technology, energy production and end-use technologies, biological and environmental science, and scientific computing. With these capabilities ORNL conducts basic and applied research and development (R&D) to support DOE's overarching national security mission, which encompasses science, energy resources, environmental quality, and national nuclear security. As a national resource, the Laboratory also applies its capabilities and skills to the specific needs of other federal agencies and customers through the DOE Work For Others (WFO) program. Information about the Laboratory and its programs is available on the Internet at <http://www.ornl.gov/>. LDRD is a relatively small but vital DOE program that allows ORNL, as well as other multiprogram DOE laboratories, to select a limited number of R&D projects for the purpose of: (1) maintaining the scientific and technical vitality of the Laboratory; (2) enhancing the Laboratory's ability to address future DOE missions; (3) fostering creativity and stimulating exploration of forefront science and technology; (4) serving as a proving ground for new research; and (5) supporting high-risk, potentially high-value R&D. Through LDRD the Laboratory is able to improve its distinctive capabilities and enhance its ability to conduct cutting-edge R&D for its DOE and WFO sponsors. To meet the LDRD objectives and fulfill the particular needs of the Laboratory, ORNL has established a program with two components: the Director's R&D Fund and the Seed Money Fund. As outlined in Table 1, these two funds are complementary. The Director's R&D Fund develops new capabilities in support of the Laboratory initiatives, while the Seed Money Fund is open to all innovative ideas that have the potential for enhancing the Laboratory's core scientific and technical competencies. Provision for multiple routes of access to ORNL LDRD funds maximizes the likelihood that novel and seminal ideas with scientific and technological merit will be recognized and supported

Characterising pattern asymmetry in pigmented skin lesions

Abstract. In clinical diagnosis of pigmented skin lesions asymmetric pigmentation is often indicative of melanoma. This paper describes a method and measures for characterizing lesion symmetry. The estimate of mirror symmetry is computed first for a number of axes at different degrees of rotation with respect to the lesion centre. The statistics of these estimates are the used to assess the overall symmetry. The method is applied to three different lesion representations showing the overall pigmentation, the pigmentation pattern, and the pattern of dermal melanin. The best measure is a 100% sensitive and 96% specific indicator of melanoma on a test set of 33 lesions, with a separate training set consisting of 66 lesions

Hope College Abstracts: 18th Annual Celebration of Undergraduate Research and Creative Activity

The 18th Annual Celebration of Undergraduate Research and Creative Activity was held on April 12, 2019 in the Richard and Helen DeVos Fieldhouse at Hope College and featured student-faculty collaborative research projects. This program is a record reflective of those projects between the 2018-2019 academic year