New algorithm finds meaningful relationships in data

A recently published paper in Nature Biotechnology describes a simple algorithm which can potentially cut through the background noise often found in larger networks.

Networks are huge, and they are everywhere now. Your Facebook profile is part of a large network of friends, likes, and interests. In biotechnology, for example, networks are used to make sense of interacting genes. What often happens though is that items which are close (either physically or connected through a third party) are mistaken for being related. Just because two people may know the same person, doesn’t mean that they know each other. These indirect relationships can create a feedback type loop which makes them appear stronger, often obscuring the more direct connections.

There are many ways to deal with these issues, however they are specific to their problem domain and often require a great deal of computational power.

Soheil Feizi et al. (2013) have developed an algorithm which located those stronger direct connections and filters out the indirect ones. They test their algorithm by applying it to three datasets; gene expression regulatory networks, protein structure predictions, and social network of co-authorship information.

What I particularly like about this paper and the authors is that they released their code and datasets. The code is a simple MATLAB module which can easily be used by other researchers and techies interested in this type of thing. The method they describe could also be applied to a wide variety of areas which makes it quite an exciting prospect (if you’re into that kind of thing!)

Many systems (including Artificial Intelligence research) is moving away from rule based methods, to one where relationships are built by analysing big data. Think Google Translate. It isn’t built from an endless list of rules about grammar and syntax, instead it uses a vast array of multi-language data (e.g. books printed in multiple languages) to build a network of related words and phrases. Amazon’s recommendation engine works in a similar way. Using the information they have on “similar people”, they dig through their large datasets and produce items which they think you might also enjoy. Even the ads and “people you might know” you see on Facebook are discovered in this way.

Feizi’s algorithm provides a simple mathematical way to fine tune these recommendations by filtering out the indirect, transient connections from the truer, more meaningful ones. It could turn out to be quite a powerful mechanism, not only when applied to biological processes (e.g. drug effects on gene expression) but also to social networks such as Twitter and LinkedIn, recommendation engines, translation tools, and trust metrics.

The Broad Institute have published an article which summarises the research nicely.


Feizi, S., Marbach, D., Médard, M., & Kellis, M., Nature Biotechnology, 31, 726 (link)



Semester one down

A month after finishing first semester, and I find myself longing for more brain food. It’s been good to have a break from the study, but I’m keen to get back into it again soon. My first semester with SAO was amazing. I did two subjects, one which focused on stars and their evolution, the other on galaxies.

It was tough work with a lot of material to cover. I found myself studying every night, and most weekends. I’ve had little to no time behind the telescope as well which is a bit of a shame, although the poor weather we’ve had in Melbourne this year has made my guilt more bearable.

— Read More —


Newsgroups for learning

The post grad I’m undertaking is online. This is great because I can manage my study time much more effectively around work and home, and I also get the influence of people from all over the world in my class as well. The course has a requirement that you post a certain number of questions and answers each fortnight to the forums. I was expecting that people would do the bare minimum for this item and therefore the value of the newsgroups would be limited. Was I mistaken!

Newsgroup postings

Newsgroup postings

Less than one week into the official semester my two subjects have 41 posts between them. Some are simple few line answers and comments. There are however some which are of quite a high quality and very informative. What has surprised me most was how much learning I have already gotten from crafting my own responses to questions.


A question was posed asking why Shapley considered Globular Clusters to be a part of our galaxy and not external to it. I thought this was an interesting question and began to do a little research about it. Before I realised, 4 hours had flown by, it was past midnight and I had explored a wonderful world of mistakes, friends and alliances, a great debate and a reconciliation. Through those four hours I learnt more about this topic than I had read in our course material and elsewhere.

I’ll write more about engagement through the newsgroups at a later date, but suffice to say, so far I’m finding them very useful to my learning.


Organising my reading materials

In starting my studies in Astronomy this week, I found it necessary to get myself organised. More specifically, organising the course materials, research papers and web sites. My process for this will definitely evolve and change over time, however here is what I’m working with at the moment.

What I needed

A short summary of my requirements:

  • Course materials and readings (in PDF) should be stored in a central location
  • Can be accessed through my Mac or iPad
  • Must be able to highlight and make annotations on the PDFs
  • Files can be categorised by tags/labels
  • Citation/Source for papers can be stored

— Read More —


Comet C/2011 W3 (Lovejoy)

I haven’t updated here in a while so thought it was about time. Summer is here in Australia which means more time outside at night under the stars. La Niña is here which means a not so hot and not so dry climate which doesn’t bode to well for those with their eyes fixated on the heavens. I’m planning on fixing that in other ways, but more on that later.

In the meantime, here’s a pic I took of Comet C/2011 W3 (Lovejoy). I woke up at 4am for a number of nights in a row hoping the skies would be clear. So on the 23rd of December, I wasn’t expecting much but on walking out into my backyard, I saw the comet. There she was, blazing brightly above the horizon. Clear to the naked eye. I ran inside, grabbed my camera gear and tripod. Threw on some shoes, grabbed my keys and ran out of the house into my car.

Driving like a speed demon around the suburbs at 4am in the morning, I found a dark place on an unsealed road in-front of a large property. I pulled up in the middle of the street, turned off my light, set up my gear and started the camera shooting. As I sat down on the gravel I realised something. I looked like a real dork. Shorts, tattered t-shirt, runners without socks, camera gear and retainer. Yes, a retainer. In my defence I was excited and I forgot to take it out. Also in my defence, I was in the midst of getting a root canal and crown replaced. Finally in my defence, I got to see my first comet so there, I don’t care much what you think!

C/2011 W3 (Lovejoy)

C/2011 W3 (Lovejoy)




First night with a camera and telescope

Like many young boys, I wanted one day to be an astronaut. Now at 30 something the closest I might get is looking through a telescope.

Last night was my first night at the Briars as a member of the Mornington Peninsula Astronomical Society (MPAS). The Briars is a 96 hectare historic park in Mt Martha. As well as a 1840s Homestead full of Napoleonic memorabilia, MPAS has its observation site based there.

After a bit of a chat with some other friendly members, setting up our scopes and doing something called “polar alignment” I was ready to start playing. The view through the StellarVue 105 f/6.3 Triplet APO Refractor is quite gorgeous. I decided to mount my basic Nikon D40 camera onto my scope and see if I could get some photographs.

Now, these definitely aren’t the best photos out there and I’m a little embarrassed to post them publicly given the spectacular images some people are producing these days. BUT … I’m quite happy with my first result and it will be a good reference point for me in the future to see how I might improve.

Great Orion Nebula

One of the most photographed sights in the night sky. This photograph by comparison could be classified as really bad, but for me, it was my first shot so I’m happy none-the-less!

Scope: StellarVue 105 f/6.3 Triplet APO Refractor
Camera: Nikon D40
Exposure: 2 x 30 seconds
ISO: 1600

Great Orion Nebula (M42 / NGC 1976)

Great Orion Nebula (M42 / NGC 1976)

Tucanae 47

One of my favourite sights in the night sky. Looks like a single star with the naked eye but on closer inspection it’s a collection of stars (globular cluster) some 120 light years wide! This photograph unfortunately is quite out of focus and has a fair bit of drift present. All items to keep practicing at!

Scope: StellarVue 105 f/6.3 Triplet APO Refractor
Camera: Nikon D40
Exposure: Single 30 second
ISO: 1600

47 Tucanae (NGC 104)


One thing I quite enjoyed seeing but didn’t get a photograph of was Saturn. Rising quite late, it was the last object I viewed that night. What a spectacular sight. The view through the StellarVue was incredibly crisp. I had to push the magnification a bit to get a larger view but even then it was surprisingly bright and clear. For those number inclined …

Normal viewing through the StellarVue:

105mm aperture
f/6.3 focal ratio
661.5mm focal length

With the 2x barlow & a 6mm eyepiece:

1.323 metre focal length
Magnification of 220x

All in all, a quite successful first light for me as a MPAS member.



Starting a family history

Over the last month, I’ve started to piece together my family history. As I come to publishing it online I realise how much private information it exposes. With a date of birth and a maiden name you can do a whole lot of damage to a person’s identity. So, with that realisation I have decided not to publicly publish this information. I will however write up some of the interesting facts and resources I encounter along the way.

My virtual family tree

My virtual family tree

What software am I using?

I researched and tried a small variety of genealogy software which is out there. In the end I settled on a product called Mac Family Tree.

It is extremely easy to use and seems to be quite powerful too. One of the most important features is that it is GEDCOM compatible. GEDCOM is a file format used to transfer genealogical data between various products.

One thing I intend to do with this GEDCOM format is to export it from Mac Family Tree and run it through a kind of website generator which will turn all the data into a navigable website for my family to use.

I also like this product because it can store all manner of factual information (e.g. dates, places, events) as well as more fluid types like stories, images, files, etc.

It displays a whole variety of reports and charts too which have already helped me pick up on some interesting facts and statistics occurring in my family.

What have I discovered so far?

There are some quite interesting stories about my maternal grandparents, my maternal grandfather and his father in-law. Discovering this didn’t require any digging through national archives. It was simply reaching out and asking people for any interesting stories and things they know.

Well, my grandparents were married by proxy. My grandfather had already moved to Australia (Queensland) and my grandmother was still in Italy. Before she would come to Australia she insisted that they get married. So they did, and it happened on opposite sides of the world.

My maternal great-grandfather (on my grandmother’s side) was Italian. In 1909 he jumped onto a boat and travelled to the USA to visit a family member there. He came through the Ellis Island port in New York so his entry records are available online. He was 29 at the time and travelled by himself from Sicily.

My maternal grandfather also had an interesting time during war times in Italy, but more on that another day.

On my father’s side, at my grandmother’s recent funeral, I saw a picture of my great-grandfather. The picture would have been taken in the late 1800s. The similarity between him, one of my uncles and my father is quite striking. Even more striking is how similar he looks to Mark Twain!

What’s next?

My next step is to fill in as many of the facts as I can. Mainly birth and death dates and locations. With this information I should be in a good position to start searching for various official documents like birth certificates and military records.


Obligatory start of year post

I’m not one for new year’s resolutions, but not wanting to feel left out, here are my current goals for the time ahead. Yes, alright, well these are “goals” as such and they don’t fit that S.M.A.R.T. method crap, but they are things which are in my head at the moment, so take them as they come …

New Year Resolutions

Language learning

I am aiming to reach a conversational level of proficiency with both Czech and Italian.

Over the years of listening to Italian (and speaking small amounts of it) I have acquired that intrinsic feel for the grammar and structure. Improving my Italian will be a matter of “becoming comfortable” with it and learning more vocabulary, rather than learning any formal rules and the like. The most difficult part for me will be to better understand and separate the various dialectical differences spoken amongst my older family members.

My learning of the Czech language will take a slightly different course. I still need to become more comfortable with the sound and rhythm of the language. Much more vocabulary and significantly more real life conversational practice is required. I also intend to watch more Czech films this year which should be fun.


James Krenov at work

James Krenov at work

I have already done a small number of commissions but I don’t want to take on too many of them. There are just so many other styles and things I would like to explore at the same time. I do intend to make a few pieces of “fine furniture” and sell them. Either smaller things like boxes, picture frames and lamps, or larger things like hall tables and cabinets.

There are three things I do want to build this year:

  1. Krenov style cabinet
  2. A new André Jacob Roubo workbench
  3. Another hall table

Brain food

A couple of months ago, I finally found a Masters Degree I was keen to undertake. My interests are a little esoteric so finding a degree which is broad enough to hold my interest has been a challenge. The Masters in Organisational Dynamics seems to cover a number of aspects I am interested in as well as provide enough flexibility to keep it interesting for me. Cognition, psychology, identity of self, learning theory and meditation are all part of it.

Unfortunately they have cancelled the degree for 2011 and will be recommencing it in 2012 under a new banner.

The National Institute of Organisation Dynamics Australia (NIODA) is a spin off of the Organisational Dynamics department at RMIT. They kick off the new degree in 2012 so I need to find something to study and keep my brain going this year. I’ve been toying with the idea of a Psychology (diploma or certificate) so I will see where that takes me in the meantime.


I was born an Australian citizen and have Italian heritage. One day I would like to move to Europe and even live in Italy for a while. To do this easily, I will need to get my Italian citizenship.

Italian passportNow, for those of you against the whole “dual-citizenship” caper, let me tell you these two things:

  1. I believe every naturally born Australian should partake in an Australian Oath of Citizenship, or at least have an option to affirm their allegiance when they turn 18.
  2. I am an Italian citizen and have always been one since I took that first breath after birth.

Italy is one of the few nations who bestow citizenship jure sanguinis (right of blood). So as long as one of my parents was still an Italian citizen (i.e. didn’t renounce their citizenship) when I was born, then I am automatically an Italian citizen. It doesn’t matter than I was born in Australia.

So, I just have to fill in the requisite paperwork and then apply for my EU passport. Easy!

Other stuff

All the other stuff which is currently occupying my thoughts and will hopefully lead somewhere soon …

  • Get bike riding again
  • Commence and publish online a family history (i.e. of my own family and ancestry)
  • Build a deck, pergola, garden beds and tidy up the backyard overall
  • Meditate more and meditate regularly

The spectacle behind the spectacle …

A few times now I have witnessed quite a humorous sight. The mechanics of the Pražský Orloj (Astronomical Clock) are to be admired especially for the period in which it was made. The clock mechanism itself is amazingly complex and quite beautiful. There is even an iphone app for that which gives you a good feel for what the clock actually communicates (aside from the time of day!)

The little dance the figurines do every hour however is something else entirely …

The most spectacular thing about witnessing this hourly display is by far the crowd. In the evenings as people are out for dinner (or beginning night tours), crowds of literally hundreds of people all look up through their cameras at the clock.

Crowd watching the Orloj

Crowd watching the Orloj

The bells ding, dads grab their children and rush them into prime viewing position, the little figurines do their little figurine dance and the golden chicken pokes its head out of a little doorway.

Then out of the sound of ringing bells comes … (now this is the part I like most) … a spontaneous cheer and round of applause from the crowd. Hoorah! The golden chicken lives another hour! Hoorah!

The golden chicken content with its reception retires into its room, the little doorway closes and the place is deserted once again.

It’s the spectacle of the crowd which keeps drawing me back to this place and not the hourly jiggling of ancient mechanical puppets. If you’re interested, there is an online version of the clock which gives you a sense of all the parts – except of course for those cute figurines and the captivating crowd. For that, you really need to visit Praha in person.


My little language test – Do gestures make a difference?

I always knew that body language made up a huge part of communication. So today I tried a little experiment to see how important it is when speaking in a language you only know a little about.

At my hotel in Boskovice, I had a great, but short, conversation with the receptionist. It was partly in Czech and partly in English but I forced myself to use as much Czech as possible. We spoke about music and I learnt that she was studying multi-media at university and had a 5 year old daughter named Ann. On saying goodbye (once my lift arrived) Lucie lamented that the conversation was too short.

Church in Boskovice

Church in Boskovice

So, here began my experiment. This morning I decided to call the hotel on the phone with the pretence that I was thinking of visiting again in a week. I figured since I knew we could have a conversation in person, having one over the phone would remove the visual aspects and truly test my language skills.

This phone conversation was close to a disaster. It was full of “sorrys” and much nervous laughter from both sides. At one point I was speaking broken English, as if that would help. To at least rescue the situation and finish things up nicely I resorted to using Google translator.

One nights sleep and a successful conversation turns into mud.

The inability to use facial expressions and hand gestures really did make things very difficult. Whilst not a true scientific experiment, I realise now first hand that whilst learning more vocabulary might be good, it isn’t the complete picture. You can fill many gaps in your limited language knowledge by being confident, animated and by using hand gestures.

Luckily for me I’m Italian so this comes naturally!

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