We examine the extent to which modified Kohonen self-organizing maps (SOMs) can learn unique repr... more We examine the extent to which modified Kohonen self-organizing maps (SOMs) can learn unique representations of temporal sequences while still supporting map formation. Two biologically inspired extensions are made to traditional SOMs: selection of multiple simultaneous rather than single "winners" and the use of local intramap connections that are trained according to a temporally asymmetric Hebbian learning rule. The extended SOM is then trained with variable-length temporal sequences that are composed of phoneme feature vectors, with each sequence corresponding to the phonetic transcription of a noun. The model transforms each input sequence into a spatial representation (final activation pattern on the map). Training improves this transformation by, for example, increasing the uniqueness of the spatial representations of distinct sequences, while still retaining map formation based on input patterns. The closeness of the spatial representations of two sequences is found to correlate significantly with the sequences' similarity. The extended model presented here raises the possibility that SOMs may ultimately prove useful as visualization tools for temporal sequences and as preprocessors for sequence pattern recognition systems.
In a number of multi-agent artificial life studies where agents interact over limited distances, ... more In a number of multi-agent artificial life studies where agents interact over limited distances, the emergence and/or evolution of a specific behavior may depend critically upon interagent distances. Little theoretical analysis has been done previously concerning how to predict such distances. In this paper, we derive a probabilistic method that, for an agent at an arbitrary location in a two-dimensional cellular world, predicts the expected distance to a nearest other agent. Our method works for many world topologies, and we apply it to determine the expected distance for six commonly used ones. Further, the method is readily adapted to handle special restrictions. Over a wide variety of agent densities we show that the theoretically predicted distances are largely in agreement with the distances measured in computational experiments with randomly placed agents. We then utilize our prediction method to interpret recent observations that an imprecise threshold in the density of agents exists for the evolution of communication. We thus illustrate that, despite its conceptual simplicity, our method can aid the analysis and even the design of complex artificial environments populated by agents that have the potential to interact with one another.
Background Crossing plants of the same species but different ploidies can have dramatic effects o... more Background Crossing plants of the same species but different ploidies can have dramatic effects on seed growth, but little is known about the alterations to transcriptional programmes responsible for this. Parental genomic imbalance particularly affects proliferation of the endosperm, with an increased ratio of paternally to maternally contributed genomes ('paternal excess') associated with overproliferation, while maternal excess inhibits endosperm growth. One interpretation is that interploidy crosses disrupt the balance in the seed of active copies of parentally imprinted genes. This is supported by the observation that mutations in imprinted FIS-class genes of Arabidopsis thaliana share many features of the paternal excess phenotype. Here we investigated gene expression underlying parent-of-origin effects in Arabidopsis through transcriptional profiling of siliques generated by interploidy crosses and FIS-class mutants. Results We found that fertilized fis1 mutant seeds have similar profiles to seeds with paternal excess, showing that the shared phenotypes are underpinned by similar patterns of gene expression. We identified genes strongly associated with enhanced or inhibited seed growth; this provided many candidates for further investigation including MADS-box transcription factors, cell cycle genes, and genes involved in hormone pathways. Conclusions The work presented here is a step towards understanding the effects on seed development of the related phenomena of parental genome balance and imprinting.
Aneuploidy results from nondisjunction of chromosomes in meiosis and is the leading cause of deve... more Aneuploidy results from nondisjunction of chromosomes in meiosis and is the leading cause of developmental disabilities and mental retardation in humans. Therefore, understanding aspects of chromosome segregation in a genetic model is of value. Mice heterozygous for a (2.8) Robertsonian translocation were intercrossed with chromosomally normal mice and Chromosome 2 was genotyped for number and parental origin in 836 individuals at 8.5 dpc. The frequency of nondisjunction of this Robertsonian chromosome is 1.58%. Trisomy of Chromosome 2 with two maternally derived chromosomes is the most developmentally successful aneuploid karyotype at 8.5 dpc. Trisomy of Chromosome 2 with two paternally derived chromosomes is developmentally delayed and less frequent than the converse. Individuals with maternal or paternal uniparental disomy of Chromosome 2 were not detected at 8.5 dpc. Nondisjunction events were distributed randomly across litters, i.e., no evidence for clustering was found. Transmission ratio distortion is frequently observed in Robertsonian chromosomes and a bias against the transmission of the (2.8) Chromosome was detected. Interestingly, this was observed for female and male transmitting parents.
We examine the extent to which modified Kohonen self-organizing maps (SOMs) can learn unique repr... more We examine the extent to which modified Kohonen self-organizing maps (SOMs) can learn unique representations of temporal sequences while still supporting map formation. Two biologically inspired extensions are made to traditional SOMs: selection of multiple simultaneous rather than single "winners" and the use of local intramap connections that are trained according to a temporally asymmetric Hebbian learning rule. The extended SOM is then trained with variable-length temporal sequences that are composed of phoneme feature vectors, with each sequence corresponding to the phonetic transcription of a noun. The model transforms each input sequence into a spatial representation (final activation pattern on the map). Training improves this transformation by, for example, increasing the uniqueness of the spatial representations of distinct sequences, while still retaining map formation based on input patterns. The closeness of the spatial representations of two sequences is found to correlate significantly with the sequences' similarity. The extended model presented here raises the possibility that SOMs may ultimately prove useful as visualization tools for temporal sequences and as preprocessors for sequence pattern recognition systems.
In a number of multi-agent artificial life studies where agents interact over limited distances, ... more In a number of multi-agent artificial life studies where agents interact over limited distances, the emergence and/or evolution of a specific behavior may depend critically upon interagent distances. Little theoretical analysis has been done previously concerning how to predict such distances. In this paper, we derive a probabilistic method that, for an agent at an arbitrary location in a two-dimensional cellular world, predicts the expected distance to a nearest other agent. Our method works for many world topologies, and we apply it to determine the expected distance for six commonly used ones. Further, the method is readily adapted to handle special restrictions. Over a wide variety of agent densities we show that the theoretically predicted distances are largely in agreement with the distances measured in computational experiments with randomly placed agents. We then utilize our prediction method to interpret recent observations that an imprecise threshold in the density of agents exists for the evolution of communication. We thus illustrate that, despite its conceptual simplicity, our method can aid the analysis and even the design of complex artificial environments populated by agents that have the potential to interact with one another.
Background Crossing plants of the same species but different ploidies can have dramatic effects o... more Background Crossing plants of the same species but different ploidies can have dramatic effects on seed growth, but little is known about the alterations to transcriptional programmes responsible for this. Parental genomic imbalance particularly affects proliferation of the endosperm, with an increased ratio of paternally to maternally contributed genomes ('paternal excess') associated with overproliferation, while maternal excess inhibits endosperm growth. One interpretation is that interploidy crosses disrupt the balance in the seed of active copies of parentally imprinted genes. This is supported by the observation that mutations in imprinted FIS-class genes of Arabidopsis thaliana share many features of the paternal excess phenotype. Here we investigated gene expression underlying parent-of-origin effects in Arabidopsis through transcriptional profiling of siliques generated by interploidy crosses and FIS-class mutants. Results We found that fertilized fis1 mutant seeds have similar profiles to seeds with paternal excess, showing that the shared phenotypes are underpinned by similar patterns of gene expression. We identified genes strongly associated with enhanced or inhibited seed growth; this provided many candidates for further investigation including MADS-box transcription factors, cell cycle genes, and genes involved in hormone pathways. Conclusions The work presented here is a step towards understanding the effects on seed development of the related phenomena of parental genome balance and imprinting.
Aneuploidy results from nondisjunction of chromosomes in meiosis and is the leading cause of deve... more Aneuploidy results from nondisjunction of chromosomes in meiosis and is the leading cause of developmental disabilities and mental retardation in humans. Therefore, understanding aspects of chromosome segregation in a genetic model is of value. Mice heterozygous for a (2.8) Robertsonian translocation were intercrossed with chromosomally normal mice and Chromosome 2 was genotyped for number and parental origin in 836 individuals at 8.5 dpc. The frequency of nondisjunction of this Robertsonian chromosome is 1.58%. Trisomy of Chromosome 2 with two maternally derived chromosomes is the most developmentally successful aneuploid karyotype at 8.5 dpc. Trisomy of Chromosome 2 with two paternally derived chromosomes is developmentally delayed and less frequent than the converse. Individuals with maternal or paternal uniparental disomy of Chromosome 2 were not detected at 8.5 dpc. Nondisjunction events were distributed randomly across litters, i.e., no evidence for clustering was found. Transmission ratio distortion is frequently observed in Robertsonian chromosomes and a bias against the transmission of the (2.8) Chromosome was detected. Interestingly, this was observed for female and male transmitting parents.
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Papers by Reiner Schulz