CAVASS: A Computer-Assisted Visualization and Analysis Software System

The Medical Image Processing Group at the University of Pennsylvania has been developing (and distributing with source code) medical image analysis and visualization software systems for a long period of time. Our most recent system, 3DVIEWNIX, was first released in 1993. Since that time, a number of significant advancements have taken place with regard to computer platforms and operating systems, networking capability, the rise of parallel processing standards, and the development of open-source toolkits. The development of CAVASS by our group is the next generation of 3DVIEWNIX. CAVASS will be freely available and open source, and it is integrated with toolkits such as Insight Toolkit and Visualization Toolkit. CAVASS runs on Windows, Unix, Linux, and Mac but shares a single code base. Rather than requiring expensive multiprocessor systems, it seamlessly provides for parallel processing via inexpensive clusters of work stations for more time-consuming algorithms. Most importantly, CAVASS is directed at the visualization, processing, and analysis of 3-dimensional and higher-dimensional medical imagery, so support for digital imaging and communication in medicine data and the efficient implementation of algorithms is given paramount importance

Machine Learning for Instance Segmentation

Volumetric Electron Microscopy images can be used for connectomics, the study of brain connectivity at the cellular level. A prerequisite for this inquiry is the automatic identification of neural cells, which requires machine learning algorithms and in particular efficient image segmentation algorithms. In this thesis, we develop new algorithms for this task. In the first part we provide, for the first time in this field, a method for training a neural network to predict optimal input data for a watershed algorithm. We demonstrate its superior performance compared to other segmentation methods of its category. In the second part, we develop an efficient watershed-based algorithm for weighted graph partitioning, the \emph{Mutex Watershed}, which uses negative edge-weights for the first time. We show that it is intimately related to the multicut and has a cutting edge performance on a connectomics challenge. Our algorithm is currently used by the leaders of two connectomics challenges. Finally, motivated by inpainting neural networks, we create a method to learn the graph weights without any supervision

Improved modelling of the human cerebral vasculature

Ph.DDOCTOR OF PHILOSOPH

Inductive Pattern Formation

With the extended computational limits of algorithmic recursion, scientific investigation is transitioning away from computationally decidable problems and beginning to address computationally undecidable complexity. The analysis of deductive inference in structure-property models are yielding to the synthesis of inductive inference in process-structure simulations. Process-structure modeling has examined external order parameters of inductive pattern formation, but investigation of the internal order parameters of self-organization have been hampered by the lack of a mathematical formalism with the ability to quantitatively define a specific configuration of points. This investigation addressed this issue of quantitative synthesis. Local space was developed by the Poincare inflation of a set of points to construct neighborhood intersections, defining topological distance and introducing situated Boolean topology as a local replacement for point-set topology. Parallel development of the local semi-metric topological space, the local semi-metric probability space, and the local metric space of a set of points provides a triangulation of connectivity measures to define the quantitative architectural identity of a configuration and structure independent axes of a structural configuration space. The recursive sequence of intersections constructs a probabilistic discrete spacetime model of interacting fields to define the internal order parameters of self-organization, with order parameters external to the configuration modeled by adjusting the morphological parameters of individual neighborhoods and the interplay of excitatory and inhibitory point sets. The evolutionary trajectory of a configuration maps the development of specific hierarchical structure that is emergent from a specific set of initial conditions, with nested boundaries signaling the nonlinear properties of local causative configurations. This exploration of architectural configuration space concluded with initial process-structure-property models of deductive and inductive inference spaces. In the computationally undecidable problem of human niche construction, an adaptive-inductive pattern formation model with predictive control organized the bipartite recursion between an information structure and its physical expression as hierarchical ensembles of artificial neural network-like structures. The union of architectural identity and bipartite recursion generates a predictive structural model of an evolutionary design process, offering an alternative to the limitations of cognitive descriptive modeling. The low computational complexity of these models enable them to be embedded in physical constructions to create the artificial life forms of a real-time autonomously adaptive human habitat

Emergent Design

Explorations in Systems Phenomenology in Relation to Ontology, Hermeneutics and the Meta-dialectics of Design SYNOPSIS A Phenomenological Analysis of Emergent Design is performed based on the foundations of General Schemas Theory. The concept of Sign Engineering is explored in terms of Hermeneutics, Dialectics, and Ontology in order to define Emergent Systems and Metasystems Engineering based on the concept of Meta-dialectics. ABSTRACT Phenomenology, Ontology, Hermeneutics, and Dialectics will dominate our inquiry into the nature of the Emergent Design of the System and its inverse dual, the Meta-system. This is an speculative dissertation that attempts to produce a philosophical, mathematical, and theoretical view of the nature of Systems Engineering Design. Emergent System Design, i.e., the design of yet unheard of and/or hitherto non-existent Systems and Metasystems is the focus. This study is a frontal assault on the hard problem of explaining how Engineering produces new things, rather than a repetition or reordering of concepts that already exist. In this work the philosophies of E. Husserl, A. Gurwitsch, M. Heidegger, J. Derrida, G. Deleuze, A. Badiou, G. Hegel, I. Kant and other Continental Philosophers are brought to bear on different aspects of how new technological systems come into existence through the midwifery of Systems Engineering. Sign Engineering is singled out as the most important aspect of Systems Engineering. We will build on the work of Pieter Wisse and extend his theory of Sign Engineering to define Meta-dialectics in the form of Quadralectics and then Pentalectics. Along the way the various ontological levels of Being are explored in conjunction with the discovery that the Quadralectic is related to the possibility of design primarily at the Third Meta-level of Being, called Hyper Being. Design Process is dependent upon the emergent possibilities that appear in Hyper Being. Hyper Being, termed by Heidegger as Being (Being crossed-out) and termed by Derrida as Differance, also appears as the widest space within the Design Field at the third meta-level of Being and therefore provides the most leverage that is needed to produce emergent effects. Hyper Being is where possibilities appear within our worldview. Possibility is necessary for emergent events to occur. Hyper Being possibilities are extended by Wild Being propensities to allow the embodiment of new things. We discuss how this philosophical background relates to meta-methods such as the Gurevich Abstract State Machine and the Wisse Metapattern methods, as well as real-time architectural design methods as described in the Integral Software Engineering Methodology. One aim of this research is to find the foundation for extending the ISEM methodology to become a general purpose Systems Design Methodology. Our purpose is also to bring these philosophical considerations into the practical realm by examining P. Bourdieu’s ideas on the relationship between theoretical and practical reason and M. de Certeau’s ideas on practice. The relationship between design and implementation is seen in terms of the Set/Mass conceptual opposition. General Schemas Theory is used as a way of critiquing the dependence of Set based mathematics as a basis for Design. The dissertation delineates a new foundation for Systems Engineering as Emergent Engineering based on General Schemas Theory, and provides an advanced theory of Design based on the understanding of the meta-levels of Being, particularly focusing upon the relationship between Hyper Being and Wild Being in the context of Pure and Process Being

Automated Reasoning

This volume, LNAI 13385, constitutes the refereed proceedings of the 11th International Joint Conference on Automated Reasoning, IJCAR 2022, held in Haifa, Israel, in August 2022. The 32 full research papers and 9 short papers presented together with two invited talks were carefully reviewed and selected from 85 submissions. The papers focus on the following topics: Satisfiability, SMT Solving,Arithmetic; Calculi and Orderings; Knowledge Representation and Jutsification; Choices, Invariance, Substitutions and Formalization; Modal Logics; Proofs System and Proofs Search; Evolution, Termination and Decision Prolems. This is an open access book

System of Systems Engineering for Policy Design

A system of systems (SoS) framework is proposed for policy design that takes into account the value systems of multiple participants, harnesses the complexity of strategic interactions among participants, and confronts the risks and uncertainties present in participants’ decision making. SoS thinking provides an integrative and adaptive mindset, which is needed to tackle policy challenges characterized by conflict, complexity, and uncertainty. With the aim of putting SoS thinking into practice, operational methods and tools are presented herein. Specifically, SoS engineering methodologies to create value system models, agent-based models of competitive and cooperative behaviour under conflict, and risk management models are developed and integrated into the framework. The proposed structure, methods and tools can be utilized to organize policy design discourse. Communication among participants involved in the policy discussion is structured around SoS models, which are used to integrate multiple perspectives of a system and to test the effectiveness of policies in achieving desirable outcomes under varying conditions. In order to demonstrate the proposed methods and tools that have been developed to enliven policy design discourse, a theoretical common-pool resources dilemma is utilized. The generic application illustrates the methodology of constructing ordinal preferences from values. Also, it is used to validate the agent-based modeling and simulation platform as a tool to investigate strategic interactions among participants and harness the potential to influence and enable participants to achieve desirable outcomes. A real-world common pool resources dilemma in the provisioning and security considerations of the Straits of Malacca and Singapore is examined and employed as a case study for applying strategic conflict models in risk management. Overall, this thesis advances the theory and application of SoS engineering and focuses on understanding value systems, handling complexity in terms of conflict dynamics, and finally, enhancing risk management

From Logic to Realism to Brighter Future for Humanity

This collection of articles explores a wide range of subject, from Godel’s incompleteness theorem, to possible technocalypse and neutrofuturology. Articles on historical debates on irrational number to electroculture, on vortex particle, or on different Neutrosophic applications are included

Collected Papers (Neutrosophics and other topics), Volume XIV

This fourteenth volume of Collected Papers is an eclectic tome of 87 papers in Neutrosophics and other fields, such as mathematics, fuzzy sets, intuitionistic fuzzy sets, picture fuzzy sets, information fusion, robotics, statistics, or extenics, comprising 936 pages, published between 2008-2022 in different scientific journals or currently in press, by the author alone or in collaboration with the following 99 co-authors (alphabetically ordered) from 26 countries: Ahmed B. Al-Nafee, Adesina Abdul Akeem Agboola, Akbar Rezaei, Shariful Alam, Marina Alonso, Fran Andujar, Toshinori Asai, Assia Bakali, Azmat Hussain, Daniela Baran, Bijan Davvaz, Bilal Hadjadji, Carlos Díaz Bohorquez, Robert N. Boyd, M. Caldas, Cenap Özel, Pankaj Chauhan, Victor Christianto, Salvador Coll, Shyamal Dalapati, Irfan Deli, Balasubramanian Elavarasan, Fahad Alsharari, Yonfei Feng, Daniela Gîfu, Rafael Rojas Gualdrón, Haipeng Wang, Hemant Kumar Gianey, Noel Batista Hernández, Abdel-Nasser Hussein, Ibrahim M. Hezam, Ilanthenral Kandasamy, W.B. Vasantha Kandasamy, Muthusamy Karthika, Nour Eldeen M. Khalifa, Madad Khan, Kifayat Ullah, Valeri Kroumov, Tapan Kumar Roy, Deepesh Kunwar, Le Thi Nhung, Pedro López, Mai Mohamed, Manh Van Vu, Miguel A. Quiroz-Martínez, Marcel Migdalovici, Kritika Mishra, Mohamed Abdel-Basset, Mohamed Talea, Mohammad Hamidi, Mohammed Alshumrani, Mohamed Loey, Muhammad Akram, Muhammad Shabir, Mumtaz Ali, Nassim Abbas, Munazza Naz, Ngan Thi Roan, Nguyen Xuan Thao, Rishwanth Mani Parimala, Ion Pătrașcu, Surapati Pramanik, Quek Shio Gai, Qiang Guo, Rajab Ali Borzooei, Nimitha Rajesh, Jesús Estupiñan Ricardo, Juan Miguel Martínez Rubio, Saeed Mirvakili, Arsham Borumand Saeid, Saeid Jafari, Said Broumi, Ahmed A. Salama, Nirmala Sawan, Gheorghe Săvoiu, Ganeshsree Selvachandran, Seok-Zun Song, Shahzaib Ashraf, Jayant Singh, Rajesh Singh, Son Hoang Le, Tahir Mahmood, Kenta Takaya, Mirela Teodorescu, Ramalingam Udhayakumar, Maikel Y. Leyva Vázquez, V. Venkateswara Rao, Luige Vlădăreanu, Victor Vlădăreanu, Gabriela Vlădeanu, Michael Voskoglou, Yaser Saber, Yong Deng, You He, Youcef Chibani, Young Bae Jun, Wadei F. Al-Omeri, Hongbo Wang, Zayen Azzouz Omar