1,721,067 research outputs found
jHOLES
No full textjHoles implements the clique weight rank persistent homology algorithm. jHoles fills the lack of an efficient implementation of the filtering process for clique weight rank homology. For a complete description of the approach at the basis of the software tool refer to: Jacopo Binchi, Emanuela Merelli, Matteo Rucco, Giovanni Petri, and Francesco Vaccarino. jHoles: A tool for understanding biological complex networks via clique weight rank persistent homology. Electronic Notes in Theoretical Computer Science , 306:5–18, 201
Transactions on Computational Systems Biology III
No full textSpecial Issue of the "Transactions on Computational Systems Biology", vol. III. 4th International Workshop on NETwork Tools and Applications in Biology (NETTAB 2004), Camerino, MC, Italy, September 2004. Revised Selected & Invited Papers. LNBI 3737
Topological Interpretation of Interactive Computation
Full text linkIt is a great pleasure to write this tribute in honor of Scott A. Smolka on his 65th birthday. We revisit Goldin, Smolka hypothesis that persistent Turing machine (PTM) can capture the intuitive notion of sequential interaction computation. We propose a topological setting to model the abstract concept of environment. We use it to define a notion of a topological Turing machine (TTM) as a universal model for interactive computation and possible model for concurrent computation
Topological Field Theory of Data: Mining Data Beyond Complex Networks
No full textPreface: Modern science is witnessing a peak of intense activity toward the study
of complex systems. This new topic is a very heterogeneous variety of ap-
proaches, methods and perspectives that share the common attempt to un-
derstand the collective behavior of a very large number of units correlated
by simple competitive and cooperative interactions. These type of investi-
gations have indeed appeared several times in the past. Recently tough, the
availability of large databases and the advent of unprecedented computer
facilities have created a fertile ground for the current boost. Moreover the
progress made in the studies of non-homogenous, disordered systems of the
last two decades has produced new promising approaches and technical tools
for applied research topics. The analysis of such objects has led to a fruitful
dialog involving mathematics and physics as founding and guiding disciplines,
with an increasingly growing contribution of specic problems from the socio-
economical, biological and other sciences. The present book is a collection of
selected contributions by leading world experts toward the process of build-
ing up a rigorous conceptual framework within these new ideas that have
irrigated the exact sciences, revealing a host of new questions, strategies and
solutions.
The volume opens with the contribution by Mario Rasetti and Emanuela
Merelli that focuses on a a new approach to Data Science that challenges
the traditional ones. ..
Front Matter, Table of Contents, Preface, Conference Organization
No full textFront Matter, Table of Contents, Preface, Conference Organizatio
Using Topological Data Analysis for diagnosis pulmonary embolism
No full textPulmonary Embolism (PE) is a common and potentially lethal condition. Most
patients die within the first few hours from the event. Despite diagnostic
advances, delays and underdiagnosis in PE are common.To increase the diagnostic
performance in PE, current diagnostic work-up of patients with suspected acute
pulmonary embolism usually starts with the assessment of clinical pretest
probability using plasma d-Dimer measurement and clinical prediction rules. The
most validated and widely used clinical decision rules are the Wells and Geneva
Revised scores. We aimed to develop a new clinical prediction rule (CPR) for PE
based on topological data analysis and artificial neural network. Filter or
wrapper methods for features reduction cannot be applied to our dataset: the
application of these algorithms can only be performed on datasets without
missing data. Instead, we applied Topological data analysis (TDA) to overcome
the hurdle of processing datasets with null values missing data. A topological
network was developed using the Iris software (Ayasdi, Inc., Palo Alto). The PE
patient topology identified two ares in the pathological group and hence two
distinct clusters of PE patient populations. Additionally, the topological
netowrk detected several sub-groups among healthy patients that likely are
affected with non-PE diseases. TDA was further utilized to identify key
features which are best associated as diagnostic factors for PE and used this
information to define the input space for a back-propagation artificial neural
network (BP-ANN). It is shown that the area under curve (AUC) of BP-ANN is
greater than the AUCs of the scores (Wells and revised Geneva) used among
physicians. The results demonstrate topological data analysis and the BP-ANN,
when used in combination, can produce better predictive models than Wells or
revised Geneva scores system for the analyzed cohor
X-Klaim Is Back
Full text linkKlaim is a coordination language specifically designed to model and program distributed systems consisting of mobile components interacting through multiple distributed tuple spaces. The Klaim’s theoretical foundations provided a solid ground for the implementation of the Klaim’s programming model. To practically program Klaim-based applications, the X-Klaim programming language has been proposed. It extends Klaim with enriched primitives and standard control flow constructs, and is compiled in Java to be executed. However, due to the limits of X-Klaim in terms of usability and the aging of the technology at the basis of its compiler, X-Klaim has been progressively neglected. Motivated by the success that Klaim has gained, the popularity that still has in teaching distributed computing, and its possible future exploitations in the development of modern ICT systems, in this paper we propose a renewed and enhanced version of X-Klaim. The new implementation, coming together with an Eclipse-based IDE tooling, relies on recent powerful frameworks for the development of programming languages
Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13), Florence, Italy, 6 June 2013
No full textThis ENTCS volume contains the post-proceedings of the Fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio’13) held
in Florence on the 6th of June 2013. This workshop was organized as an affiliated event of the eighth International Federated Conferences on Distributed Computing
Techniques (DisCoTec 2013).
For the fourth edition of CS2Bio, the program consisted of two invited lectures
by Giuseppe Longo (ENS Paris, France) and Mario Rasetti (ISI Foundation, Italy)
complemented by eight technical contributions (five regular papers and three tool
presentations), with an accompanying paper in this proceedings, and five short
presentations as disseminations of projects results. In line with the theme of the
workshop the presentations addressed topics in the area of formal languages and
methods for the representation of biological systems and their dynamics, and of
analysis and simulation approaches to biological case-studies. Moreover, in this
CS2Bio edition, novel computational paradigms for understanding biological com-
plex systems where addressed, as Quantum information and life sciences; Geometry,
algebraic and computational topology and biomathematics; Information processing
and biomedicine; Statistical mechanics and biophysics.
In his invited talk Giuseppe Longo spoke about randomness, variability and di-
versity in biological dynamics. The dynamic instability of living systems and the
superposition of different forms of randomness have been presented as components
of the contingently changing, or even increasing, organization of life through onto-
genesis or evolution. The lecture of Mario Rasetti focused on Big Data, Topology
and Field Theory as main ingredients towards a quantum model of life. He argued
that a molecule does not become a message only because of its shape or struc-
ture, but in the wider context of the system of physical constraints (a“symmetry”)
whereby information plays a dynamical role; living molecules extract information
from large sets of data and manipulate it, thus the goal is to understand not molec-
ular structures, but the structure of the language molecules mutually communicate
with.
The four short presentations have been an opportunity to learn interesting
projects results. Mara Sangiovanni reported on “A Spin-based Model Checking
Approach for Genome-Scale Metabolic Networks Validation and Analysis”, a novel method which integrates Flux Balance Analysis and Model Checking to address the
problem of verifying if a metabolic model fulfills the expected biological features.
By using a human hepatocyte metabolic network as a case study, it can be proven
that presented approach is useful in the validation and analysis of genome-scale
metabolic models. It followed a roundup of presentations about the European FET
project “TOPDRIM: topology driven methods for complex systems”, sponsor of
the CS2BIO 2013. The project has the objective to define an algebraic framework
for modeling multilevel complex systems, it aims to exploit theories from topology,
combinatorics and statistical mechanics and formal languages whose role is central
for building a global vision of big data, the huge amount of information flowing
around complex systems. The project aims to contribute to the Big Data Science.
Luca Tesei presented preliminary results on a research where the geometrical-based
interactions between DNA and a restriction enzyme are modeled to prove the ex-
istence of long-range interactions at molecular level. Francesco Vaccarino reported
on the study made about the structure of brain functional networks obtained from
fMRI data through their homological properties. Matteo Rucco informed about a
data-driven approach for modeling clinical predictive rule for Pulmonary Embolism.
Finally, Hillary Han discussed the bijective proof for a relation between uni- bi- and
tricellular maps of certain topological genus, where the uni-, bi- and tricellular maps
corresponds to RNA structures over one, two and three backbones. Result that has
immediate consequences for the folding of RNA interaction structures.
The workshop in Florence attracted more than 40 participants and the inter-
disciplinary atmosphere was productive and pleasant. The organizers express their
thanks to all speakers and participants of CS2Bio’13 for their contributions that
made this year’s edition a success. In particular, we are grateful to Giuseppe Longo
and Mario Rasetti for their interesting talks and inspiring contribution to the in-
terdisciplinary discussions. We also acknowledge the efforts of the members of the
program committee for the reviewing process.
The Program Committee of CS2Bio’13 was composed by:
•
Luca Cardelli (Microsoft Research Cambridge, UK)
•
Erik de Vink (Technische Universiteit Eindhoven, the Netherlands)
•
Jasmin Fisher (Microsoft Research Cambridge, UK)
•
Paola Giannini (Universit del Piemonte Orientale, Italy)
•
Radu Grosu (Vienna University of Technology, Austria)
•
Jean Krivine (CNRS and Universit Paris Diderot, France)
•
Pietro Lio’ (University of Cambridge, UK)
•
Daniele Manini (Universit di Torino, Italy)
•
Emanuela Merelli (Universit di Camerino, Italy)
Co-chair
•
Paolo Milazzo (Università di Pisa, Italy)
•
Ion Petre (bo Akademi University, Finland)
•
Marco Pettini (Universit de Marseille, France)
•
Christian Reidys (University of Southern Denmark, Denmark)
•
David Safranek (Masaryk University, Czech Republic)
•
Luca Tesei (Università di Camerino, Italy)
•
Angelo Troina (Università di Torino, Italy)
Co-chair
•
Verena Wolf (Saarland University, Germany)
Emanuela Merelli
Angelo Troin
Interactions between Computer Science and Biology
No full textThis special issue contains five articles based on papers presented at the 4th International Workshop on Interactions between Computer Science and Biology, CS2Bio’13. The workshop series aims at exploring the “interactions” between computer science, in particular formal methods, and biology at system level. The workshop gathered researchers interested in the convergence of Computer Science and Life Sciences.
The five selected papers contained in this special issue concern the design and analysis of behavioural properties typical of biological systems. Compared with the workshop papers, the articles have been strongly revised and extended with additional results. They underwent a further rigourous reviewing process, following the standard of the TCS journal
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