New Techniques in Deep Representation Learning

Thesis (Ph.D.)--University of Washington, 2016-06

Spreading and synchronization of intrinsic signals in visual cortex of macaque monkey evoked by a localized visual stimulus

Spatio-temporal maps of the occipital cortex of macaque monkeys were analyzed using optical imaging of intrinsic signals. The images obtained during localized visual stimulation (IS) were compared with the images obtained on presentation of a blank screen (IB). We first investigated spontaneous variations of the intrinsic signals by analyzing the 100 IBs for each of the three cortical areas. Slow periodical activation was observed in alternation over the cortical areas. Cross-correlation analysis indicated that synchronization of spontaneous activation only took place within each cortical area, but not between them. When a small, drifting grating (2degreesX2degrees) was presented on the fovea. a dark spot appeared in the optical image at the cortical representation of this retinal location. It spread bilaterally along the border between V1 and V2, continuing as a number of parallel dark bands covering a large area of the lateral surface of V1. Cross-correlation analysis showed that during visual stimulation the intrinsic signals over all of the three cortical areas were synchronized, with in-phase activation of V1 and V2 and anti-phase activation of V4 and V1/V2. The significance of these extensive synergistic and antagonistic interactions between different cortical areas is discussed. (C) 2003 Elsevier B.V. All rights reserved.

A study of pyramidal cell structure in the cingulate cortex of the macaque monkey with comparative notes on inferotemporal and primary visual cortex

Recent studies have revealed a marked degree of variation in the pyramidal cell phenotype in visual, somatosensory, motor and prefrontal cortical areas in the brain of different primates, which are believed to subserve specialized cortical function. In the present study we carried out comparisons of dendritic structure of layer III pyramidal cells in the anterior and posterior cingulate cortex and compared their structure with those sampled from inferotemporal cortex (IT) and the primary visual area (V1) in macaque monkeys. Cells were injected with Lucifer Yellow in flat-mounted cortical slices, and processed for a light-stable DAB reaction product. Size, branching pattern, and spine density of basal dendritic arbors was determined, and somal areas measured. We found that pyramidal cells in anterior cingulate cortex were more branched and more spinous than those in posterior cingulate cortex, and cells in both anterior and posterior cingulate were considerably larger, more branched, and more spinous than those in area V1. These data show that pyramidal cell structure differs between posterior dysgranular and anterior granular cingulate cortex, and that pyramidal neurons in cingulate cortex have different structure to those in many other cortical areas. These results provide further evidence for a parallel between structural and functional specialization in cortex.

Visual thalamocortical projections in the flying fox: Parallel pathways to striate and extrastriate areas

We studied thalamic projections to the visual cortex in flying foxes, animals that share neural features believed to resemble those present in the brains of early primates. Neurones labeled by injections of fluorescent tracers in striate and extrastriate cortices were charted relative to the architectural boundaries of thalamic nuclei. Three main findings are reported: First, there are parallel lateral geniculate nucleus (LGN) projections to striate and extrastriate cortices. Second, the pulvinar complex is expansive, and contains multiple subdivisions. Third, across the visual thalamus, the location of cells labeled after visual cortex injections changes systematically, with caudal visual areas receiving their strongest projections from the most lateral thalamic nuclei, and rostral areas receiving strong projections from medial nuclei. We identified three architectural layers in the LGN, and three subdivisions of the pulvinar complex. The outer LGN layer contained the largest cells, and had strong projections to the areas V1, V2 and V3. Neurones in the intermediate LGN layer were intermediate in size, and projected to V1 and, less densely, to V2. The layer nearest to the origin of the optic radiation contained the smallest cells, and projected not only to V1, V2 and V3, but also, weakly, to the occipitotemporal area (OT, which is similar to primate middle temporal area) and the occipitoparietal area (OP, a third tier area located near the dorsal midline). V1, V2 and V3 received strong projections from the lateral and intermediate subdivisions of the pulvinar complex, while OP and OT received their main thalamic input from the intermediate and medial subdivisions of the pulvinar complex. These results suggest parallels with the carnivore visual system, and indicate that the restriction of the projections of the large- and intermediatesized LGN layers to V1, observed in present-day primates, evolved from a more generalized mammalian condition. (C) 2004 IBRO. Published by Elsevier Ltd. All rights reserved.

Detection of fruit and the selection of primate visual pigments for color vision

Primates have X chromosome genes for cone photopigments with sensitivity maxima from 535 to 562 nm. Old World monkeys and apes (catarrhines) and the New World ( platyrrhine) genus Alouatta have separate genes for 535-nm ( medium wavelength; M) and 562-nm ( long wavelength; L) pigments. These pigments, together with a 425-nm ( short wavelength) pigment, permit trichromatic color vision. Other platyrrhines and prosimians have a single X chromosome gene but often with alleles for two or three M/L photopigments. Consequently, heterozygote females are trichromats, but males and homozygote females are dichromats. The criteria that affect the evolution of M/L alleles and maintain genetic polymorphism remain a puzzle, but selection for finding food may be important. We compare different types of color vision for detecting more than 100 plant species consumed by tamarins ( Saguinus spp.) in Peru. There is evidence that both frequency-dependent selection on homozygotes and heterozygote advantage favor M/L polymorphism and that trichromatic color vision is most advantageous in dim light. Also, whereas the 562-nm allele is present in all species, the occurrence of 535- to 556-nm alleles varies between species. This variation probably arises because trichromatic color vision favors widely separated pigments and equal frequencies of 535/543- and 562-nm alleles, whereas in dichromats, long-wavelength pigment alleles are fitter.

Pyramidal cell specialization in the occipitotemporal cortex of the vervet monkey

Pyramidal cells were injected intracellularly in fixed, flat-mounted cortical slices taken from the first and fourth visual areas (VI and V4, respectively) and cytoarchitectonic areas TEO and TE of two age and gender-matched vervet monkeys and the size, branching complexity and spine density of their basal dendritic trees determined. In both animals, we found marked differences in the pyramidal cell phenotype between cortical areas. More specifically, a consistent trend for larger, more branched and more spinous pyramidal cells with progression through VI, V4, TEO and TE was observed. These findings support earlier reports of interareal specialization in pyramidal cell structure in occipitotemporal visual areas in the macaque monkey. (c) 2005 Lippincott Williams & Wilkins.

Pyramidal cell specialization in the occipitotemporal cortex of the Chacma baboon (Papio ursinus)

Pyramidal cell structure varies systematically in occipitotemporal visual areas in monkeys. The dendritic trees of pyramidal cells, on average, become larger, more branched and more spinous with progression from the primary visual area (V1) to the second visual area (V2), the fourth (V4, or dorsolateral DL visual area) and inferotemporal (IT) cortex. Presently available data reveal that the extent of this increase in complexity parallels the expansion of occipitotemporal cortex. Here we extend the basis for comparison by studying pyramidal cell structure in occipitotemporal cortical areas in the chacma baboon. We found a systematic increase in the size of and branching complexity in the basal dendritic trees, as well as a progressive increase in the spine density along the basal dendrites of layer III pyramidal cells through V1, V2 and V4. These data suggest that the trend for more complex pyramidal cells with anterior progression through occipitotemporal visual areas is not a feature restricted to monkeys and prosimians, but is a widespread feature of occipitotemporal cortex in primates.

Brain maps, great and small: lessons from comparative studies of primate visual cortical organization

In this paper, we review evidence from comparative studies of primate cortical organization, highlighting recent findings and hypotheses that may help us to understand the rules governing evolutionary changes of the cortical map and the process of formation of areas during development. We argue that clear unequivocal views of cortical areas and their homologies are more likely to emerge for 'core' fields, including the primary sensory areas, which are specified early in development by precise molecular identification steps. In primates, the middle temporal area is probably one of these primordial cortical fields. Areas that form at progressively later stages of development correspond to progressively more recent evolutionary events, their development being less firmly anchored in molecular specification. The certainty with which areal boundaries can be delimited, and likely homologies can be assigned, becomes increasingly blurred in parallel with this evolutionary/developmental sequence. For example, while current concepts for the definition of cortical areas have been vindicated in allowing a clarification of the organization of the New World monkey 'third tier' visual cortex (the third and dorsomedial areas, V3 and DM), our analyses suggest that more flexible mapping criteria may be needed to unravel the organization of higher-order visual association and polysensory areas.

West Nile and St. Louis encephalitis virus antibody seroconversion, prevalence, and persistence in naturally infected pig-tailed macaques (Macaca nemestrina)

Pig-tailed macaques (Macaca nemestrina) naturally infected with West Nile virus were monitored from 1999 to 2005 to determine virus-specific antibody seroconversion, prevalence, and persistence. Antibodies persisted for up to 36 months, as detected by epitope-blocking enzyme-linked immunosorbent and hemagglutination inhibition assays. Exposure to cocirculating St. Louis encephalitis virus was evaluated by Western blotting and immunofluorescence assays.

Integration of semantically annotated data by the KnoFuss architecture

Most of the existing work on information integration in the Semantic Web concentrates on resolving schema-level problems. Specific issues of data-level integration (instance coreferencing, conflict resolution, handling uncertainty) are usually tackled by applying the same techniques as for ontology schema matching or by reusing the solutions produced in the database domain. However, data structured according to OWL ontologies has its specific features: e.g., the classes are organized into a hierarchy, the properties are inherited, data constraints differ from those defined by database schema. This paper describes how these features are exploited in our architecture KnoFuss, designed to support data-level integration of semantic annotations.

Disturbing visual working memory:electrophysiological evidence for a role of the prefrontal cortex in recovery from interference

Single cell recordings in monkeys support the notion that the lateral prefrontal cortex (PFC) controls reactivation of visual working memory representations when rehearsal is disrupted. In contrast, recent fMRI findings yielded a double dissociation for PFC and the medial temporal lobe (MTL) in a letter working memory task. PFC was engaged in interference protection during reactivation while MTL was prominently involved in the retrieval of the letter representations. We present event-related potential data (ERP) that support PFC involvement in the top-down control of reactivation during a visual working memory task with endogenously triggered recovery after visual interference. A differentiating view is proposed for the role of PFC in working memory with respect to endogenous/exogenous control and to stimulus type. General implications for binding and retention mechanisms are discussed.

Semantic reasoning for autonomic IT systems

Autonomic systems are required to adapt continually to changing environments and user goals. This process involves the real-Time update of the system's knowledge base, which should therefore be stored in a machine-readable format and automatically checked for consistency. OWL ontologies meet both requirements, as they represent collections of knowl- edge expressed in FIrst order logic, and feature embedded reasoners. To take advantage of these OWL ontology char- acteristics, this PhD project will devise a framework com- prising a theoretical foundation, tools and methods for de- veloping knowledge-centric autonomic systems. Within this framework, the knowledge storage and maintenance roles will be fulfilled by a specialised class of OWL ontologies. ©2014 ACM.

Онтологический Метод Доопределения Имитационной Модели

В докладе представлена подсистема доопределения имитационной модели. Подсистема является компонентом системы имитации и автоматизированного проектирования вычислительных систем Triad.Net. В Triad.Net на ранних стадиях проектирования пользователь может опустить некоторые детали при описании модели проектируемого объекта. Тем не менее, ему необходимо получить оценки (пусть и приближенные) функционирования этого объекта. Подсистема доопределения по определенным критериям осуществляет поиск фрагмента программного кода, позволяющего доопределить модель. Различают автоматическое и полуавтоматическое доопределение модели. В статье приводится архитектура подсистемы доопределения, описаны алгоритмы автоматического доопределения, основанные на онтологическом подходе, указаны особенности полуавтоматического доопределения.

A survey of semantic web services formalisms

The field of Semantic Web Services (SWS) has been recognized as one of the most promising areas of emergent research within the Semantic Web initiative, exhibiting an extensive commercial potential and attracting significant attention from both industry and the research community. Currently, there exist several different frameworks and languages for formally describing a Web Service: Web Ontology Language for Services (OWL-S), Web Service Modelling Ontology (WSMO) and Semantic Annotations for the Web Services Description Language (SAWSDL) are the most important approaches. To the inexperienced user, choosing the appropriate platform for a specific SWS application may prove to be challenging, given a lack of clear separation between the ideas promoted by the associated research communities. In this paper, we systematically compare OWL-S, WSMO and SAWSDL from various standpoints, namely, that of the service requester and provider as well as the broker-based view. The comparison is meant to help users to better understand the strengths and limitations of these different approaches to formalizing SWS, and to choose the most suitable solution for a given application. Copyright © 2015 John Wiley & Sons, Ltd.

BOWL:augmenting the semantic web with beliefs

As the Semantic Web is an open, complex and constantly evolving medium, it is the norm, but not exception that information at different sites is incomplete or inconsistent. This poses challenges for the engineering and development of agent systems on the Semantic Web, since autonomous software agents need to understand, process and aggregate this information. Ontology language OWL provides core language constructs to semantically markup resources on the Semantic Web, on which software agents interact and cooperate to accomplish complex tasks. However, as OWL was designed on top of (a subset of) classic predicate logic, it lacks the ability to reason about inconsistent or incomplete information. Belief-augmented Frames (BAF) is a frame-based logic system that associates with each frame a supporting and a refuting belief value. In this paper, we propose a new ontology language Belief-augmented OWL (BOWL) by integrating OWL DL and BAF to incorporate the notion of confidence. BOWL is paraconsistent, hence it can perform useful reasoning services in the presence of inconsistencies and incompleteness. We define the abstract syntax and semantics of BOWL by extending those of OWL. We have proposed reasoning algorithms for various reasoning tasks in the BOWL framework and we have implemented the algorithms using the constraint logic programming framework. One example in the sensor fusion domain is presented to demonstrate the application of BOWL.