Orlando, Gabriele; Raimondi, Daniele; Lenaerts, Tom; Vranken, Wim F
Rigapollo, a HMM-SVM based approach to sequence alignment Miscellaneous
2016, (Conference: European Conference on Computational Biology(3-7 September 2016: Den Hague, the Netherlands)).
@misc{info:hdl:2013/243714,
title = {Rigapollo, a HMM-SVM based approach to sequence alignment},
author = {Gabriele Orlando and Daniele Raimondi and Tom Lenaerts and Wim F Vranken},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243714},
year = {2016},
date = {2016-01-01},
note = {Conference: European Conference on Computational Biology(3-7 September 2016: Den Hague, the Netherlands)},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
Grembergen, Olivier Van; Bizet, Martin; de Bony, Eric James; Calonne, Emilie; Putmans, Pascale; Brohée, Sylvain; Olsen, Catharina; Guo, Mingzhou; Bontempi, Gianluca; Sotiriou, Christos; Defrance, Matthieu; cois Fuks, Franc
Portraying breast cancers with long noncoding RNAs Journal Article
In: Science advances, vol. 2, no. 9, 2016, (DOI: 10.1126/sciadv.1600220).
@article{info:hdl:2013/236112,
title = {Portraying breast cancers with long noncoding RNAs},
author = {Olivier Van Grembergen and Martin Bizet and Eric James de Bony and Emilie Calonne and Pascale Putmans and Sylvain Brohée and Catharina Olsen and Mingzhou Guo and Gianluca Bontempi and Christos Sotiriou and Matthieu Defrance and Fran{c c}ois Fuks},
url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/236112/1/doi_219739.pdf},
year = {2016},
date = {2016-01-01},
journal = {Science advances},
volume = {2},
number = {9},
abstract = {Evidence is emerging that long noncoding RNAs (lncRNAs) may play a role in cancer development, but this role is not yet clear. We performed a genome-wide transcriptional survey to explore the lncRNA landscape across 995 breast tissue samples. We identified 215 lncRNAs whose genes are aberrantly expressed in breast tumors, as compared to normal samples. Unsupervised hierarchical clustering of breast tumors on the basis of their lncRNAs revealed four breast cancer subgroups that correlate tightly with PAM50-defined mRNA-based subtypes. Using multivariate analysis, we identified no less than 210 lncRNAs prognostic of clinical outcome. By analyzing the coexpression of lncRNA genes and protein-coding genes, we inferred potential functions of the 215 dysregulated lncRNAs. We then associated subtype-specific lncRNAs with key molecular processes involved in cancer. A correlation was observed, on the one hand, between luminal A--specific lncRNAs and the activation of phosphatidylinositol 3-kinase, fibroblast growth factor, and transforming growth factor--β pathways and, on the other hand, between basal-like--specific lncRNAs and the activation of epidermal growth factor receptor (EGFR)--dependent pathways and of the epithelial-to-mesenchymal transition. Finally, we showed that a specific lncRNA, which we called CYTOR, plays a role in breast cancer. We confirmed its predicted functions, showing that it regulates genes involved in the EGFR/mammalian target of rapamycin pathway and is required for cell proliferation, cell migration, and cytoskeleton organization. Overall, our work provides the most comprehensive analyses for lncRNA in breast cancers. Our findings suggest a wide range of biological functions associated with lncRNAs in breast cancer and provide a foundation for functional investigations that could lead to new therapeutic approaches.},
note = {DOI: 10.1126/sciadv.1600220},
keywords = {},
pubstate = {published},
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}
Zisis, Ioannis; Guida, Sibilla Di; Han, The Anh T A H; Kirchsteiger, Georg; Lenaerts, Tom
Generocity motivated by acceptance - evolutionary analysis of an anticipation game Journal Article
In: Scientific Reports, vol. 5, 2015, (Language of publication: en).
@article{info:hdl:2013/228071,
title = {Generocity motivated by acceptance - evolutionary analysis of an anticipation game},
author = {Ioannis Zisis and Sibilla Di Guida and The Anh T A H Han and Georg Kirchsteiger and Tom Lenaerts},
url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/228071/3/2015SR-Pair-formation-dictator.pdf},
year = {2015},
date = {2015-01-01},
journal = {Scientific Reports},
volume = {5},
note = {Language of publication: en},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Faust, Karoline; Mendez, Gipsi Lima; Lerat, Jean-Sébastien; Sathirapongsasuti, Jarupon Fah; Knight, Rob; Huttenhower, Curtis; Lenaerts, Tom; Raes, Jeroen JR
Cross-biome comparison of microbial association networks Journal Article
In: Frontiers in microbiology, vol. 6, no. OCT, 2015, (DOI: 10.3389/fmicb.2015.01200).
@article{info:hdl:2013/226810,
title = {Cross-biome comparison of microbial association networks},
author = {Karoline Faust and Gipsi Lima Mendez and Jean-Sébastien Lerat and Jarupon Fah Sathirapongsasuti and Rob Knight and Curtis Huttenhower and Tom Lenaerts and Jeroen JR Raes},
url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/226810/4/doi_210437.pdf},
year = {2015},
date = {2015-01-01},
journal = {Frontiers in microbiology},
volume = {6},
number = {OCT},
abstract = {Clinical and environmental meta-omics studies are accumulating an ever-growing amount of microbial abundance data over a wide range of ecosystems. With a sufficiently large sample number, these microbial communities can be explored by constructing and analyzing co-occurrence networks, which detect taxon associations from abundance data and can give insights into community structure. Here, we investigate how co-occurrence networks differ across biomes and which other factors influence their properties. For this, we inferred microbial association networks from 20 different 16S rDNA sequencing data sets and observed that soil microbial networks harbor proportionally fewer positive associations and are less densely interconnected than host-associated networks. After excluding sample number, sequencing depth and beta-diversity as possible drivers, we found a negative correlation between community evenness and positive edge percentage. This correlation likely results from a skewed distribution of negative interactions, which take place preferentially between less prevalent taxa. Overall, our results suggest an under-appreciated role of evenness in shaping microbial association networks.},
note = {DOI: 10.3389/fmicb.2015.01200},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pozzolo, Andrea Dal; Caelen, Olivier; Johnson, Reid; Bontempi, Gianluca
Calibrating Probability with Undersampling for Unbalanced Classification Proceedings Article
In: 2015 IEEE Symposium on Computational Intelligence and Data Mining, 2015, (Language of publication: en).
@inproceedings{info:hdl:2013/221670,
title = {Calibrating Probability with Undersampling for Unbalanced Classification},
author = {Andrea Dal Pozzolo and Olivier Caelen and Reid Johnson and Gianluca Bontempi},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/221670},
year = {2015},
date = {2015-01-01},
booktitle = {2015 IEEE Symposium on Computational Intelligence and Data Mining},
note = {Language of publication: en},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Huculeci, Radu; Garcia-Pino, Abel; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico A J
Structural insights into the intertwined dimer of fyn SH2. Journal Article
In: Protein science, vol. 24, no. 12, pp. 1964-1978, 2015, (DOI: 10.1002/pro.2806).
@article{info:hdl:2013/225650,
title = {Structural insights into the intertwined dimer of fyn SH2.},
author = {Radu Huculeci and Abel Garcia-Pino and Lieven Buts and Tom Lenaerts and Nico A J van Nuland},
url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/225650/3/225650.pdf},
year = {2015},
date = {2015-01-01},
journal = {Protein science},
volume = {24},
number = {12},
pages = {1964-1978},
abstract = {Src homology 2 domains are interaction modules dedicated to the recognition of phosphotyrosine sites incorporated in numerous proteins found in intracellular signaling pathways. Here we provide for the first time structural insight into the dimerization of Fyn SH2 both in solution and in crystalline conditions, providing novel crystal structures of both the dimer and peptide-bound structures of Fyn SH2. Using nuclear magnetic resonance chemical shift analysis, we show how the peptide is able to eradicate the dimerization, leading to monomeric SH2 in its bound state. Furthermore, we show that Fyn SH2's dimer form differs from other SH2 dimers reported earlier. Interestingly, the Fyn dimer can be used to construct a completed dimer model of Fyn without any steric clashes. Together these results extend our understanding of SH2 dimerization, giving structural details, on one hand, and suggesting a possible physiological relevance of such behavior, on the other hand.},
note = {DOI: 10.1002/pro.2806},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pozzolo, Andrea Dal; Boracchi, Giacomo; Caelen, Olivier; Alippi, Cesare; Bontempi, Gianluca
Credit Card Fraud Detection and Concept-Drift Adaptation with Delayed Supervised Information Proceedings Article
In: Neural Networks (IJCNN), 2015 International Joint Conference on, 2015, (DOI: 10.1109/IJCNN.2015.7280527).
@inproceedings{info:hdl:2013/221668,
title = {Credit Card Fraud Detection and Concept-Drift Adaptation with Delayed Supervised Information},
author = {Andrea Dal Pozzolo and Giacomo Boracchi and Olivier Caelen and Cesare Alippi and Gianluca Bontempi},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/221668},
year = {2015},
date = {2015-01-01},
booktitle = {Neural Networks (IJCNN), 2015 International Joint Conference on},
abstract = {Most fraud-detection systems (FDSs) monitor streams of credit card transactions by means of classifiers returning alerts for the riskiest payments. Fraud detection is notably a challenging problem because of concept drift (i.e. customers' habits evolve) and class unbalance (i.e. genuine transactions far outnumber frauds). Also, FDSs differ from conventional classification because, in a first phase, only a small set of supervised samples is provided by human investigators who have time to assess only a reduced number of alerts. Labels of the vast majority of transactions are made available only several days later, when customers have possibly reported unauthorized transactions. The delay in obtaining accurate labels and the interaction between alerts and supervised information have to be carefully taken into consideration when learning in a concept-drifting environment. In this paper we address a realistic fraud-detection setting and we show that investigator's feedbacks and delayed labels have to be handled separately. We design two FDSs on the basis of an ensemble and a sliding-window approach and we show that the winning strategy consists in training two separate classifiers (on feedbacks and delayed labels, respectively), and then aggregating the outcomes. Experiments on large dataset of real-world transactions show that the alert precision, which is the primary concern of investigators, can be substantially improved by the proposed approach.},
note = {DOI: 10.1109/IJCNN.2015.7280527},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Han, The Anh T A H; Lenaerts, Tom
The efficient interaction of costly punishment and commitment Journal Article
In: Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS, vol. 3, pp. 1657-1658, 2015, (Language of publication: en).
@article{info:hdl:2013/220750,
title = {The efficient interaction of costly punishment and commitment},
author = {The Anh T A H Han and Tom Lenaerts},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220750},
year = {2015},
date = {2015-01-01},
journal = {Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS},
volume = {3},
pages = {1657-1658},
abstract = {To ensure cooperation in the Prisoner's Dilemma, agents may require prior commitments from others, subject to compensations when defecting after agreeing to commit. Alternatively, agents may prefer to behave reactively, without arranging prior commitments, by simply punishing those who misbehave. These two mechanisms have been shown to promote the emergence of cooperation, yet are complementary in the way they aim to instigate cooperation. In this work, using Evolutionary Game Theory, we describe a computational model showing that there is a wide range of parameters where the combined strategy is better than either strategy by itself, leading to a significantly higher level of cooperation. Interestingly, the improvement is most significant when the cost of arranging commitments is sufficiently high and the penalty reaches a certain threshold, thereby overcoming the weaknesses of both strategies.},
note = {Language of publication: en},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Han, The Anh T A H; Pereira, Lu'is Moniz; Santos, Francisco C; Lenaerts, Tom
Emergence of cooperation via intention recognition, commitment and apology-A research summary Journal Article
In: AI communications, vol. 28, no. 4, pp. 709-715, 2015, (DOI: 10.3233/AIC-150672).
@article{info:hdl:2013/220724,
title = {Emergence of cooperation via intention recognition, commitment and apology-A research summary},
author = {The Anh T A H Han and Lu{'i}s Moniz Pereira and Francisco C Santos and Tom Lenaerts},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220724},
year = {2015},
date = {2015-01-01},
journal = {AI communications},
volume = {28},
number = {4},
pages = {709-715},
abstract = {The mechanisms of emergence and evolution of cooperation in populations of abstract individuals, with diverse behavioral strategies in co-presence, have been undergoing mathematical study via evolutionary game theory, inspired in part on evolutionary psychology. Their systematic study resorts to simulation techniques, thus enabling the study of aforesaid mechanisms under a variety of conditions, parameters and alternative virtual games. The theoretical and experimental results have continually been surprising, rewarding and promising. In our recent work, we initiated the introduction, in such groups of individuals, of cognitive abilities inspired on techniques and theories of Artificial Intelligence, namely those pertaining to Intention Recognition, Commitment and Apology (separately and jointly), encompassing errors in decision-making and communication noise. As a result, both the emergence and stability of cooperation become reinforced comparatively to the absence of such cognitive abilities. This holds separately for Intention Recognition, for Commitment and for Apology, and even more so when they are jointly engaged. Our presentation aims to sensitize the reader to these evolutionary game theory based issues, results and prospects, which are accruing in importance for the modeling of minds with machines, with impact on our understanding of the evolution of mutual tolerance and cooperation. Recognition of someone's intentions, which may include imagining the recognition others have of our own intentions, and may comprise not just some error tolerance, but also a penalty for unfulfilled commitment though allowing for apology, can lead to evolutionary stable win/win equilibriums within groups of individuals, and perhaps amongst groups. The recognition and the manifestation of intentions, plus the assumption of commitment-even whilst paying a cost for putting it in place-and the acceptance of apology, are all facilitators in that respect, each of them singly and, above all, in collusion.},
note = {DOI: 10.3233/AIC-150672},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gazzo, Andrea; Daneels, Dorien; Cilia, Elisa; Bonduelle, Maryse; Abramowicz, Marc; Dooren, Sonia Van; Smits, Guillaume; Lenaerts, Tom
DIDA: A curated and annotated digenic diseases database. Journal Article
In: Nucleic acids research, 2015, (DOI: 10.1093/nar/gkv1068).
@article{info:hdl:2013/220549,
title = {DIDA: A curated and annotated digenic diseases database.},
author = {Andrea Gazzo and Dorien Daneels and Elisa Cilia and Maryse Bonduelle and Marc Abramowicz and Sonia Van Dooren and Guillaume Smits and Tom Lenaerts},
url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/220549/3/doi_204176.pdf},
year = {2015},
date = {2015-01-01},
journal = {Nucleic acids research},
abstract = {DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. The database is accessible via http://dida.ibsquare.be and currently includes 213 digenic combinations involved in 44 different digenic diseases. These combinations are composed of 364 distinct variants, which are distributed over 136 distinct genes. The web interface provides browsing and search functionalities, as well as documentation and help pages, general database statistics and references to the original publications from which the data have been collected. The possibility to submit novel digenic data to DIDA is also provided. Creating this new repository was essential as current databases do not allow one to retrieve detailed records regarding digenic combinations. Genes, variants, diseases and digenic combinations in DIDA are annotated with manually curated information and information mined from other online resources. Next to providing a unique resource for the development of new analysis methods, DIDA gives clinical and molecular geneticists a tool to find the most comprehensive information on the digenic nature of their diseases of interest.},
note = {DOI: 10.1093/nar/gkv1068},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pozzolo, Andrea Dal; Boracchi, Giacomo; Caelen, Olivier; Alippi, Cesare; Bontempi, Gianluca
Credit Card Fraud Detection and Concept-Drift Adaptation with Delayed Supervised Information Proceedings Article
In: Neural Networks (IJCNN), 2015 International Joint Conference on, 2015, (DOI: 10.1109/IJCNN.2015.7280527).
@inproceedings{info:hdl:2013/221668b,
title = {Credit Card Fraud Detection and Concept-Drift Adaptation with Delayed Supervised Information},
author = {Andrea Dal Pozzolo and Giacomo Boracchi and Olivier Caelen and Cesare Alippi and Gianluca Bontempi},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/221668},
year = {2015},
date = {2015-01-01},
booktitle = {Neural Networks (IJCNN), 2015 International Joint Conference on},
note = {DOI: 10.1109/IJCNN.2015.7280527},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Sekara, Mateusz; Kowalski, Michael; Byrski, Aleksander; Indurkhya, Bipin; Kisiel-Dorohinicki, Marek; Samson, Dana; Lenaerts, Tom
Multi-pheromone ant Colony Optimization for Socio-cognitive Simulation Purposes Journal Article
In: Procedia Computer Science, vol. 51, pp. 954-963, 2015, (DOI: 10.1016/j.procs.2015.05.234).
@article{info:hdl:2013/206321,
title = {Multi-pheromone ant Colony Optimization for Socio-cognitive Simulation Purposes},
author = {Mateusz Sekara and Michael Kowalski and Aleksander Byrski and Bipin Indurkhya and Marek Kisiel-Dorohinicki and Dana Samson and Tom Lenaerts},
url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/206321/1/Elsevier_189948.pdf},
year = {2015},
date = {2015-01-01},
journal = {Procedia Computer Science},
volume = {51},
pages = {954-963},
abstract = {We present an application of Ant Colony Optimisation (ACO) to simulate socio-cognitive features of a population. We incorporated perspective taking ability to generate three different proportions of ant colonies: Control Sample, High Altercentricity Sample, and Low Altercentricity Sample. We simulated their performances on the Travelling Salesman Problem and compared them with the classic ACO. Results show that all three 'cognitively enabled' ant colonies require less time than the classic ACO. Also, though the best solution is found by the classic ACO, the Control Sample finds almost as good a solution but much faster. This study is offered as an example to illustrate an easy way of defining inter-individual interactions based on stigmergic features of the environment.},
note = {DOI: 10.1016/j.procs.2015.05.234},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pozzolo, Andrea Dal; Caelen, Olivier; Johnson, Reid; Bontempi, Gianluca
Calibrating Probability with Undersampling for Unbalanced Classification Proceedings Article
In: 2015 IEEE Symposium on Computational Intelligence and Data Mining, 2015, (Language of publication: en).
@inproceedings{info:hdl:2013/221670b,
title = {Calibrating Probability with Undersampling for Unbalanced Classification},
author = {Andrea Dal Pozzolo and Olivier Caelen and Reid Johnson and Gianluca Bontempi},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/221670},
year = {2015},
date = {2015-01-01},
booktitle = {2015 IEEE Symposium on Computational Intelligence and Data Mining},
note = {Language of publication: en},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Han, The Anh T A H; Pereira, Lu'is Moniz; Lenaerts, Tom
Avoiding or restricting defectors in public goods games? Journal Article
In: Journal of the Royal Society interface, vol. 12, no. 103, pp. 20141203, 2015, (DOI: 10.1098/rsif.2014.1203).
@article{info:hdl:2013/205981,
title = {Avoiding or restricting defectors in public goods games?},
author = {The Anh T A H Han and Lu{'i}s Moniz Pereira and Tom Lenaerts},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/205981},
year = {2015},
date = {2015-01-01},
journal = {Journal of the Royal Society interface},
volume = {12},
number = {103},
pages = {20141203},
abstract = {When creating a public good, strategies or mechanisms are required to handle defectors. We first show mathematically and numerically that prior agreements with posterior compensations provide a strategic solution that leads to substantial levels of cooperation in the context of public goods games, results that are corroborated by available experimental data. Notwithstanding this success, one cannot, as with other approaches, fully exclude the presence of defectors, raising the question of how they can be dealt with to avoid the demise of the common good. We show that both avoiding creation of the common good, whenever full agreement is not reached, and limiting the benefit that disagreeing defectors can acquire, using costly restriction mechanisms, are relevant choices. Nonetheless, restriction mechanisms are found the more favourable, especially in larger group interactions. Given decreasing restriction costs, introducing restraining measures to cope with public goods free-riding issues is the ultimate advantageous solution for all participants, rather than avoiding its creation.},
note = {DOI: 10.1098/rsif.2014.1203},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Martinez-Vaquero, Luis L A; Han, The Anh T A H; Pereira, Lu'is Marcelo; Lenaerts, Tom
Apology and forgiveness evolve to resolve failures in cooperative agreements Journal Article
In: Scientific reports, vol. 5, 2015, (DOI: 10.1038/srep10639).
@article{info:hdl:2013/205370,
title = {Apology and forgiveness evolve to resolve failures in cooperative agreements},
author = {Luis L A Martinez-Vaquero and The Anh T A H Han and Lu{'i}s Marcelo Pereira and Tom Lenaerts},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/205370},
year = {2015},
date = {2015-01-01},
journal = {Scientific reports},
volume = {5},
abstract = {Making agreements on how to behave has been shown to be an evolutionarily viable strategy in one-shot social dilemmas. However, in many situations agreements aim to establish long-term mutually beneficial interactions. Our analytical and numerical results reveal for the first time under which conditions revenge, apology and forgiveness can evolve and deal with mistakes within ongoing agreements in the context of the Iterated Prisoners Dilemma. We show that, when the agreement fails, participants prefer to take revenge by defecting in the subsisting encounters. Incorporating costly apology and forgiveness reveals that, even when mistakes are frequent, there exists a sincerity threshold for which mistakes will not lead to the destruction of the agreement, inducing even higher levels of cooperation. In short, even when to err is human, revenge, apology and forgiveness are evolutionarily viable strategies which play an important role in inducing cooperation in repeated dilemmas.},
note = {DOI: 10.1038/srep10639},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Han, The Anh T A H; Santos, Francisco C; Lenaerts, Tom; Pereira, Lu'is Marcelo
Synergy between intention recognition and commitments in cooperation dilemmas Journal Article
In: Scientific Reports, vol. 5, 2015, (DOI: 10.1038/srep09312).
@article{info:hdl:2013/197743,
title = {Synergy between intention recognition and commitments in cooperation dilemmas},
author = {The Anh T A H Han and Francisco C Santos and Tom Lenaerts and Lu{'i}s Marcelo Pereira},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/197743},
year = {2015},
date = {2015-01-01},
journal = {Scientific Reports},
volume = {5},
abstract = {Commitments have been shown to promote cooperation if, on the one hand, they can be sufficiently enforced, and on the other hand, the cost of arranging them is justified with respect to the benefits of cooperation. When either of these constraints is not met it leads to the prevalence of commitment free-riders, such as those who commit only when someone else pays to arrange the commitments. Here, we show how intention recognition may circumvent such weakness of costly commitments. We describe an evolutionary model, in the context of the one-shot Prisoner's Dilemma, showing that if players first predict the intentions of their co-player and propose a commitment only when they are not confident enough about their prediction, the chances of reaching mutual cooperation are largely enhanced. We find that an advantageous synergy between intention recognition and costly commitments depends strongly on the confidence and accuracy of intention recognition. In general, we observe an intermediate level of confidence threshold leading to the highest evolutionary advantage, showing that neither unconditional use of commitment nor intention recognition can perform optimally. Rather, our results show that arranging commitments is not always desirable, but that they may be also unavoidable depending on the strength of the dilemma.},
note = {DOI: 10.1038/srep09312},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Huculeci, Radu; Garcia-Pino, Abel; Buts, Lieven; Lenaerts, Tom; Nuland, Nico A J
Structural insights into the intertwined dimer of fyn SH2. Journal Article
In: Protein science, vol. 24, no. 12, pp. 1964-1978, 2015, (DOI: 10.1002/pro.2806).
@article{info:hdl:2013/225650b,
title = {Structural insights into the intertwined dimer of fyn SH2.},
author = {Radu Huculeci and Abel Garcia-Pino and Lieven Buts and Tom Lenaerts and Nico A J Nuland},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/225650},
year = {2015},
date = {2015-01-01},
journal = {Protein science},
volume = {24},
number = {12},
pages = {1964-1978},
note = {DOI: 10.1002/pro.2806},
keywords = {},
pubstate = {published},
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}
Zisis, Ioannis; Guida, Sibilla Di; Han, The Anh T. A. H.; Kirchsteiger, Georg; Lenaerts, Tom
Generocity motivated by acceptance - evolutionary analysis of an anticipation game Journal Article
In: Scientific Reports, vol. 5, 2015, (Language of publication: en).
@article{info:hdl:2013/228071b,
title = {Generocity motivated by acceptance - evolutionary analysis of an anticipation game},
author = {Ioannis Zisis and Sibilla Di Guida and The Anh T. A. H. Han and Georg Kirchsteiger and Tom Lenaerts},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/228071},
year = {2015},
date = {2015-01-01},
journal = {Scientific Reports},
volume = {5},
note = {Language of publication: en},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Colaprico, Antonio; Silva, Tiago Da; Olsen, Catharina; Garofano, Luciano; Cava, Claudia; Garolini, Davide; Sabedot, Thais TS; Malta, Tathiane TM; Pagnotta, Stefano SM; Castiglioni, Isabella; Ceccarelli, M.; Bontempi, Gianluca; Noushmehr, Houtan
TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Journal Article
In: Nucleic acids research, 2015, (DOI: 10.1093/nar/gkv1507).
@article{info:hdl:2013/222877b,
title = {TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.},
author = {Antonio Colaprico and Tiago Da Silva and Catharina Olsen and Luciano Garofano and Claudia Cava and Davide Garolini and Thais TS Sabedot and Tathiane TM Malta and Stefano SM Pagnotta and Isabella Castiglioni and M. Ceccarelli and Gianluca Bontempi and Houtan Noushmehr},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/222877},
year = {2015},
date = {2015-01-01},
journal = {Nucleic acids research},
note = {DOI: 10.1093/nar/gkv1507},
keywords = {},
pubstate = {published},
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Lerman, Liran; Bontempi, Gianluca; Markowitch, Olivier
The bias–variance decomposition in profiled attacks Journal Article
In: Journal of Cryptographic Engineering, vol. 5, no. 4, pp. 255-267, 2015, (DOI: 10.1007/s13389-015-0106-1).
@article{info:hdl:2013/220673b,
title = {The bias–variance decomposition in profiled attacks},
author = {Liran Lerman and Gianluca Bontempi and Olivier Markowitch},
url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220673},
year = {2015},
date = {2015-01-01},
journal = {Journal of Cryptographic Engineering},
volume = {5},
number = {4},
pages = {255-267},
note = {DOI: 10.1007/s13389-015-0106-1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}