These are the slides for a tutorial talk about "multilayer networks" that I gave at NetSci 2014.
I walk people through a review article that I wrote with my PLEXMATH collaborators: http://comnet.oxfordjournals.org/content/2/3/203
Opinion Dynamics on Generalized NetworksMason Porter
This is a talk on opinion dynamics (especially bounded-confidence models) on generalized networks.
It is part of the MIX-NEXT III (Multiscale & Integrative compleX Networks: EXperiments & Theories) satellite at NetSci 2022.
(Thursday 14 July 2022)
Mathematical Models of the Spread of Diseases, Opinions, Information, and Mis...Mason Porter
This is my general-audience talk at DiscCon III (2021 WorldCon).
My talk overlapped with the Hugo Award ceremony, but the video will be posted later on the DisCon website for attendees who want to see it.
This is a colloquium that I presented on 4/22/21: Stockholm University, Nordic Institute for Theoretical Physics (NORDITA), WINQ–AlbaNova Colloquium
Here is a video of my talk: http://video.albanova.se/ALBANOVA20210422/video.mp4
These are the slides for a tutorial talk about "multilayer networks" that I gave at NetSci 2014.
I walk people through a review article that I wrote with my PLEXMATH collaborators: http://comnet.oxfordjournals.org/content/2/3/203
Opinion Dynamics on Generalized NetworksMason Porter
This is a talk on opinion dynamics (especially bounded-confidence models) on generalized networks.
It is part of the MIX-NEXT III (Multiscale & Integrative compleX Networks: EXperiments & Theories) satellite at NetSci 2022.
(Thursday 14 July 2022)
Mathematical Models of the Spread of Diseases, Opinions, Information, and Mis...Mason Porter
This is my general-audience talk at DiscCon III (2021 WorldCon).
My talk overlapped with the Hugo Award ceremony, but the video will be posted later on the DisCon website for attendees who want to see it.
This is a colloquium that I presented on 4/22/21: Stockholm University, Nordic Institute for Theoretical Physics (NORDITA), WINQ–AlbaNova Colloquium
Here is a video of my talk: http://video.albanova.se/ALBANOVA20210422/video.mp4
Introduction to Topological Data AnalysisMason Porter
Here are slides for my 3/14/21 talk on an introduction to topological data analysis.
This is the first talk in our Short Course on topological data analysis at the 2021 American Physical Society (APS) March Meeting: https://march.aps.org/program/dsoft/gsnp-short-course-introduction-to-topological-data-analysis/
Topological Data Analysis of Complex Spatial SystemsMason Porter
These are slides from a seminar I gave in "Cardiff" (for the mathematics department at University of Cardiff) on 4/15/20.
You can also find a recording of a similar talk that I gave in March 2020 for MBI (Mathematical Biosciences Institute): https://mbi.osu.edu/events/online-colloquium-mason-porter-spatial-systems-and-topological-data-analysis
Here are my slides (though the animated gifs on a couple of them are stills in this version) of my talk on an introduction to the science of "chaos" at WorldCon 77 in Dublin, Ireland.
This is my attempt to give a gentle introduction to the notion of chaos to a science-fiction audience.
Centrality in Time- Dependent NetworksMason Porter
My slides for my keynote talk at the NetSci 2018 (#NetSci2018) conference in Paris, France (June 2018). This talk will take place on Thursday 13 June in the morning.
Paper Writing in Applied Mathematics (slightly updated slides)Mason Porter
Here are my slides (which I have updated very slightly) in writing papers in applied mathematics.
There will be an accompanying oral presentation and discussion on Friday 20 April. I am recording the video for that and plan to post it along with these (or a further updated version of these) slides.
Tutorial on Paper-Writing in Applied Mathematics (Preliminary Draft of Slides)Mason Porter
These are preliminary slides for a tutorial and discussion on "Writing Papers in Applied Mathematics" that I'll be giving at UCLA, first for a few of my own PhD students on 4/6 and later (on 4/20 ?) in a recorded session to a larger UCLA group.
Several people have expressed interest, so I will post the recorded session online and circulate it.
These slides are for my talk for the Somerville College Mathematics Reunion ("Somerville Maths Reunion", 6/24/17): http://www.some.ox.ac.uk/event/somerville-maths-reunion/
My talk at the 2017 SIAM "Snowbird" conference on applications of dynamical systems (#SIAMDS17).
I spoke in a session on topological data analysis (TDA). My talk concerned persistent homology and its application to Brexit data (including voting data) and "functional networks" from coupled time series from both experiments and output of dynamical systems.
Eventually, a version of these slides that is synchronized with the audio of my talk is supposed to be posted online.
This is my attempt at an introduction to data ethics for mathematicians. Mathematicians increasingly need to deal with these kinds of issues, but we don't have the tradition of ethics training from other disciplines.
I welcome comments on how to improve these slides. Did I miss any salient points? Do you want to offer a different perspective on any of these? Do you want to offer any counterpoints? (Please e-mail me directly with comments and suggestions.)
Eventually, I hope to develop these slides further into an article for a venue aimed at mathematical scientists, and of course I would love to have knowledgeable coauthors who can offer a different perspective from mine.
My slides from my 3-hour tutorial on mesoscale structures in networks from the 2016 Lake Como School on Complex Networks (http://ntmb.lakecomoschool.org/).
After my talk, Tiago Peixoto gave a talk on statistical inference of large-scale mesoscale structures in networks. His presentation, which takes a complementary perspective from mine, is available at the following website: https://speakerdeck.com/count0/statisical-inference-of-generative-network-models
This is a presentation I gave in a workshop on "Language, concepts, history" organized by historian Joanna Innes. It took place on Friday 4/22/16 in Somerville College, Oxford.
I was one of the only people present who was not from the humanities, so it was a rather different-than-usual audience and set of participants for me.
I drew some of these slides from other presentations to rather different audiences. I emphasized rather different parts of some of those slides, so I am not sure if the slides on their own give an accurate reflection of the difference between this presentation and some of my other ones.
I thought the presentation went rather well.
Networks in Space: Granular Force Networks and BeyondMason Porter
This is my talk for the Network Geometry Workshop (http://ginestra-bianconi-6flt.squarespace.com) at QMUL on 16 July 2015.
(A few of the slides are adapted from slides by my coauthors Dani Bassett and Karen Daniels.)
These are slides for my tutorial talk on network dynamics. (The colors are fine in the downloaded version, though there seem to be color issues if you view the slides directly in slideshare.)
Slides from my talk on a systems-level investigation of long-term human migration in Korea. Our paper is available at the following page: http://journals.aps.org/prx/abstract/10.1103/PhysRevX.4.041009
I adapted these slides from the ones created by my coauthor Sang Hoon Lee.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Introduction to Topological Data AnalysisMason Porter
Here are slides for my 3/14/21 talk on an introduction to topological data analysis.
This is the first talk in our Short Course on topological data analysis at the 2021 American Physical Society (APS) March Meeting: https://march.aps.org/program/dsoft/gsnp-short-course-introduction-to-topological-data-analysis/
Topological Data Analysis of Complex Spatial SystemsMason Porter
These are slides from a seminar I gave in "Cardiff" (for the mathematics department at University of Cardiff) on 4/15/20.
You can also find a recording of a similar talk that I gave in March 2020 for MBI (Mathematical Biosciences Institute): https://mbi.osu.edu/events/online-colloquium-mason-porter-spatial-systems-and-topological-data-analysis
Here are my slides (though the animated gifs on a couple of them are stills in this version) of my talk on an introduction to the science of "chaos" at WorldCon 77 in Dublin, Ireland.
This is my attempt to give a gentle introduction to the notion of chaos to a science-fiction audience.
Centrality in Time- Dependent NetworksMason Porter
My slides for my keynote talk at the NetSci 2018 (#NetSci2018) conference in Paris, France (June 2018). This talk will take place on Thursday 13 June in the morning.
Paper Writing in Applied Mathematics (slightly updated slides)Mason Porter
Here are my slides (which I have updated very slightly) in writing papers in applied mathematics.
There will be an accompanying oral presentation and discussion on Friday 20 April. I am recording the video for that and plan to post it along with these (or a further updated version of these) slides.
Tutorial on Paper-Writing in Applied Mathematics (Preliminary Draft of Slides)Mason Porter
These are preliminary slides for a tutorial and discussion on "Writing Papers in Applied Mathematics" that I'll be giving at UCLA, first for a few of my own PhD students on 4/6 and later (on 4/20 ?) in a recorded session to a larger UCLA group.
Several people have expressed interest, so I will post the recorded session online and circulate it.
These slides are for my talk for the Somerville College Mathematics Reunion ("Somerville Maths Reunion", 6/24/17): http://www.some.ox.ac.uk/event/somerville-maths-reunion/
My talk at the 2017 SIAM "Snowbird" conference on applications of dynamical systems (#SIAMDS17).
I spoke in a session on topological data analysis (TDA). My talk concerned persistent homology and its application to Brexit data (including voting data) and "functional networks" from coupled time series from both experiments and output of dynamical systems.
Eventually, a version of these slides that is synchronized with the audio of my talk is supposed to be posted online.
This is my attempt at an introduction to data ethics for mathematicians. Mathematicians increasingly need to deal with these kinds of issues, but we don't have the tradition of ethics training from other disciplines.
I welcome comments on how to improve these slides. Did I miss any salient points? Do you want to offer a different perspective on any of these? Do you want to offer any counterpoints? (Please e-mail me directly with comments and suggestions.)
Eventually, I hope to develop these slides further into an article for a venue aimed at mathematical scientists, and of course I would love to have knowledgeable coauthors who can offer a different perspective from mine.
My slides from my 3-hour tutorial on mesoscale structures in networks from the 2016 Lake Como School on Complex Networks (http://ntmb.lakecomoschool.org/).
After my talk, Tiago Peixoto gave a talk on statistical inference of large-scale mesoscale structures in networks. His presentation, which takes a complementary perspective from mine, is available at the following website: https://speakerdeck.com/count0/statisical-inference-of-generative-network-models
This is a presentation I gave in a workshop on "Language, concepts, history" organized by historian Joanna Innes. It took place on Friday 4/22/16 in Somerville College, Oxford.
I was one of the only people present who was not from the humanities, so it was a rather different-than-usual audience and set of participants for me.
I drew some of these slides from other presentations to rather different audiences. I emphasized rather different parts of some of those slides, so I am not sure if the slides on their own give an accurate reflection of the difference between this presentation and some of my other ones.
I thought the presentation went rather well.
Networks in Space: Granular Force Networks and BeyondMason Porter
This is my talk for the Network Geometry Workshop (http://ginestra-bianconi-6flt.squarespace.com) at QMUL on 16 July 2015.
(A few of the slides are adapted from slides by my coauthors Dani Bassett and Karen Daniels.)
These are slides for my tutorial talk on network dynamics. (The colors are fine in the downloaded version, though there seem to be color issues if you view the slides directly in slideshare.)
Slides from my talk on a systems-level investigation of long-term human migration in Korea. Our paper is available at the following page: http://journals.aps.org/prx/abstract/10.1103/PhysRevX.4.041009
I adapted these slides from the ones created by my coauthor Sang Hoon Lee.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Cascades and Social Influence on Networks, UCSB, 3 Oct 2014
1. Collaborators:
Davide
Cellai,
James
Gleeson,
Adam
Hackett,
Heather
Harrington,
Florian
Klimm,
Miroslav
Kramar,
Sergey
Melnik,
Konstantin
Mischaikow,
Peter
Mucha,
JP
Onnela,
Felix
Reed-‐Tsochas,
Dane
Taylor,
Jonathan
Ward
2.
3.
4. MAP
&
J.
P
Gleeson,
“Dynamical
Systems
on
Networks:
A
Tutorial”,
submitted
to
Frontiers
in
Applied
Dynamical
Systems,
arXiv:
1403.7663
5.
6.
7.
8.
9.
10.
11.
12.
13. S.
Melnik,
J.
A.
Ward,
J.
P.
Gleeson,
&
MAP,
“Multi-‐Stage
Complex
Contagions”,
Chaos,
23(1),
013124
(2013)
14. Active
(S1)
Hyper-‐active
(S2)
Influences
neighbors
Influences
neighbors,
but
with
bonus
influence
compared
to
Active
nodes
No
influence
Note:
S2
⊆
S1
but
Si
⊈
S0
for
i
>
0
43. #FXGTVKUGOGPV/$+5GOGUVGT2TQITCO
QP0GVYQTMU
5RTKPI
• Mathematical Biosciences
Institute, The Ohio State
University, USA!
• Semester program on “Dynamics of
Biologically Inspired Networks”!
– http://mbi.osu.edu/programs/
emphasis-programs/future-programs/
spring-2016-dynamics-biologically-inspired-
networks/!
• Focuses on theoretical questions
on networks that arise from
biology!