Institut für Informatik und Computational Science
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teaspoon
(2018)
Answer Set Programming (ASP) is an approach to declarative problem solving, combining a rich yet simple modeling language with high performance solving capacities. We here develop an ASP-based approach to curriculum-based course timetabling (CB-CTT), one of the most widely studied course timetabling problems. The resulting teaspoon system reads a CB-CTT instance of a standard input format and converts it into a set of ASP facts. In turn, these facts are combined with a first-order encoding for CB-CTT solving, which can subsequently be solved by any off-the-shelf ASP systems. We establish the competitiveness of our approach by empirically contrasting it to the best known bounds obtained so far via dedicated implementations. Furthermore, we extend the teaspoon system to multi-objective course timetabling and consider minimal perturbation problems.
The course timetabling problem can be generally defined as the task of assigning a number of lectures to a limited set of timeslots and rooms, subject to a given set of hard and soft constraints. The modeling language for course timetabling is required to be expressive enough to specify a wide variety of soft constraints and objective functions. Furthermore, the resulting encoding is required to be extensible for capturing new constraints and for switching them between hard and soft, and to be flexible enough to deal with different formulations. In this paper, we propose to make effective use of ASP as a modeling language for course timetabling. We show that our ASP-based approach can naturally satisfy the above requirements, through an ASP encoding of the curriculum-based course timetabling problem proposed in the third track of the second international timetabling competition (ITC-2007). Our encoding is compact and human-readable, since each constraint is individually expressed by either one or two rules. Each hard constraint is expressed by using integrity constraints and aggregates of ASP. Each soft constraint S is expressed by rules in which the head is the form of penalty (S, V, C), and a violation V and its penalty cost C are detected and calculated respectively in the body. We carried out experiments on four different benchmark sets with five different formulations. We succeeded either in improving the bounds or producing the same bounds for many combinations of problem instances and formulations, compared with the previous best known bounds.
Regardless of what is intended by government curriculum
specifications and advised by educational experts, the competencies
taught and learned in and out of classrooms can vary considerably.
In this paper, we discuss in particular how we can investigate the
perceptions that individual teachers have of competencies in ICT,
and how these and other factors may influence students’ learning. We
report case study research which identifies contradictions within the
teaching of ICT competencies as an activity system, highlighting issues
concerning the object of the curriculum, the roles of the participants and
the school cultures. In a particular case, contradictions in the learning
objectives between higher order skills and the use of application tools
have been resolved by a change in the teacher’s perceptions which
have not led to changes in other aspects of the activity system. We look
forward to further investigation of the effects of these contradictions in
other case studies and on forthcoming curriculum change.
Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types
(2021)
Background:
There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually.
Methods:
In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data.
Results:
We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: .
Conclusions:
Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs.
Computational methods for the design of effective therapies against drug resistant HIV strains
(2005)
The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective pressure exerted by the human immune system and by combination drug therapy. We have developed several computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genomic data
Ein handlungsorientiertes, didaktisches Training für Tutoren im Bachelorstudium der Informatik
(2009)
Die didaktisch-pädagogische Ausbildung studentischer Tutoren für den Einsatz im Bachelorstudium der Informatik ist Gegenstand dieser Arbeit. Um die theoretischen Inhalte aus Sozial- und Lernpsychologie handlungsorientiert und effizient zu vermitteln, wird das Training als Lehrform gewählt. Die in einer Tutorübung zentrale Methode der Gruppenarbeit wird dabei explizit und implizit vermittelt. Erste praktische Erfahrungen mit ihrer zukünftigen Rolle gewinnen die Tutoren in Rollenspielen, wobei sowohl Standardsituationen als auch fachspezifisch und pädagogisch problematische Situationen simuliert werden. Während die Vermittlung der genannten Inhalte und die Rollenspiele im Rahmen einer Blockveranstaltung vor Beginn des Semesters durchgeführt werden, finden während des Semesters Hospitationen statt, in der die Fähigkeiten der Tutoren anhand eines standardisierten Bewertungsbogens beurteilt werden.
Workshop "Formale Methoden der Linguistik" und "14. Theorietag Automaten und Formale Sprachen"
(2004)
We introduce and investigate input-revolving finite automata, which are (nondeterministic) finite state automata with the additional ability to shift the remaining part of the input. Three different modes of shifting are considered, namely revolving to the left, revolving to the right, and circular-interchanging. We investigate the computational capacities of these three types of automata and their deterministic variants, comparing any of the six classes of automata with each other and with further classes of well-known automata. In particular, it is shown that nondeterminism is better than determinism, that is, for all three modes of shifting there is a language accepted by the nondeterministic model but not accepted by any deterministic automaton of the same type. Concerning the closure properties most of the deterministic language families studied are not closed under standard operations. For example, we show that the family of languages accepted by deterministic right-revolving finite automata is an anti-AFL which is not closed under reversal and intersection.
Die Studienanfänger der Informatik haben in Deutschland sehr unterschiedliche Grundkenntnisse in der Programmierung. Dies führt immer wieder zu Schwierigkeiten in der Ausrichtung der Einführungsveranstaltungen. An der TU München wird seit dem Wintersemester 2008/2009 nun eine neue Art von Vorkursen angeboten. In nur 2,5 Tagen erstellen die Teilnehmer ein kleines objektorientiertes Programm. Dabei arbeiten sie weitestgehend alleine, unterstützt von einem studentischen Tutor. In dieser Arbeit sollen nun das Konzept der sogenannten „Vorprojekte“ sowie erste Forschungsansätze vorgestellt werden
Wir stellen die Konzeption und erste Ergebnisse einer neuartigen Informatik- Lehrveranstaltung für Studierende der Geodäsie vor. Das Konzept verbindet drei didaktische Ideen: Kontextorientierung, Peer-Tutoring und Praxisbezug (Course). Die Studierenden sollen dabei in zwei Semestern wichtige Grundlagen der Informatik verstehen und anzuwenden lernen. Durch enge Verzahnung der Aufgaben mit einem für Nichtinformatiker relevanten Kontext, sowie einem sehr hohen Anteil von Selbsttätigkeit der Studierenden soll die Motivation für fachfremde Themen gesteigert werden. Die Ergebnisse zeigen, dass die Veranstaltung sehr erfolgreich war.
Es wird ein Informatik-Wettbewerb für Schülerinnen und Schüler der Sekundarstufe II beschrieben, der über mehrere Wochen möglichst realitätsnah die Arbeitswelt eines Informatikers vorstellt. Im Wettbewerb erarbeiten die Schülerteams eine Android-App und organisieren ihre Entwicklung durch Projektmanagementmethoden, die sich an professionellen, agilen Prozessen orientieren. Im Beitrag werden der theoretische Hintergrund zu Wettbewerben, die organisatorischen und didaktischen Entscheidung, eine erste Evaluation sowie Reflexion und Ausblick dargestellt.
Graded paraconsistency
(2000)
Circumscribing inconsistency
(1997)
Significant inferences
(2000)
Compressions and extensions
(1998)
One of the main problems in machine learning is to train a predictive model from training data and to make predictions on test data. Most predictive models are constructed under the assumption that the training data is governed by the exact same distribution which the model will later be exposed to. In practice, control over the data collection process is often imperfect. A typical scenario is when labels are collected by questionnaires and one does not have access to the test population. For example, parts of the test population are underrepresented in the survey, out of reach, or do not return the questionnaire. In many applications training data from the test distribution are scarce because they are difficult to obtain or very expensive. Data from auxiliary sources drawn from similar distributions are often cheaply available. This thesis centers around learning under differing training and test distributions and covers several problem settings with different assumptions on the relationship between training and test distributions-including multi-task learning and learning under covariate shift and sample selection bias. Several new models are derived that directly characterize the divergence between training and test distributions, without the intermediate step of estimating training and test distributions separately. The integral part of these models are rescaling weights that match the rescaled or resampled training distribution to the test distribution. Integrated models are studied where only one optimization problem needs to be solved for learning under differing distributions. With a two-step approximation to the integrated models almost any supervised learning algorithm can be adopted to biased training data. In case studies on spam filtering, HIV therapy screening, targeted advertising, and other applications the performance of the new models is compared to state-of-the-art reference methods.
We address classification problems for which the training instances are governed by an input distribution that is allowed to differ arbitrarily from the test distribution-problems also referred to as classification under covariate shift. We derive a solution that is purely discriminative: neither training nor test distribution are modeled explicitly. The problem of learning under covariate shift can be written as an integrated optimization problem. Instantiating the general optimization problem leads to a kernel logistic regression and an exponential model classifier for covariate shift. The optimization problem is convex under certain conditions; our findings also clarify the relationship to the known kernel mean matching procedure. We report on experiments on problems of spam filtering, text classification, and landmine detection.
We address classification problems for which the training instances are governed by an input distribution that is allowed to differ arbitrarily from the test distribution-problems also referred to as classification under covariate shift. We derive a solution that is purely discriminative: neither training nor test distribution are modeled explicitly. The problem of learning under covariate shift can be written as an integrated optimization problem. Instantiating the general optimization problem leads to a kernel logistic regression and an exponential model classifier for covariate shift. The optimization problem is convex under certain conditions; our findings also clarify the relationship to the known kernel mean matching procedure. We report on experiments on problems of spam filtering, text classification, and landmine detection.
Die gelungene Durchführung einer Vorlesung „Informatik I – Einführung in die Programmierung“ ist schwierig, trotz einer Vielfalt existierender Materialien und erprobter didaktischer Methoden. Gerade aufgrund dieser vielfältigen Auswahl hat sich bisher noch kein robustes Konzept durchgesetzt, das unabhängig von den Durchführenden eine hohe Erfolgsquote garantiert. An den Universitäten Tübingen und Freiburg wurde die Informatik I aus den gleichen Lehrmaterialien und unter ähnlichen Bedingungen durchgeführt, um das verwendete Konzept auf Robustheit zu überprüfen. Die Grundlage der Vorlesung bildet ein systematischer Ansatz zum Erlernen des Programmierens, der von der PLTGruppe in USA entwickelt worden ist. Hinzu kommen neue Ansätze zur Betreuung, insbesondere das Betreute Programmieren, bei dem die Studierenden eine solide Basis für ihre Programmierfähigkeiten entwickeln. Der vorliegende Bericht beschreibt hierbei gesammelte Erfahrungen, erläutert die Entwicklung der Unterrichtsmethodik und der Inhaltsauswahl im Vergleich zu vorangegangenen Vorlesungen und präsentiert Daten zum Erfolg der Vorlesung.
Through the use of next generation sequencing (NGS) technology, a lot of newly sequenced organisms are now available. Annotating those genes is one of the most challenging tasks in sequence biology. Here, we present an automated workflow to find homologue proteins, annotate sequences according to function and create a three-dimensional model.
The Berlin Brain-Computer Interface (BBCI) project develops a noninvasive BCI system whose key features are 1) the use of well-established motor competences as control paradigms, 2) high-dimensional features from 128-channel electroencephalogram (EEG), and 3) advanced machine learning techniques. As reported earlier, our experiments demonstrate that very high information transfer rates can be achieved using the readiness potential (RP) when predicting the laterality of upcoming left-versus right-hand movements in healthy subjects. A more recent study showed that the RP similarily accompanies phantom movements in arm amputees, but the signal strength decreases with longer loss of the limb. In a complementary approach, oscillatory features are used to discriminate imagined movements (left hand versus right hand versus foot). In a recent feedback study with six healthy subjects with no or very little experience with BCI control, three subjects achieved an information transfer rate above 35 bits per minute (bpm), and further two subjects above 24 and 15 bpm, while one subject could not achieve any BCI control. These results are encouraging for an EEG-based BCI system in untrained subjects that is independent of peripheral nervous system activity and does not rely on evoked potentials even when compared to results with very well-trained subjects operating other BCI systems
Interest in developing a new method of man-to-machine communication-a brain-computer interface (BCI)-has grown steadily over the past few decades. BCIs create a new communication channel between the brain and an output device by bypassing conventional motor output pathways of nerves and muscles. These systems use signals recorded from the scalp, the surface of the cortex, or from inside the brain to enable users to control a variety of applications including simple word-processing software and orthotics. BCI technology could therefore provide a new communication and control option for individuals who cannot otherwise express their wishes to the outside world. Signal processing and classification methods are essential tools in the development of improved BCI technology. We organized the BCI Competition 2003 to evaluate the current state of the art of these tools. Four laboratories well versed in EEG-based BCI research provided six data sets in a documented format. We made these data sets (i.e., labeled training sets and unlabeled test sets) and their descriptions available on the Internet. The goal in the competition was to maximize the performance measure for the test labels. Researchers worldwide tested their algorithms and competed for the best classification results. This paper describes the six data sets and the results and function of the most successful algorithms
A brain-computer interface (BCI) is a system that allows its users to control external devices with brain activity. Although the proof-of-concept was given decades ago, the reliable translation of user intent into device control commands is still a major challenge. Success requires the effective interaction of two adaptive controllers: the user's brain, which produces brain activity that encodes intent, and the BCI system, which translates that activity into device control commands. In order to facilitate this interaction, many laboratories are exploring a variety of signal analysis techniques to improve the adaptation of the BCI system to the user. In the literature, many machine learning and pattern classification algorithms have been reported to give impressive results when applied to BCI data in offline analyses. However, it is more difficult to evaluate their relative value for actual online use. BCI data competitions have been organized to provide objective formal evaluations of alternative methods. Prompted by the great interest in the first two BCI Competitions, we organized the third BCI Competition to address several of the most difficult and important analysis problems in BCI research. The paper describes the data sets that were provided to the competitors and gives an overview of the results.