Journal articles
- Johannes Textor, Maciej Liskiewicz:
Adjustment Criteria in Causal Diagrams: An Algorithmic Perspective.
CoRR, (abs/1202.3764)2012.
Go to website - Michael Elberfeld, Johannes Textor:
Negative Selection Algorithms on Strings with Efficient Training and Linear-Time Classification.
Theoretical Computer Science, 412(6):534-542, 2011.
Show PDF | Go to website | Show abstract
A string-based negative selection algorithm is an immune-inspired
classifier that infers a partitioning of a string space $\Sigma^\ell$
into ``normal'' and ``anomalous'' partitions from a training set $S$
containing only samples from the ``normal'' partition.
The algorithm generates a set of patterns, called ``detectors'', to cover
regions of the string space containing none of the training samples.
Strings that match at least one of these detectors are then
classified as ``anomalous''. A major problem with existing
implementations of this approach is that the detector generation step suffers
from exponential worst-case time complexity.
Hence, researchers have found negative selection to be of
limited use for real-world problems such as network intrusion detection.
Here we show that for the two most widely used kinds of detectors, the
$r$-chunk and $r$-contiguous detectors based on partial matching
to substrings of length $r$, negative selection can be
implemented efficiently by avoiding generating detectors
altogether: For each detector type, training set
$S\subseteq\Sigma^\ell$ and parameter $r \leq \ell$ one can construct an
automaton whose acceptance behaviour is
equivalent to the algorithm's
classification outcome. The resulting runtime
is $O(|S|\ell r|\Sigma|)$ for constructing the automaton in
the training phase and $O(\ell)$ for classifying a string.
- Johannes Textor, Juliane Hardt, Sven Knüppel:
DAGitty: A Graphical Tool for Analyzing Causal Diagrams.
Epidemiology, 5(22):745, 2011.
Go to website - Johannes Textor, Antonio Peixoto, Sarah E. Henrickson, Mathieu Sinn, Ulrich H. von Andrian, Jürgen Westermann:
Defining the Quantitative Limits of Intravital Two-Photon Lymphocyte Tracking.
Proceedings of the National Academy of Sciences of the United States of America, 108(30):12401-12406, 2011.
Go to website | Show abstract
Two-photon microscopy has substantially advanced our understanding of cellular dynamics in the immune system. Cell migration can now be imaged in real time in the living animal. Strikingly, the migration of naive lymphocytes in secondary lymphoid tissue appears predominantly random. It is unclear, however, whether directed migration may escape detection in this random background. Using a combination of mathematical modeling and experimental data, we investigate the extent to which modern two-photon imaging can rule out biologically relevant directed migration. For naive T cells migrating in uninfected lymph nodes (LNs) at average 3D speeds of around 18 ?m/min, we rule out uniform directed migration of more than 1.7 ?m/min at the 95% confidence level, confirming that T cell migration is indeed mostly random on a timescale of minutes. To investigate whether this finding still holds for longer timescales, we use a 3D simulation of the naive T cell LN transit. A pure random walk predicts a transit time of around 16 h, which is in good agreement with experimental results. A directional bias of only 0.5 ?m/min—less than 3% of the cell speed—would already accelerate the transit twofold. These results jointly strengthen the random walk analogy for naive T cell migration in LNs, but they also emphasize that very small deviations from random migration can still be important. Our methods are applicable to cells of any type and can be used to reanalyze existing datasets.
- Johannes Textor, Björn Hansen:
Hybrid Simulation Algorithms for an Agent Based Model of the Immune Response.
Cybernetics and Systems, 40(5):390-417, 2009.
Go to website | Show PDF | Show abstract
The immune system is of central interest for the life sciences, but its high complexity makes it
a challenging system to study. Computational models of the immune system can help to
improve our understanding of its fundamental principles. In this paper, we analyze and extend
the Celada-Seiden model, a simple and elegant agent-based model of the entire immune
response, which, however, lacks biophysically sound simulation methodology. We extend the
stochastic model to a stochastic-deterministic hybrid, and link the deterministic version to
continuous physical and chemical laws. This gives precise meanings to all simulation
processes, and helps to increase performance. To demonstrate an application for the model,
we implement and study two different hypotheses about T cell-mediated immune memory.
In contrast to the more informal role of conferences in almost every
other field, conference proceedings are the main route
of publication for computer science papers.
I recommend reading Lance Fortnow's article on this subject for a viewpoint
and further information.
Conference papers
- Rüdiger Reischuk, Johannes Textor:
Stochastic Search With Locally Clustered Targets: Learning from T Cells.
In 10th International Conference on Artificial Immune Systems (ICARIS 2011), Volume 6825 of Lecture Notes in Computer Science, pp. 146-159.
Springer,
2011.
- Johannes Textor, Maciej Liskiewicz:
Adjustment Criteria in Causal Diagrams: An Algorithmic Perspective.
In Proceedings of the 27th Conference on Uncertainty in Artificial Intelligence (UAI 2011), pp. 681-688.
AUAI Press,
2011.
Show PDF | Go to website - Maciej Liskiewicz, Johannes Textor:
Negative Selection Algorithms Without Generating Detectors.
In Proceedings of the 12th annual conference on Genetic and evolutionary computation (GECCO'10), pp. 1047-1054.
ACM,
2010.
Show PDF | Go to website | Show abstract
Negative selection algorithms are immune-inspired classifiers
that are trained on negative examples only. Classification
is performed by generating detectors that match none
of the negative examples, and these detectors are then
matched against the elements to be classified. This can be
a performance bottleneck: A large number of detectors may be required
for acceptable sensitivity, or finding detectors that match none of
the negative examples may be difficult.
In this paper, we show how negative selection can be implemented
without generating detectors explicitly, which for many detector
types leads to polynomial time algorithms whereas the common approach to
sample detectors randomly takes exponential time in the
worst case.
In particular, we show that negative selection on strings with
generating all detectors can be efficiently
simulated without detectors if, and only if, an associated
decision problem can be answered efficiently, regardless
the detector type. We also show how to efficiently
simulate the more general case in which only a limited
number of detectors is generated. For many detector types,
this non-exhaustive negative selection is more meaningful
but it can be computationally more difficult, which we illustrate
using Boolean monomials.
- Michael Elberfeld, Johannes Textor:
Efficient Algorithms for String-Based Negative Selection.
In Proceedings of the 8th International Conference on Artificial Immune Systems (ICARIS 2009), Volume 5666 of Lecture Notes in Computer Science, pp. 109-121.
Springer,
2009.
Show PDF | Go to website | Show abstract
String-based negative selection is an immune-inspired classification scheme: Given a self-set S of strings, generate a set D of detectors that do not match any element of S. Then, use these detectors to partition a monitor set M into self and non-self elements. Implementations of this scheme are often impractical because they need exponential time in the size of S to construct D. Here, we consider r-chunk and r-contiguous detectors, two common implementations that suffer from this problem, and show that compressed representations of D are constructible in polynomial time for any given S and r. Since these representations can themselves be used to classify the elements in M, the worst-case running time of r-chunk and r-contiguous detector based negative selection is reduced from exponential to polynomial.
- Johannes Textor, Benjamin Feldner:
An XML Pipeline Based System Architecture for Managing Bibliographic Metadata.
In Metadata and Semantics Research (MTSR'09), Volume 46 of Communications in Computer and Information Science, pp. 130-140.
Springer,
2009.
Show PDF | Go to website | Show abstract
In our knowledge-based society, bibliographic metadata is everywhere. Although several metadata standards for bibliographic information have been developed and established by the professional librarian community, home-grown ad-hoc solutions are still widespread in small to medium-sized institutions. This paper presents a framework for storing, indexing, and browsing bibliographic metadata that is designed to lower the barrier for metadata standard adoption by facilitating legacy data import and integration into existing infrastructure. These goals are achieved using XML pipelines as a central design paradigm. As a practical use case, we discuss the implementation of the described architecture at a research institute in our university, where it is now in productive use for managing publication lists and the local library.
- Johannes Textor, Björn Hansen:
Improved Simulation Algorithms for Agent Based Models of the Immune Response.
In Proceedings of the 19th European Meeting on Cybernetics and Systems (EMCSR 2008), pp. 476-481.
Austrian Society for Cybernetic Studies,
2008.
Show PDF | Go to website | Show abstract
The immune response is a complex process
which involves large numbers of highly diverse cells, making it a well suited application for agent based modelling. A major
problem with current models is the lack of
biophysically sound simulation methodology.
In this paper, we analyze the key algorithms
of an important agent based model of the
immune system, point out methodological
de?ciencies and propose alternatives which
correspond to discrete versions of established
continuous models. To analyze the e?ects
of these modi?cations, a detailed simulation
of the immune response based on the
proposed algorithms has been implemented and
tested.
- Johannes Textor, Jürgen Westermann:
Modeling Migration, Compartmentalization, and Exit of Naive T Cells in Lymph Nodes Without Chemotaxis.
In 6th International Conference on Artificial Immune Systems (ICARIS 2007), Volume 4628 of Lecture Notes in Computer Science, pp. 228-239.
Springer,
2007.
Show PDF | Go to website | Show abstract
The migration of lymphocytes through secondary lymphoid
organs was believed to be mainly controlled by chemokine gradients.
This theory has recently been called into question since naive lymphocytes observed in vivo by two-photon microscopy show no evidence of
directed migration. We have constructed a simple mathematical model
of naive T cell migration in lymph nodes that is solely based on local
mechanisms. The model was validated against ?ndings from histological
analysis and experimentally determined lymphocyte recirculation kinetics. Our results suggest that T cell compartmentalization in lymph nodes
can be explained without long-range chemokine gradients. However, the
T cell residence time predicted by our model is signi?cantly lower than
observed in vivo, indicating the existence of a mechanism which alters
the T cell random walk over time.
- Mario Muñoz, Jesus A. Fisteus, Johannes Textor, Carlos Delgado Kloos, Carlos Turmo, Clara Cala:
Characterizing and Categorizing Internal Administrative Processes in an e-Government Setting.
In IADIS International Conference e-Commerce 2004, IADIS,
2004.
Show PDF | Go to website | Show abstract
The new millennium has brought among its most important changes the evolution of the electronic administration as one of the major enablers for the information society. Some initiatives like the IDA project have concentrated on the data exchange among different public administrations. Others, like eGOV have focused on the definition of e-services for citizens and enterprises. Others, like OSCI in Germany, have tried to define a security framework for e-administration, while others like the eGIF framework in the UK have combined several of the previous features. In this paper, we tackle a different aspect, which has not been fully studied yet, but which is of uppermost importance in e-government: the internal processes in electronic administration. We present a general model for categorizing administrative documents using XML and the results of the use of this model in the Spanish Science and Technology Ministry’s ACADIA project for the administrative documents inside this Ministry. The model takes into account how signatures shall be generated, attached and validated inside e-administrative processes and illustrates the concepts with practical examples taken from the processes inside this Ministry.
Invited Talks at International Meetings
- Johannes Textor:
Antigen Detection as a Distributed Randomized Search Process: A Multiscale Approach.
SMB 2009
– Annual Meeting of the Society for Mathematical Biology, Vancouver, Canada, 2009.
Selected Talks at International Meetings
- Johannes Textor:
A Unified View of T Cell Recirculation and Stochastic Search in the Lymph
Node Microenvironment.
IDRN meeting on T lymphocyte dynamics in acute and chronic viral infection, London, UK, 2011.
Posters at International Meetings
- Andreas Gebert, Dorthe von Smolinski, Maike Blessenohl, Anna Schueth,
Regina Orzekowsky-Schroeder, Johannes Textor, Antje Klinger, Geroen Huettmann:
Intravital Lymphocyte Trafficking in the Intestinal Epithelium:
A Novel Experimental Model Based on High-Resolution Autofluorescence 2-Photon Microscopy.
2nd European Congress of Immunology, Berlin, Germany, 2009.
- Andreas Gebert, Maike Blessenohl, Dorthe von Smolinski, Anna Schueth,
Regina Orzekowsky-Schroeder, Johannes Textor, Geroen Huettmann, Antje Klinger:
In Vivo Dynamics of Intraepithelial Lymphocytes in the Gut: A
Novel Experimental Approach Based on High-Resolution Autofluorescence 2-Photon Microscopy.
16th Germinal Center Conference, Frankfurt, Germany, 2009.
- Johannes Textor, Jürgen Westermann:
Simulating the Lymph Node Transit of Naive T cells.
IDRN meeting on Lymphocyte Kinetics in Health and Disease, London, UK, 2008.
