title: Learning Petri net models of non-linear gene interactions

authors: Mayo, Michael

subjects: computer science

abstract: Understanding how an individual's genetic make-up influences their risk of disease is a problem of paramount importance. Although machine-learning techniques are able to uncover the relationships between genotype and disease, the problem of automatically building the best biochemical model or “explanation” of the relationship has received less attention. In this paper, I describe a method based on random hill climbing that automatically builds Petri net models of non-linear (or multi-factorial) disease-causing gene–gene interactions. Petri nets are a suitable formalism for this problem, because they are used to model concurrent, dynamic processes analogous to biochemical reaction networks. I show that this method is routinely able to identify perfect Petri net models for three disease-causing gene–gene interactions recently reported in the literature.

text: Learning Petri net models of non-linear gene interactions Understanding how an individual's genetic make-up influences their risk of disease is a problem of paramount importance. Although machine-learning techniques are able to uncover the relationships between genotype and disease, the problem of automatically building the best biochemical model or “explanation” of the relationship has received less attention. In this paper, I describe a method based on random hill climbing that automatically builds Petri net models of non-linear (or multi-factorial) disease-causing gene–gene interactions. Petri nets are a suitable formalism for this problem, because they are used to model concurrent, dynamic processes analogous to biochemical reaction networks. I show that this method is routinely able to identify perfect Petri net models for three disease-causing gene–gene interactions recently reported in the literature.

year: 2005

title: Investigating Gravity and Electromagnetism on a 10 Dimensional Manifold with Local Symmetry so(2,3)

authors: Ussher, Matthew Neville

abstract: The Hawthorn model [1] is built upon the idea that the Lie algebra so(2, 3) is a more natural description of the local structure of space-time than the Poincare Lie algebra, with the former contracting to the latter in the limit of the contraction parameter r tending to infinity. This notion is explored in the context of a 10-dimensional space-time referred to as an ADS manifold. Here we build on the work of Crump [2] and try to incorporate field equations for gravity into the model. We derive two apparently different equations describing gravitational phenomena, demonstrate an intimate connection between gravity and electromagnetism and provide a first estimate as to the value of the contraction parameter r.

text: Investigating Gravity and Electromagnetism on a 10 Dimensional Manifold with Local Symmetry so(2,3) The Hawthorn model [1] is built upon the idea that the Lie algebra so(2, 3) is a more natural description of the local structure of space-time than the Poincare Lie algebra, with the former contracting to the latter in the limit of the contraction parameter r tending to infinity. This notion is explored in the context of a 10-dimensional space-time referred to as an ADS manifold. Here we build on the work of Crump [2] and try to incorporate field equations for gravity into the model. We derive two apparently different equations describing gravitational phenomena, demonstrate an intimate connection between gravity and electromagnetism and provide a first estimate as to the value of the contraction parameter r.

year: 2013

title: Pupuritia ngā purapura i mahue mai rā: Te waiata-ā-ringa 1960 - 1990

authors: Papesch, Te Rita

subjects: Māori history

abstract: I tēnei tuhinga kei te āta titiro ahau ki te waiata-ā-ringa. Kei te hoki ahau ki te tīmatanga, ā, kei te whai ahau i te tipuranga me te oranga o tēnei mea, o te waiata-ā-ringa. Hei āwhina i ahau, kei te titiro ahau ki ētahi o ngā waiata-ā-ringa kua titoa e ngā kaitito mai i te tau 1960 tae noa ki te tau 1990. Kei te whakamārama hoki ahau i te whānui o ngā rerengakētanga o ēnei waiata-ā-ringa. Ka titiro hoki ahau ki te mahi ā ringa āhua reka hoki o ēnei waiata-ā-ringa, arā te mahi ngahau, te mahi whakataetae, te mahi i ēnei waiata-ā-ringa hei kīnaki i ngā whaikōrero, hei kīnaki i ngā kōrero kua kōrerohia i ngā hui, hei taonga pupuri i ngā kōrero o te iwi whānui, mō te iwi whānui me ngā mahi kua mahia i te ao i aua tuangahurutoru o ngā tau.
I tōku tau tuawhā i roto i te Tari Māori o Te Whare Wānanga o Waikato, i haere mātou ngā ākonga me tō mātou kaiwhakaako, me Hirini Melbourne, ki te kōrero ki ngā kaitito rongonui o te motu. I aua wā i hopukina ā rātou kōrero ki te mīhini. I roto i tēnei tuhinga kei te hoki ahau ki ā rātou kōrero i mau i a mātou. Ko ētahi o rātou kei te ora tonu, ko ētahi kua mate kē, kua haere ki tua o te ārai, ki te kāinga tūturu mō tātou katoa. Nō reira, e ngā whaea, nā koutou ahau i awhi, i mirimiri ki ō koutou ringa me ō koutou mōhiotanga ki tēnei taonga a tātou, ki te waiata-ā-ringa, moe mai rā i roto i ngā ringa o Hine-nui-te-pō.
Mai i aua wā i a au e ako ana i roto i te Tari Māori o Te Whare Wānanga o Waikato, i haere hoki ahau ki te pātai atu, ki te kōrero atu ki ētahi atu kaitito. Nā rātou ā rātou whakahoki ki aku pātai i tuhi ki runga i te pepa, ā, i mau hoki ki te rīpene. Nā, kua tae ki te wā me whakapuaki e ahau ōku māramatanga, mōhiotanga hoki ki ā rātou kōrero. Nō reira, e ngā mātua, he mihi kau anō tēnei ki a koutou i whai wā ki te whakahoki i ngā pātai, i ngā tono a tēnei tā koutou mōkai. Kua tukua e koutou tōku reo hei kawe i ō koutou whakaaro mō ā koutou mahi whakahirahira.
Kei te tuhi kōrero hoki ahau hei tautoko i tāku i whakapae, i whakahautia ēnei kaitito e ngā mahi waiata-ā-ringa i Te Tairāwhiti, e ngā tāngata o reira hoki, pērā i a Tā Apirana Ngata, i a Tuini Ngawai, i a wai, i a wai. Hei tautoko i tōku whakapae kua pātai atu ahau ki ēnei kaitito mō ō rātou whakaaro mō tōku whakapae, ā, kua tuhia ō rātou whakaaro.
Kei te whai hoki ahau i ōku whakaaro, mā tēnei taonga, mā te waiata-ā-ringa ka ako ai te tangata i tō tātou reo rangatira me ōna āhuatanga katoa.
Ki ahau nei kei reira, kei ngā waiata-ā-ringa e takoto ana ngā kōrero ātaahua o mua rā, arā, ngā whakataukī, ngā pepeha. Kei reira hoki e mahia ana te reo tūturu, te reo tawhito, tae noa ki te reo o nāianei. He ātaahua katoa ēnei reo, he akoranga hoki mā te tangata.
Ki te pātai mai te tangata, e hia te roa atu o tāku mahi rangahau i tēnei kaupapa, ka whakahoki au ki a ia, mai i te wā tuatahi ka mahi au i te waiata-ā-ringa, tae noa ki tēnei tau tonu, ā, e toru tekau ngā tau au e whakaaro ana, e mahi ana i te waiata-ā-ringa. Kātahi anō au ka whai wā ki te tuhi mō te waiata-ā-ringa.
Nā, hei kōrero whakamutunga, kei te titiro ahau kei whea e tū ana te waiata-ā-ringa i ēnei rā, ā, kei whea hoki e haere ana, ka whai hua anō, ā, ki whea?
Kia ora tātou mō tēnei wā.

text: Pupuritia ngā purapura i mahue mai rā: Te waiata-ā-ringa 1960 - 1990 I tēnei tuhinga kei te āta titiro ahau ki te waiata-ā-ringa. Kei te hoki ahau ki te tīmatanga, ā, kei te whai ahau i te tipuranga me te oranga o tēnei mea, o te waiata-ā-ringa. Hei āwhina i ahau, kei te titiro ahau ki ētahi o ngā waiata-ā-ringa kua titoa e ngā kaitito mai i te tau 1960 tae noa ki te tau 1990. Kei te whakamārama hoki ahau i te whānui o ngā rerengakētanga o ēnei waiata-ā-ringa. Ka titiro hoki ahau ki te mahi ā ringa āhua reka hoki o ēnei waiata-ā-ringa, arā te mahi ngahau, te mahi whakataetae, te mahi i ēnei waiata-ā-ringa hei kīnaki i ngā whaikōrero, hei kīnaki i ngā kōrero kua kōrerohia i ngā hui, hei taonga pupuri i ngā kōrero o te iwi whānui, mō te iwi whānui me ngā mahi kua mahia i te ao i aua tuangahurutoru o ngā tau.
I tōku tau tuawhā i roto i te Tari Māori o Te Whare Wānanga o Waikato, i haere mātou ngā ākonga me tō mātou kaiwhakaako, me Hirini Melbourne, ki te kōrero ki ngā kaitito rongonui o te motu. I aua wā i hopukina ā rātou kōrero ki te mīhini. I roto i tēnei tuhinga kei te hoki ahau ki ā rātou kōrero i mau i a mātou. Ko ētahi o rātou kei te ora tonu, ko ētahi kua mate kē, kua haere ki tua o te ārai, ki te kāinga tūturu mō tātou katoa. Nō reira, e ngā whaea, nā koutou ahau i awhi, i mirimiri ki ō koutou ringa me ō koutou mōhiotanga ki tēnei taonga a tātou, ki te waiata-ā-ringa, moe mai rā i roto i ngā ringa o Hine-nui-te-pō.
Mai i aua wā i a au e ako ana i roto i te Tari Māori o Te Whare Wānanga o Waikato, i haere hoki ahau ki te pātai atu, ki te kōrero atu ki ētahi atu kaitito. Nā rātou ā rātou whakahoki ki aku pātai i tuhi ki runga i te pepa, ā, i mau hoki ki te rīpene. Nā, kua tae ki te wā me whakapuaki e ahau ōku māramatanga, mōhiotanga hoki ki ā rātou kōrero. Nō reira, e ngā mātua, he mihi kau anō tēnei ki a koutou i whai wā ki te whakahoki i ngā pātai, i ngā tono a tēnei tā koutou mōkai. Kua tukua e koutou tōku reo hei kawe i ō koutou whakaaro mō ā koutou mahi whakahirahira.
Kei te tuhi kōrero hoki ahau hei tautoko i tāku i whakapae, i whakahautia ēnei kaitito e ngā mahi waiata-ā-ringa i Te Tairāwhiti, e ngā tāngata o reira hoki, pērā i a Tā Apirana Ngata, i a Tuini Ngawai, i a wai, i a wai. Hei tautoko i tōku whakapae kua pātai atu ahau ki ēnei kaitito mō ō rātou whakaaro mō tōku whakapae, ā, kua tuhia ō rātou whakaaro.
Kei te whai hoki ahau i ōku whakaaro, mā tēnei taonga, mā te waiata-ā-ringa ka ako ai te tangata i tō tātou reo rangatira me ōna āhuatanga katoa.
Ki ahau nei kei reira, kei ngā waiata-ā-ringa e takoto ana ngā kōrero ātaahua o mua rā, arā, ngā whakataukī, ngā pepeha. Kei reira hoki e mahia ana te reo tūturu, te reo tawhito, tae noa ki te reo o nāianei. He ātaahua katoa ēnei reo, he akoranga hoki mā te tangata.
Ki te pātai mai te tangata, e hia te roa atu o tāku mahi rangahau i tēnei kaupapa, ka whakahoki au ki a ia, mai i te wā tuatahi ka mahi au i te waiata-ā-ringa, tae noa ki tēnei tau tonu, ā, e toru tekau ngā tau au e whakaaro ana, e mahi ana i te waiata-ā-ringa. Kātahi anō au ka whai wā ki te tuhi mō te waiata-ā-ringa.
Nā, hei kōrero whakamutunga, kei te titiro ahau kei whea e tū ana te waiata-ā-ringa i ēnei rā, ā, kei whea hoki e haere ana, ka whai hua anō, ā, ki whea?
Kia ora tātou mō tēnei wā.

year: 1990