Eigenvector Synchronization, Graph Rigidity and the Molecule Problem

The graph realization problem has received a great deal of attention in recent years, due to its importance in applications such as wireless sensor networks and structural biology. In this paper, we extend on previous work and propose the 3D-ASAP algorithm, for the graph realization problem in $\mathbb{R}^3$, given a sparse and noisy set of distance measurements. 3D-ASAP is a divide and conquer, non-incremental and non-iterative algorithm, which integrates local distance information into a global structure determination. Our approach starts with identifying, for every node, a subgraph of its 1-hop neighborhood graph, which can be accurately embedded in its own coordinate system. In the noise-free case, the computed coordinates of the sensors in each patch must agree with their global positioning up to some unknown rigid motion, that is, up to translation, rotation and possibly reflection. In other words, to every patch there corresponds an element of the Euclidean group Euc(3) of rigid transformations in $\mathbb{R}^3$, and the goal is to estimate the group elements that will properly align all the patches in a globally consistent way. Furthermore, 3D-ASAP successfully incorporates information specific to the molecule problem in structural biology, in particular information on known substructures and their orientation. In addition, we also propose 3D-SP-ASAP, a faster version of 3D-ASAP, which uses a spectral partitioning algorithm as a preprocessing step for dividing the initial graph into smaller subgraphs. Our extensive numerical simulations show that 3D-ASAP and 3D-SP-ASAP are very robust to high levels of noise in the measured distances and to sparse connectivity in the measurement graph, and compare favorably to similar state-of-the art localization algorithms.Comment: 49 pages, 8 figure

Into Complexity. A Pattern-oriented Approach to Stakeholder Communities

The NWO-programme ”the societal aspects of genomics”, has called for stronger means of collaboration and deliberative involvement between the various stakeholders of genomics research. Within the project group assembled at the University for Humanistics, this call was translated to the ‘lingua democratica’, in which the prerequisites of such deliberative efforts were put to scrutiny. The contribution of this thesis has taken a more or less abstract angle to this task, and sought to develop a vocabulary that can be shared amongst various stakeholders with different backgrounds, interests and stakes for any complex theme, although genomics has more or less been in focus throughout the research. As ‘complexity thinking’ is currently a theme in both the ‘hard’ sciences as the social sciences and the humanities, and has always been an issue for professionals, this concept was pivotal in achieving such an inclusive angle. However, in order to prevent that complexity would become fragmented due to disciplinary boundaries, it is essential that those aspects of complexity that seem to return in many discussions would be made clear, and stand out with respect to the complexities of specialisation. The thesis has argued that the concept of ‘patterns’ applies for these aspects, and they form the backbone of the vocabulary that has been developed. Especially patterns of feedback have been given much attention, as this concept is pivotal for many complex themes. However, although patterns are implicitly or explicitly used in many areas, there is little methodological (and philosophical) underpinning of what they are and why they are able to do what they do. As a result, quite some attention has been given to these issues, and how they relate to concepts such as ‘information’,‘order’ and complexity itself. From these explorations, the actual vocabulary was developed, including the methodological means to use this vocabulary. This has taken the shape of a recursive development of a so-called pattern-library, which has crossed disciplinary boundaries, from technological areas, through biology, psychology and the social sciences, to a topic that is typical of the humanities. This journey across the divide of C.P. Snow’s ‘two cultures’ is both a test for a lingua democratica, as well as aimed to demonstrate how delicate, and balanced such a path must be in order to be effective, especially if one aims to retain certain coherence along the way. Finally, the methodology has been applied in a very practical way, to a current development that hinges strongly on research in genomics, which is trans-humanist movement

Machine Learning

Machine Learning can be defined in various ways related to a scientific domain concerned with the design and development of theoretical and implementation tools that allow building systems with some Human Like intelligent behavior. Machine learning addresses more specifically the ability to improve automatically through experience

AccuSyn: Using Simulated Annealing to Declutter Genome Visualizations

We apply Simulated Annealing, a well-known metaheuristic for obtaining near-optimal solutions to optimization problems, to discover conserved synteny relations (similar features) in genomes. The analysis of synteny gives biologists insights into the evolutionary history of species and the functional relationships between genes. However, as even simple organisms have huge numbers of genomic features, syntenic plots initially present an enormous clutter of connections, making the structure difficult to understand. We address this problem by using Simulated Annealing to minimize link crossings. Our interactive web-based synteny browser, AccuSyn, visualizes syntenic relations with circular plots of chromosomes and draws links between similar blocks of genes. It also brings together a huge amount of genomic data by integrating an adjacent view and additional tracks, to visualize the details of the blocks and accompanying genomic data, respectively. Our work shows multiple ways to manually declutter a synteny plot and then thoroughly explains how we integrated Simulated Annealing, along with human interventions as a human-in-the-loop approach, to achieve an accurate representation of conserved synteny relations for any genome. The goal of AccuSyn was to make a fairly complete tool combining ideas from four major areas: genetics, information visualization, heuristic search, and human-in-the-loop. Our results contribute to a better understanding of synteny plots and show the potential that decluttering algorithms have for syntenic analysis, adding more clues for evolutionary development. At this writing, AccuSyn is already actively used in the research being done at the University of Saskatchewan and has already produced a visualization of the recently-sequenced Wheat genome

The Meaning of Music-Making for Computer Scientists with a Serious Musing-Making Avocation: A Phenomenological Case Study

This study explores the meaning of music-making in the lives of computer scientists who play classical music as their serious avocation. In particular, it investigates their tendencies and capacities to concurrently engage in two such distinct disciplines on a regular basis, by exploring the cognitive, social, and cultural aspects of their concurrent engagement. While current research literature approaches the affinities between mathematicians/scientists and musicians through the presence of mathematical properties of music and through anecdotal evidence involving known persona and their innovations, this study provides a deeper look at the individuals who combine such worlds, in order to better understand how music-making is situated in their lives. Framing this research as a phenomenological case-study, narratives of seven study participants (and two pilot-study participants) are constructed through open-ended interviews, in which the participants relive their experiences of this phenomenon of embracing the two disciplines within a vocation/avocation framework. Using narrative analysis, and to a limited extent sociolinguistic analysis, the essence of this phenomenon is extracted from their narratives in the form of three major themes: participation in musical groups, sharing of cognitive skills across both disciplines, and tendencies to bring the two disciplines together. Given these themes, this study demonstrates the rich lives of these individuals, their high sense of self, ability to give to society, and their occasional ability to reach creative peaks. This study can motivate educators and educational institutions to encourage and support individuals with interdisciplinary interests, and calls for such individuals not to leave behind their artistic passions despite the role pragmatism plays in their career choices. This study can also help educators better understand individuals who are attracted to or engaged in multiple disciplines, and can complement or reaffirm scientific research on cognitive skills used in the disciplines of music-making and computer-science

Molecular Formula Identification using High Resolution Mass Spectrometry: Algorithms and Applications in Metabolomics and Proteomics

Wir untersuchen mehrere theoretische und praktische Aspekte der Identifikation der Summenformel von Biomolekülen mit Hilfe von hochauflösender Massenspektrometrie. Durch die letzten Forschritte in der Instrumentation ist die Massenspektrometrie (MS) zur einen der Schlüsseltechnologien für die Analyse von Biomolekülen in der Proteomik und Metabolomik geworden. Sie misst die Massen der Moleküle in der Probe mit hoher Genauigkeit, und ist für die Messdatenerfassung im Hochdurchsatz gut geeignet. Eine der Kernaufgaben in der MS-basierten Proteomik und Metabolomik ist die Identifikation der Moleküle in der Probe. In der Metabolomik unterliegen Metaboliten der Strukturaufklärung, beginnend bei der Summenformel eines Moleküls, d.h. der Anzahl der Atome jedes Elements. Dies ist der entscheidende Schritt in der Identifikation eines unbekannten Metabolits, da die festgelegte Formel die Anzahl der möglichen Molekülstrukturen auf eine viel kleinere Menge reduziert, die mit Methoden der automatischen Strukturaufklärung weiter analysiert werden kann. Nach der Vorverarbeitung ist die Ausgabe eines Massenspektrometers eine Liste von Peaks, die den Molekülmassen und deren Intensitäten, d.h. der Anzahl der Moleküle mit einer bestimmten Masse, entspricht. Im Prinzip können die Summenformel kleiner Moleküle nur mit präzisen Massen identifiziert werden. Allerdings wurde festgestellt, dass aufgrund der hohen Anzahl der chemisch legitimer Formeln in oberen Massenbereich eine exzellente Massengenaugkeit alleine für die Identifikation nicht genügt. Hochauflösende MS erlaubt die Bestimmung der Molekülmassen und Intensitäten mit hervorragender Genauigkeit. In dieser Arbeit entwickeln wir mehrere Algorithmen und Anwendungen, die diese Information zur Identifikation der Summenformel der Biomolekülen anwenden

Informed consent in personalized medicine

Thesis (S.M. in Science Writing)--Massachusetts Institute of Technology, Dept. of Comparative Media Studies, 2013.Vita. Cataloged from PDF version of thesis.Includes bibliographical references (pages 27-30).The next era of medicine will be one of personalization, scientists and physicians promise. Personalized medicine is a refined clinical approach in which clinicians will utilize your genomic information to help you prevent disease, and tailor targeted therapies for you when you fall ill. This is the future science has slowly been approaching. However, the human genome is not enough, not unless we can decipher its language. One ambitious study to this effect is the Personal Genome Project, led by Dr. George Church at Harvard Medical School. This project will eventually recruit 100,000 volunteers to donate their genomes and a full body of information concerning their biological health. With this data, Church hopes others can cross-analyze these profiles and better determine the role in disease of each gene of the human genome. However, the Personal Genome Project is as much a study in the ethical, legal and social aspects of genomic studies as it is an effort toward personalized medicine. Church envisions a future where privacy cannot be guaranteed. Society is becoming more open and technology is more invasive than ever. Considering this, Church has informed his participants that their information will likely not remain anonymous. With their fully informed consent, he has in turn made all this data public, to promote open science. This ethical approach raises several important questions about expansive genomic studies. The scientific community will have to decide on an approach that will eventually deliver personalized medicine. On one end of the spectrum, there is Church's open approach, and the other, more security, more firewalls and more legislation. In order for personalized medicine to become a reality, society will have to prepare itself for our ever-changing ethical, technological and scientific landscape.by Abdul-Kareem H. Ahmed.S.M.in Science Writin