2022 |
Klejda, Adam; Komosinski, Maciej; Mensfelt, Agnieszka Diversification Techniques and Distance Measures in Evolutionary Design of 3D Structures Conference Genetic and Evolutionary Computation Conference Companion (GECCO'22), ACM, Boston, USA, 2022. @conference{130, title = {Diversification Techniques and Distance Measures in Evolutionary Design of 3D Structures}, author = {Adam Klejda and Maciej Komosinski and Agnieszka Mensfelt}, doi = {10.1145/3520304.3528948}, year = {2022}, date = {2022-01-01}, booktitle = {Genetic and Evolutionary Computation Conference Companion (GECCO'22)}, publisher = {ACM}, address = {Boston, USA}, abstract = {Evolutionary algorithms are among the most successful metaheuristics for hard optimization problems. Nonetheless, there is still much room for improvement of their effectiveness, especially in the multimodal problems, where the algorithms are prone to falling into unsatisfactory local optima. One of the solutions to this problem may be to encourage a broader exploration of the solution space. Motivated by this premise, we compare the evolutionary algorithm without niching, with niching, the novelty search, and the two-criteria optimization (NSGA-II) where the criteria of fitness and diversity are not aggregated. We investigate these methods in the context of automated design of three-dimensional structures, which is one of the hardest optimization problems, often characterized by a rugged fitness landscape arising from a complex genotype to phenotype mapping. In the experiments we optimize 3D structures towards two different goals, height and velocity, using two genetic encodings and three distance measures: two phenetic ones and a genetic one. We demonstrate how different distance measures and diversity promotion mechanisms influence the fitness of the obtained solutions.}, keywords = {}, pubstate = {published}, tppubtype = {conference} } Evolutionary algorithms are among the most successful metaheuristics for hard optimization problems. Nonetheless, there is still much room for improvement of their effectiveness, especially in the multimodal problems, where the algorithms are prone to falling into unsatisfactory local optima. One of the solutions to this problem may be to encourage a broader exploration of the solution space. Motivated by this premise, we compare the evolutionary algorithm without niching, with niching, the novelty search, and the two-criteria optimization (NSGA-II) where the criteria of fitness and diversity are not aggregated. We investigate these methods in the context of automated design of three-dimensional structures, which is one of the hardest optimization problems, often characterized by a rugged fitness landscape arising from a complex genotype to phenotype mapping. In the experiments we optimize 3D structures towards two different goals, height and velocity, using two genetic encodings and three distance measures: two phenetic ones and a genetic one. We demonstrate how different distance measures and diversity promotion mechanisms influence the fitness of the obtained solutions. |
2021 |
Kaszuba, Piotr ; Komosinski, Maciej ; Mensfelt, Agnieszka Automated development of latent representations for optimization of sequences using autoencoders Conference 2021 IEEE Congress on Evolutionary Computation (CEC), IEEE, 2021. @conference{127, title = {Automated development of latent representations for optimization of sequences using autoencoders}, author = {Kaszuba, Piotr and Komosinski, Maciej and Mensfelt, Agnieszka}, url = {http://www.framsticks.com/files/common/LatentRepresentationsForSequencesOptimization.pdf}, doi = {10.1109/CEC45853.2021.9504910}, year = {2021}, date = {2021-01-01}, booktitle = {2021 IEEE Congress on Evolutionary Computation (CEC)}, publisher = {IEEE}, abstract = {In this paper, we propose an automated method for the development of new representations of sequences. For this purpose, we introduce a two-way mapping from variable length sequence representations to a latent representation modelled as the bottleneck of an LSTM (long short-term memory) autoencoder. Desirable properties of such mappings include smooth fitness landscapes for optimization problems and better evolvability. This work explores the capabilities of such latent encodings in the context of optimization of 3D structures. Various improvements are adopted that include manipulating the autoencoder architecture and its training procedure. The results of evolutionary algorithms that use different variants of automatically developed encodings are compared.}, keywords = {}, pubstate = {published}, tppubtype = {conference} } In this paper, we propose an automated method for the development of new representations of sequences. For this purpose, we introduce a two-way mapping from variable length sequence representations to a latent representation modelled as the bottleneck of an LSTM (long short-term memory) autoencoder. Desirable properties of such mappings include smooth fitness landscapes for optimization problems and better evolvability. This work explores the capabilities of such latent encodings in the context of optimization of 3D structures. Various improvements are adopted that include manipulating the autoencoder architecture and its training procedure. The results of evolutionary algorithms that use different variants of automatically developed encodings are compared. |
2020 |
Komosinski, Maciej; Mensfelt, Agnieszka Human perception of similarity of 3D graph structures Technical Report 2020, ISSN: RA-07/2020. @techreport{120, title = {Human perception of similarity of 3D graph structures}, author = {Maciej Komosinski and Agnieszka Mensfelt}, issn = {RA-07/2020}, year = {2020}, date = {2020-01-01}, abstract = {This report describes the study of how humans perceive similarity of simple three-dimensional graph structures. Participants of this study were required to align pairs of 3D structures the best they could, then match all vertices of these structures, evaluate their perceived similarity on a numerical scale, and justify their decisions as a textual response. The outcomes of this process were analyzed and compared to the outcomes of a heuristic computer algorithm that maximized the alignment of pairs of 3D structures and matched their vertices. The influence of personal characteristics of participants such as their gender, age, handedness, education, but also time required to complete each task, on the quality of the matching of vertices was evaluated. The consistency of human responses was also verified. The participants turned out to be more consistent (both between themselves and with the algorithm) in the degree of similarity estimated than in matching of vertices. Personal characteristics of the subjects did not have an influence on their similarity assessments.}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } This report describes the study of how humans perceive similarity of simple three-dimensional graph structures. Participants of this study were required to align pairs of 3D structures the best they could, then match all vertices of these structures, evaluate their perceived similarity on a numerical scale, and justify their decisions as a textual response. The outcomes of this process were analyzed and compared to the outcomes of a heuristic computer algorithm that maximized the alignment of pairs of 3D structures and matched their vertices. The influence of personal characteristics of participants such as their gender, age, handedness, education, but also time required to complete each task, on the quality of the matching of vertices was evaluated. The consistency of human responses was also verified. The participants turned out to be more consistent (both between themselves and with the algorithm) in the degree of similarity estimated than in matching of vertices. Personal characteristics of the subjects did not have an influence on their similarity assessments. |
2019 |
Komosinski, Maciej ; Mensfelt, Agnieszka Applications of Evolutionary Computation, Springer Springer, 2019, ISBN: 978-3-030-16692-2. @conference{102, title = {A Flexible Dissimilarity Measure for Active and Passive 3D Structures and Its Application in the Fitness–Distance Analysis}, author = {Komosinski, Maciej and Mensfelt, Agnieszka}, editor = {Kaufmann, Paul and Castillo, Pedro A.}, url = {http://www.framsticks.com/files/common/DissimilarityMeasure3DStructuresFitnessDistance.pdf}, doi = {10.1007/978-3-030-16692-2_8}, isbn = {978-3-030-16692-2}, year = {2019}, date = {2019-01-01}, booktitle = {Applications of Evolutionary Computation}, publisher = {Springer}, organization = {Springer}, abstract = {Evolutionary design of 3D structures – either static structures, or equipped with some sort of a control system – is one of the hardest optimization tasks. One of the reasons are rugged fitness landscapes resulting from complex and non-obvious genetic representations of such structures and their genetic operators. This paper investigates global convexity of fitness landscapes in optimization tasks of maximizing velocity and height of both active and passive structures. For this purpose, a new dissimilarity measure for 3D active and passive structures represented as undirected graphs is introduced. The proposed measure is general and flexible – any vertex properties can be easily incorporated as dissimilarity components. The new measure was compared against the previously introduced measure in terms of triangle inequality satisfiability, changes in raw measure values and the computational cost. The comparison revealed improvements for triangle inequality and raw values at the expense of increased computational complexity. The investigation of global convexity of the fitness landscape, involving the fitness–distance correlation analysis, revealed negative correlation between the dissimilarity of the structures and their fitness for most of the investigated cases.}, keywords = {}, pubstate = {published}, tppubtype = {conference} } Evolutionary design of 3D structures – either static structures, or equipped with some sort of a control system – is one of the hardest optimization tasks. One of the reasons are rugged fitness landscapes resulting from complex and non-obvious genetic representations of such structures and their genetic operators. This paper investigates global convexity of fitness landscapes in optimization tasks of maximizing velocity and height of both active and passive structures. For this purpose, a new dissimilarity measure for 3D active and passive structures represented as undirected graphs is introduced. The proposed measure is general and flexible – any vertex properties can be easily incorporated as dissimilarity components. The new measure was compared against the previously introduced measure in terms of triangle inequality satisfiability, changes in raw measure values and the computational cost. The comparison revealed improvements for triangle inequality and raw values at the expense of increased computational complexity. The investigation of global convexity of the fitness landscape, involving the fitness–distance correlation analysis, revealed negative correlation between the dissimilarity of the structures and their fitness for most of the investigated cases. |
2017 |
Komosinski, Maciej; Mensfelt, Agnieszka; Tyszka, Jaroslaw; Golen, Jan Multi-agent simulation of benthic foraminifera response to annual variability of feeding fluxes Journal Article Journal of Computational Science, 2017, ISSN: 1877-7503. @article{Komosinski-et-al-2017, title = {Multi-agent simulation of benthic foraminifera response to annual variability of feeding fluxes}, author = {Maciej Komosinski and Agnieszka Mensfelt and Jaroslaw Tyszka and Jan Golen}, url = {http://www.framsticks.com/files/common/SimulationForaminiferaFeedingFluxes.pdf}, doi = {10.1016/j.jocs.2016.09.009}, issn = {1877-7503}, year = {2017}, date = {2017-01-01}, journal = {Journal of Computational Science}, abstract = {In this work we describe a novel simulation model of foraminifera and their microhabitat. The simulations reported here are focused on the response of foraminiferal populations to environmental feeding fluxes. The experiments allowed to calibrate the model and to simulate realistic population patterns known from culture experiments, as well as from oceanographic and paleoecologic studies. Variability of annual food flux has a direct impact on productivity of foraminifera: population sizes closely follow the intensity of constant and seasonal food fluxes in both scenarios. This correlation between the food influx and population size is interpreted as the consequence of changing the carrying capacity of the system. Seasonal pulses of particulate organic matter enhance the population size which is represented by a higher number of fossilized shells. Our model offers a flexible experimental design to run sophisticated in silico experiments. This approach reveals a novel methodology for testing sensitivity of fossil and recent foraminiferal assemblages to environmental changes. Furthermore, it facilitates predictive applications for monitoring studies based on simulation of various scenarios.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work we describe a novel simulation model of foraminifera and their microhabitat. The simulations reported here are focused on the response of foraminiferal populations to environmental feeding fluxes. The experiments allowed to calibrate the model and to simulate realistic population patterns known from culture experiments, as well as from oceanographic and paleoecologic studies. Variability of annual food flux has a direct impact on productivity of foraminifera: population sizes closely follow the intensity of constant and seasonal food fluxes in both scenarios. This correlation between the food influx and population size is interpreted as the consequence of changing the carrying capacity of the system. Seasonal pulses of particulate organic matter enhance the population size which is represented by a higher number of fossilized shells. Our model offers a flexible experimental design to run sophisticated in silico experiments. This approach reveals a novel methodology for testing sensitivity of fossil and recent foraminiferal assemblages to environmental changes. Furthermore, it facilitates predictive applications for monitoring studies based on simulation of various scenarios. |
2016 |
Komosinski, Maciej; Mensfelt, Agnieszka Emotions perceived and emotions experienced in response to computer-generated music Journal Article Music Perception, 33 (4), pp. 432–445, 2016. @article{Komosinski-and-Mensfelt-2016, title = {Emotions perceived and emotions experienced in response to computer-generated music}, author = {Maciej Komosinski and Agnieszka Mensfelt}, url = {http://www.cs.put.poznan.pl/mkomosinski/research/music-emotions-perceived-and-experienced.pdf}, doi = {10.1525/MP.2016.33.4.432}, year = {2016}, date = {2016-04-01}, journal = {Music Perception}, volume = {33}, number = {4}, pages = {432–445}, publisher = {UC Press}, abstract = {This paper explores perceived and experienced emotions elicited by computer-generated music. During the experiments, 30 participants listened to 20 excerpts. Each of the excerpts lasted for about 16 seconds and was generated in real-time by specifically designed software. Measurements were performed using both categorical (a free verbal description) and dimensional approaches. The relationship between structural factors of music (mode, tempo, pitch height, rhythm, articulation and presence of the dissonance) and emotions was examined. Personal characteristics of the listener: gender and musical training were also taken into account. The relationship between structural factors and the perceived emotions was mostly congruent with predictions derived from the literature, and the relationship between those factors and experienced emotions was very similar. Tempo and pitch height – the cues common to music and speech – turned out to have a strong influence on the evaluation of emotion. Personal factors had a marginal effect. In the case of verbal categories comparable with the dimensional model, a strong correspondence was found.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper explores perceived and experienced emotions elicited by computer-generated music. During the experiments, 30 participants listened to 20 excerpts. Each of the excerpts lasted for about 16 seconds and was generated in real-time by specifically designed software. Measurements were performed using both categorical (a free verbal description) and dimensional approaches. The relationship between structural factors of music (mode, tempo, pitch height, rhythm, articulation and presence of the dissonance) and emotions was examined. Personal characteristics of the listener: gender and musical training were also taken into account. The relationship between structural factors and the perceived emotions was mostly congruent with predictions derived from the literature, and the relationship between those factors and experienced emotions was very similar. Tempo and pitch height – the cues common to music and speech – turned out to have a strong influence on the evaluation of emotion. Personal factors had a marginal effect. In the case of verbal categories comparable with the dimensional model, a strong correspondence was found. |
Mensfelt, Agnieszka Comparison of low level acoustic features and high level musical features as predictors of emotions elicited by computer-generated music Masters Thesis Poznan University of Technology, 2016. @mastersthesis{mastersthesis-put, title = {Comparison of low level acoustic features and high level musical features as predictors of emotions elicited by computer-generated music}, author = {Agnieszka Mensfelt}, year = {2016}, date = {2016-01-01}, school = {Poznan University of Technology}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
2015 |
Komosinski, Maciej; Mensfelt, Agnieszka; Topa, Pawel; Tyszka, Jaroslaw Application of a morphological similarity measure to the analysis of shell morphogenesis in Foraminifera Inproceedings Gruca, Aleksandra ; Brachman, Agnieszka ; Kozielski, Stanislaw ; Czachorski, Tadeusz (Ed.): Man–Machine Interactions 4, pp. 215–224, Springer Springer, 2015, ISBN: 978-3-319-23436-6. @inproceedings{Komosinski-et-al-2015, title = {Application of a morphological similarity measure to the analysis of shell morphogenesis in Foraminifera}, author = {Maciej Komosinski and Agnieszka Mensfelt and Pawel Topa and Jaroslaw Tyszka}, editor = {Gruca, Aleksandra and Brachman, Agnieszka and Kozielski, Stanislaw and Czachorski, Tadeusz}, url = {http://www.framsticks.com/files/common/ForaminiferaGenotypePhenotypeMapping.pdf}, doi = {10.1007/978-3-319-23437-3_18}, isbn = {978-3-319-23436-6}, year = {2015}, date = {2015-01-01}, booktitle = {Man–Machine Interactions 4}, volume = {391}, pages = {215–224}, publisher = {Springer}, organization = {Springer}, series = {Advances in Intelligent Systems and Computing}, abstract = {This work evaluates the genotype-to-phenotype mapping defined by one of the models of growth of foraminifera. Foraminifera are simple unicellular organisms with very diverse morphologies. To analyze the mapping, a morphological similarity measure is needed that compares 3D structures. One of the key components of the similarity estimation algorithm is Singular Value Decomposition (SVD). Since this algorithm is heavily used and its performance is important, four SVD implementations have been compared in this work. Distance matrices of the phenotypes obtained for equally distant genotypes were computed using the similarity measure. For the visualization of the phenotype space, multidimensional scaling techniques were used. Visual comparison of the genotype and the phenotype spaces revealed characteristics and potential weaknesses of the analyzed model of foraminifera growth, and demonstrated usefulness of the proposed approach.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } This work evaluates the genotype-to-phenotype mapping defined by one of the models of growth of foraminifera. Foraminifera are simple unicellular organisms with very diverse morphologies. To analyze the mapping, a morphological similarity measure is needed that compares 3D structures. One of the key components of the similarity estimation algorithm is Singular Value Decomposition (SVD). Since this algorithm is heavily used and its performance is important, four SVD implementations have been compared in this work. Distance matrices of the phenotypes obtained for equally distant genotypes were computed using the similarity measure. For the visualization of the phenotype space, multidimensional scaling techniques were used. Visual comparison of the genotype and the phenotype spaces revealed characteristics and potential weaknesses of the analyzed model of foraminifera growth, and demonstrated usefulness of the proposed approach. |
Topa, Pawel; Komosinski, Maciej ; Tyszka, Jaroslaw ; Mensfelt, Agnieszka ; Rokitta, Sebastian ; Byrski, Aleksander ; Bassara, Maciej eVolutus: A New Platform for Evolutionary Experiments Inproceedings Parallel Processing and Applied Mathematics - 11th International Conference, PPAM 2015, Krakow, Poland, September 6-9, 2015. Revised Selected Papers, Part II, pp. 570–580, 2015. @inproceedings{Topa-et-al-2015, title = {eVolutus: A New Platform for Evolutionary Experiments}, author = {Pawel Topa and Maciej Komosinski and Jaroslaw Tyszka and Agnieszka Mensfelt and Sebastian Rokitta and Aleksander Byrski and Maciej Bassara}, url = {http://dx.doi.org/10.1007/978-3-319-32152-3_53}, doi = {10.1007/978-3-319-32152-3_53}, year = {2015}, date = {2015-01-01}, booktitle = {Parallel Processing and Applied Mathematics - 11th International Conference, PPAM 2015, Krakow, Poland, September 6-9, 2015. Revised Selected Papers, Part II}, pages = {570--580}, abstract = {eVolutus is a new software platform designed for modeling evolutionary and population dynamics of living organisms. Single-celled eukaryotes, foraminifera, are selected as model organisms that have occupied the marine realm for at least 500 Ma and left an extraordinary fossil record preserved in microscopic shells. This makes them ideal objects for testing general evolutionary hypotheses based on studying multiscale genotypic, phenotypic, ecologic and macroevolutionary patterns. Our platform provides a highly configurable environment for conducting evolutionary experiments at various spatiotemporal scales.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } eVolutus is a new software platform designed for modeling evolutionary and population dynamics of living organisms. Single-celled eukaryotes, foraminifera, are selected as model organisms that have occupied the marine realm for at least 500 Ma and left an extraordinary fossil record preserved in microscopic shells. This makes them ideal objects for testing general evolutionary hypotheses based on studying multiscale genotypic, phenotypic, ecologic and macroevolutionary patterns. Our platform provides a highly configurable environment for conducting evolutionary experiments at various spatiotemporal scales. |
2014 |
Mensfelt, Agnieszka Development of the similarity measure for 3D structures and its application to the analysis of the model of foraminifera embryogeny Bachelors Thesis 2014. @bachelorsthesis{bachelorsthesis-put, title = {Development of the similarity measure for 3D structures and its application to the analysis of the model of foraminifera embryogeny}, author = {Agnieszka Mensfelt}, year = {2014}, date = {2014-01-01}, school = {Poznan University of Technology}, keywords = {}, pubstate = {published}, tppubtype = {bachelorsthesis} } |
2013 |
Mensfelt, Agnieszka Investigation of the relationship between computer-generated music and emotions perceived and experienced Masters Thesis Adam Mickiewicz University in Poznan, 2013. @mastersthesis{mastersthesis-uam, title = {Investigation of the relationship between computer-generated music and emotions perceived and experienced}, author = {Agnieszka Mensfelt}, year = {2013}, date = {2013-01-01}, school = {Adam Mickiewicz University in Poznan}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
2022 |
Diversification Techniques and Distance Measures in Evolutionary Design of 3D Structures Conference Genetic and Evolutionary Computation Conference Companion (GECCO'22), ACM, Boston, USA, 2022. |
2021 |
Automated development of latent representations for optimization of sequences using autoencoders Conference 2021 IEEE Congress on Evolutionary Computation (CEC), IEEE, 2021. |
2020 |
Human perception of similarity of 3D graph structures Technical Report 2020, ISSN: RA-07/2020. |
2019 |
Applications of Evolutionary Computation, Springer Springer, 2019, ISBN: 978-3-030-16692-2. |
2017 |
Multi-agent simulation of benthic foraminifera response to annual variability of feeding fluxes Journal Article Journal of Computational Science, 2017, ISSN: 1877-7503. |
2016 |
Emotions perceived and emotions experienced in response to computer-generated music Journal Article Music Perception, 33 (4), pp. 432–445, 2016. |
Comparison of low level acoustic features and high level musical features as predictors of emotions elicited by computer-generated music Masters Thesis Poznan University of Technology, 2016. |
2015 |
Application of a morphological similarity measure to the analysis of shell morphogenesis in Foraminifera Inproceedings Gruca, Aleksandra ; Brachman, Agnieszka ; Kozielski, Stanislaw ; Czachorski, Tadeusz (Ed.): Man–Machine Interactions 4, pp. 215–224, Springer Springer, 2015, ISBN: 978-3-319-23436-6. |
eVolutus: A New Platform for Evolutionary Experiments Inproceedings Parallel Processing and Applied Mathematics - 11th International Conference, PPAM 2015, Krakow, Poland, September 6-9, 2015. Revised Selected Papers, Part II, pp. 570–580, 2015. |
2014 |
Development of the similarity measure for 3D structures and its application to the analysis of the model of foraminifera embryogeny Bachelors Thesis 2014. |
2013 |
Investigation of the relationship between computer-generated music and emotions perceived and experienced Masters Thesis Adam Mickiewicz University in Poznan, 2013. |