Svetha Venkatesh on Svetha Venkatesh

Example Talk

Sun, 01 Jan 2017 00:00:00 +1100

Embed your slides or video here using shortcodes. Further details can easily be added using Markdown and $\rm \LaTeX$ math code.

Adaptive Experimental Design using Bayesian Optimisation

Tue, 27 Dec 2016 00:00:00 +0000

This project aims to optimise processes for manufacturing new materials, from short fibres, to alloys, to cosmetics, to food, or, in fact, any material for industry or consumer use. By using machine learning and Bayesian mathematics (a sophisticated form of probability), we have developed an abstract framework and software that achieves a faster, cheaper and more effective approach to optimising products and manufacturing processes.

The computational challenge in optimisation of novel processes arises because the mathematical relationship between the control variables and the target is often unknown - it is a classic “Black-Box Function”. Experimental data is expensive to acquire, so achieving an optimal setting with a minimum of experiments is desirable. Our framework - Adaptive Experimental Design uses machine learning to navigate complex problems with many variables. It interprets measurements and suggests settings for the next group of experiments, guiding the experimenter to the goal in fewer steps.

We have applied our method successfully to the following case studies.

Short fibre production
Alloy manufacturing
Alloy heat treatment
3D printing

Early Intervention for Autism

Wed, 27 Apr 2016 00:00:00 +0000

There is a growing gap between the number of children with autism requiring early intervention and available therapy. In this project we seek to produce the following outcomes: * Flexible frameworks for stimulus presentation and recording, for early intervention in social and cognitive/visual areas, * Open source infrastructures to leverage content and metadata from social media, constructing foundations for reusable content in early intervention, * Assistive Technologies for finding appropriate information from forums and blogs, focusing on autism, * Early warning systems of mental wellbeing, measuring affect in text-based social media (forums, blogs, etc.) and appropriate triggers for social support. * New tools for assistive support for communication and social function.

Our partners are: Autism West, Gateways, Barwon health. We do this project jointly with our colleagues at Curtin University.

Our Contributions: We present a portable platform for pervasive delivery of early intervention therapy using multi-touch interfaces and principled ways to deliver stimuli of increasing complexity and adapt to a child’s performance. Our implementation weaves Natural Environment Tasks with iPad tasks, facilitating a learning platform that integrates early intervention in the child’s daily life. The system’s construction of stimulus complexity relative to task is evaluated by therapists, together with field trials for evaluating both the integrity of the instructional design and goal of stimulus presentation and adjustment relative to performance for learning tasks. We show overwhelmingly positive results across all our stakeholders, children, parents and therapists. Our results have implications for other early learning fields that require principled ways to construct lessons across skills and adjust stimuli relative to performance. See Toby Playpad. The Technology won the 2011 Curtin University Commercialization award.

Health Analytics

Wed, 27 Apr 2016 00:00:00 +0000

With our partner Barwon Health we are embarking on questions that arise in examination of large, disparate and multimodal hospital data sets. Can we impact and inform the formation of dynamic health intervention and improved safety and care through:

Predicting hospital visitation patterns of patients with chronic disease,
Detection of sub-populations that have coherent patterns of disease, causal factors, and typical medical responses
Identify data driven characteristics of chronic patients to enable personalized care plans
Detect indicators that serve as early warning of chronic disease
Monitor key factors that deliver value to patients in the areas of care experiences, care coordination and patient safety.

Our work led to the formation of an app that allows hospital administrators and clinicians to see at a glance what’s happening in the hospital, on the ward or to their patients. This was developed over several years of research, using machine learning to mine medical and hospital data to provide hospital cost efficiencies and better predictive patient support.

Large Scale Surveillance

Wed, 27 Apr 2016 00:00:00 +0000

We are interested in the problems that arise when we examine hundreds of cameras. This big data problem opens up many new questions: Given limited operator capacity, how can select which camera I should look at? How do I select models and parameters for heterogeneous stream data - example, video feeds in varying environmental conditions? How do I evaluate algorithms in big data - training sets may exceeds 2 weeks of video data, and no realistic ground truth can be obtained from operators. How do we compare algorithms?

Our Contributions: Focusing on issues of large scale surveillance we have developed new techniques to model “normal” data from static video cameras. This allows us to detect real time “abnormal events” and thus enable operators to focus on the 1% of events in a video feed. Our algorithms drive the start-up iCetana’s innovative anomaly detection software. The software uses ideas from Compressed Sensing to enable simultaneous surveillance of many cameras deployed in diverse settings. A local city council has used our algorithms to detect loitering, anti-social behaviour and traffic violations. For more information see iCetana. The technology was: Winner, The Broadband Innovation Award Tech23,2010; Winner, 2011 WA Innovator of the Year.

Social Media Analysis

Wed, 27 Apr 2016 00:00:00 +0000

We study patterns in social media data; who is talking to who? What are they talking about? What is their sentiment? We discover latent community structures, their topics and trends. We explore not only text in blogs but also connectivity through comments. For personal media management it could be argued that social context contains the set of conceptions most often brought to bear on their contents: Where was this? Who is that? What activity were we all doing there? Who do I want to share this with? This project aims to use signals obtained from unobtrusive data sources available with today’s devices, such as location information (e.g. GPS), to extract socially meaningful indices for personal media. Social spheres are locations of significance, such as Home, Work and Recreational Area. Social networks of social ties capture the dynamic web of relationships in which we are embedded. Social rhythms arise as patterns across these former elements and allow even finer resolution categorization of activities that occur within them in space and time. All of this information can then be used, at the very least, to provide new ways to index and interact with our own, or others’, media collections. Initial work in this area focused on discovering the social spheres Work, Home and Other from raw, noisy GPS traces of everyday life, and used this information together with the presence of known persons to provide a novel personal media exploration environment called Socio-Graph. The interface aimed to allow simple search and filtering on the concepts most people innately bring to their personal media. We do this project jointly with our colleagues at Curtin University.

Getting started with the Academic framework for Hugo

Wed, 20 Apr 2016 00:00:00 +1000

The Academic framework enables you to easily create a beautifully simple personal or academic website using the Hugo static site generator.

Key features:

Easily manage your homepage, blog posts, publications, talks, and projects
Configurable widgets available for Biography, Publications, Projects, News/Blog, Talks, and Contact
Need a different section? Just use the Custom widget!
Write in Markdown for easy formatting and code highlighting, with LaTeX for mathematical expressions
Social/academic network linking, Google Analytics, and Disqus comments
Responsive and mobile friendly
Simple and refreshing one page design
Multilingual and easy to customize

Installation

Install Hugo and create a new website by typing the following commands in your Terminal or Command Prompt app:
```
hugo new site my_website
cd my_website
```
Install Academic with git:
```
git clone https://github.com/gcushen/hugo-academic.git themes/academic
```
Or alternatively, download Academic and extract it into a themes/academic folder within your Hugo website.
If you are creating a new website, copy the contents of the exampleSite folder to your website root folder, overwriting existing files if necessary. The exampleSite folder contains an example config file and content to help you get started.
```
cp -av themes/academic/exampleSite/* .
```
Start the Hugo server from your website root folder:
```
hugo server
```
Now you can go to localhost:1313 and your new Academic powered website should appear.
Customize your website - refer to the Getting Started section below
Build your site by running the hugo command. Then host it for free using Github Pages. Or alternatively, copy the generated public/ directory (by FTP, Rsync, etc.) to your production web server (such as your university’s hosting service).

Getting Started

Assuming you created a new website with the example content following the installation steps above, this section explores just a few more steps in order to customize it.

Core parameters

The core parameters for the website can be edited in the config.toml configuration file:

Set baseurl to your website URL (we recommend GitHub Pages for free hosting)
Set title to your desired website title such as your name
The example Disqus commenting variable should be cleared (e.g. disqusShortname = "") or set to your own Disqus shortname to enable commenting
Edit your details under [params]; these will be displayed mainly in the homepage about and contact widgets (if used). To disable a contact field, simply clear the value to "".
Place a square cropped portrait photo named portrait.jpg into the static/img/ folder, overwriting any defaults. Note that you can edit the avatar filepath to point to a different image name or clear the value to disable the avatar feature. Alternatively, set gravatar to true to use the Gravatar/Wordpress avatar associated with your email address.
To enable LaTeX math for your site, set math = true
Social/academic networking links are defined as multiples of [[params.social]]. They can be created or deleted as necessary.

Introduce yourself

Edit your biography in the about widget content/home/about.md that you copied across from the themes/academic/exampleSite/ folder. The research interests and qualifications are stored as interests and education variables. The academic qualifications are defined as multiples of [[education.courses]] and can be created or deleted as necessary. It’s possible to completely hide the interests and education lists by deleting their respective variables.

Customize the homepage

Refer to our guide on using widgets to customize your homepage.

Add your content

Refer to our guide on managing content to create your own publications, blog posts, talks, and projects.

Remove unused widgets and pages

How to remove unused widgets and content pages.

Themes

The following color themes are available and can be set by the color_theme option in config.toml:

`default`	`ocean`

`forest`	`coffee` + `playfair` font

`dark`

The following font styles are available and can be set by the font option in config.toml:

default (modern)
classic (original Academic v1 style)
playfair (serif)

Customization & updating

Continue reading below for advanced customization tips and instructions for keeping the framework up-to-date with any improvements that become available.

Advanced customization

It is possible to carry out many customizations without touching any files in themes/academic, making it easier to update the framework in the future.

The [[menu.main]] entries towards the bottom of config.toml define the navigation links at the top of the website. They can be added or removed as desired.

To create a dropdown sub-menu, add identifier = "something" to the parent item and parent = "something" to the child item.

Website icon

Save your main icon and mobile icon as square PNG images named icon.png and apple-touch-icon.png, respectively. Place them in your root static/img/ folder.

Analytics

To enable Google Analytics, add your tracking code in config.toml similarly to googleAnalytics = "UA-12345678-9".

Third party and local scripts (JS)

To add a third party script, create a file named head_custom.html in a layouts/partials/ folder at the root of your website (not in the themes folder). Any HTML code added to this file will be included within your website’s <head>. Therefore, it’s suitable for adding custom metadata or third party scripts specified with the async attribute.

Whereas for your own local scripts, you can link your local JS assets (relative to your root static/js) from your config.toml using custom_js = ["custom.js"].

Language and translation

The interface text (e.g. buttons) is stored in language files which are collected from Academic’s themes/academic/i18n/ folder, as well as an i18n/ folder at the root of your project.

To edit the interface text, copy themes/academic/i18n/en.yaml to i18n/en.yaml (relative to the root of your website). Open the new file and make any desired changes to the text appearing after translation:. Note that the language files are formatted in YAML syntax.

To translate the interface text to another language, follow the above instructions, but name the new file in the form i18n/X.yaml where X is the appropriate ISO/RFC5646 language identifier for the translation. Then follow the brief instructions in the Language section at the bottom of your config.toml. To change the default language used by Academic, set defaultContentLanguage to the desired language identifier in your configuration file.

To translate the navigation bar, you can edit the default [[menu.main]] instances in config.toml. However, for a multilingual site, you will need to duplicate all of the [[menu.main]] instances and rename the new instances from [[menu.main]] to [[Languages.X.menu.main]], where X is the language identifier (e.g. [[Languages.zh.menu.main]] for Simplified Chinese). Thus, the navigation bar can be displayed in multiple languages.

To translate a content file in your content/ folder into another language, copy the file to filename.X.md where filename is your existing filename and X is the appropriate ISO/RFC5646 language identifier for the translation. Then translate the content in the new file to the specified language.

For further details on Hugo’s internationalization and multilingual features, refer to the associated Hugo documentation.

Permalinks

Permalinks, or permanent links, are URLs to individual pages and posts on your website. They are permanent web addresses which can be used to link to your content. Using Hugo’s permalinks option these can be easily customized. For example, the blog post URL can be changed to the form yourURL/2016/05/01/my-post-slug by adding the following near the top of your config.toml (before [params] settings):

[permalinks]
    post = "/:year/:month/:day/:slug"

Where :slug defaults to the filename of the post, excluding the file extension. However, slug may be overridden on a per post basis if desired, simply by setting slug = "my-short-post-title" in your post preamble.

Example 2: let’s consider changing the URL path of posts from post/ to blog/. First, add the following parameters right above the [params] section of your config.toml:

[permalinks]
    post = "/blog/:slug"

Then add aliases = ["/blog/"] to your post archive page post/_index.md so that it can be accessed from the /blog/ URL.

Advanced style customization (CSS)

For advanced customization of the style, you can link custom CSS assets (relative to your root static/css) from your config.toml using custom_css = ["custom.css"].

For example, let’s override some of Academic’s default styles. First, define custom_css = ["override.css"] in config.toml. Then we can create the file static/css/override.css, relative to your website root (i.e. not in the themes directory). Add your custom CSS to this file.

Updating

Feel free to star the project on Github to help keep track of updates and check out the release notes prior to updating your site.

Before updating the framework, it is recommended to make a backup of your entire website directory, or at least your themes/academic directory.

Before updating for the first time, the remote origin repository should be renamed to upstream:

$ cd themes/academic
$ git remote rename origin upstream

To list available updates:

$ cd themes/academic
$ git fetch upstream
$ git log --pretty=oneline --abbrev-commit --decorate HEAD..upstream/master

Then, update by running:

$ git pull upstream

If you have modified files in themes/academic, git will attempt to auto-merge changes. If conflicts are reported, you will need to manually edit the files with conflicts and add them back (git add <filename>).

If there are any issues after updating, you may wish to compare your site with the latest example site to check if any settings changed in config.toml or the +++ frontmatter of content files.

Feedback & Contributing

Please use the issue tracker to let me know about any bugs or feature requests, or alternatively make a pull request.

For general questions about Hugo, there is a Hugo discussion forum.

License

Released under the MIT license.

Customizing the homepage with widgets

Tue, 19 Apr 2016 00:00:00 +1000

Homepage widgets display as sections on the homepage. They can be enabled/disabled and configured as desired. Academic has the following widgets available to use:

About/biography
Selected publications
Recent publications
Recent news/blog posts
Projects
Selected talks
Recent talks
Contact
Tag cloud
Hero (introduction)
Custom widget (demonstrated with the teaching example)

The example site that you copied to create your site uses all the different types of widget (except talks), so you can generally just delete the widgets you don’t need and customize the parameters of the widgets you wish to keep.

The parameters for each widget vary. They can be found in the preamble/frontmatter (between the pair of +++) for each widget installed in the content/home/ folder.

By default, publications will be displayed in a simple list. If you prefer a more detailed list with abstract and image, you can enable the detailed publication list on the homepage by setting list_format = 2 in content/home/publications.md.

To add a widget manually, copy the relevant widget from themes/academic/exampleSite/content/home/ to your content/home/ folder.

Widget identifiers are set to their respective filenames, so a content/home/about.md widget can be linked from the navigation bar by setting the relevant URL as "#about" in config.toml.

This means that if you want to use multiple instances of a widget, each widget will be assigned a unique ID based on the filename that you set. You can then use that ID for linking, like in the above example.

You can use the custom widget to create your own home page sections.

Simply duplicate (copy/paste) and rename the example teaching file at content/home/teaching.md. Then edit the section title, weight (refer to Ordering sections below), and content as desired.

You may also wish to add a navigation link to the top of the page that points to the new section. This can be achieved by adding something similar to the following lines to your config.toml, where the URL will consist of the first title word in lowercase:

[[menu.main]]
    name = "Research"
    url = "#research"
    weight = 10

If you do not require a particular widget, you can simply delete any associated files from the content/home/ folder.

To remove a navigation link from the top of the page, remove the associated [[menu.main]] entry in config.toml.

Ordering widgets

The order that the homepage widgets are displayed in is defined by the weight parameter in each of the files in the content/home/ directory. The widgets are displayed in ascending order of their weight, so you can simply edit the weight parameters as desired.

Managing content

Mon, 18 Apr 2016 00:00:00 +1000

This is a brief guide to managing content with the Academic framework. Content can include publications, projects, talks, news/blog articles, and widget pages. After you have read this guide about creating and managing content, you may also be interested to learn about writing content with Markdown, LaTeX, and Shortcodes.

To enable LaTeX math rendering for a page, you should include math = true in the page’s +++ preamble, as demonstrated in the included example site. Otherwise, to enable math on the homepage or for all pages, you must globally set math = true in config.toml.

To disable source code highlighting by default for all pages, set highlight = false in config.toml. You can then enable source code highlighting only on pages that need it by setting highlight = true in that page’s preamble. See the code-highlighting docs for more details.

To display a featured image in content page headers, the parameters below can be inserted towards the end of a page’s +++ preamble. It is assumed that the image is located in your static/img/ folder, so the full path in the example below will be static/img/headers/getting-started.png. The caption parameter can be used to write an image caption or credit.

[header]
image = "headers/getting-started.png"
caption = "Image credit: [**Academic**](https://github.com/gcushen/hugo-academic/)"

If you wish to prevent a featured image automatically being used for a post’s thumbnail on the homepage, the preview = false parameter can be added to [header].

Create a publication

To create a new publication:

hugo new publication/my-paper-name.md

Then edit the default variables at the top of content/publication/my-paper-name.md to include the details of your publication. The url_ variables are used to generate links associated with your publication, such as for viewing PDFs of papers. Here is an example:

+++
title = "A publication title, such as title of a paper"

# Date first published.
date = "2013-07-01"

# Authors. Comma separated list, e.g. `["Bob Smith", "David Jones"]`.
authors = ["First author's name", "Second author's name"]

# Publication type.
# Legend:
# 0 = Uncategorized
# 1 = Conference proceedings
# 2 = Journal
# 3 = Work in progress
# 4 = Technical report
# 5 = Book
# 6 = Book chapter
publication_types = ["1"]

# Publication name and optional abbreviated version.
publication = "In *International Conference on Academic*. You may use *Markdown* for italics etc."
publication_short = "In *ICA*"

# Abstract and optional shortened version.
abstract = "The abstract. Markdown and math can be used (note that math may require escaping as detailed in the red alert box below)."
abstract_short = "A short version of the abstract."

# Featured image thumbnail (optional)
image_preview = ""

# Is this a selected publication? (true/false)
selected = true

# Projects (optional).
#   Associate this publication with one or more of your projects.
#   Simply enter the filename (excluding '.md') of your project file in `content/project/`.
#   E.g. `projects = ["deep-learning"]` references `content/project/deep-learning.md`.
projects = []

# Links (optional).
url_pdf = "pdf/my-paper-name.pdf"
url_preprint = ""
url_code = ""
url_dataset = ""
url_project = ""
url_slides = ""
url_video = ""
url_poster = ""
url_source = ""

# Custom links (optional).
#   Uncomment line below to enable. For multiple links, use the form `[{...}, {...}, {...}]`.
# url_custom = [{name = "Custom Link", url = "http://example.org"}]

# Does the content use math formatting?
math = true

# Does the content use source code highlighting?
highlight = true

# Featured image
# Place your image in the `static/img/` folder and reference its filename below, e.g. `image = "example.jpg"`.
[header]
image = "headers/bubbles-wide.jpg"
caption = "My caption 😄"

+++

Further details on your publication can be written here using *Markdown* for formatting. This text will be displayed on the Publication Detail page.

The url_ links can either point to local or web content. Associated local publication content, such as PDFs, may be copied to a static/pdf/ folder and referenced like url_pdf = "pdf/my-paper-name.pdf".

You can also associate custom link buttons with the publication by adding the following block within the variable preamble above, which is denoted by +++:

url_custom = [{name = "Custom Link 1", url = "http://example.org"},
              {name = "Custom Link 2", url = "http://example.org"}]

If you set list_format=2 to enable a detailed listing of publications in the Publication Widget (home/publications.md) or Publication Archive (publication/_index.md), then there are a few more optional variables that you can include in the publication page preamble. You may use abstract_short = "friendly summary of abstract" and publication_short = "abbreviated publication details" to display a friendly summary of the abstract and abbreviate the publication details, respectively. Furthermore, there is the option to display a different image on the homepage to the publication detail page by setting image_preview = "my-image.jpg". This can be useful if you wish to scale down the image for the homepage or simply if you just wish to show a different image for the preview.

Any double quotes (") or backslashes (e.g. LaTeX \times) occurring within the value of any frontmatter parameter (such as the abstract) should be escaped with a backslash (\). For example, the symbol " and LaTeX text \times become \" and \\times, respectively. Refer to the TOML documentation for more info.

Create a blog post

To create a blog/news article:

hugo new post/my-article-name.md

Then edit the newly created file content/post/my-article-name.md with your full title and content.

Hugo will automatically generate summaries of posts that appear on the homepage. If you are dissatisfied with an automated summary, you can either limit the summary length by appropriately placing  in the article body, or completely override the automated summary by adding a summary parameter to the +++ preamble such that:

summary = "Summary of my post."

To disable commenting for a specific post, you can add disable_comments = true to the post +++ preamble. Or to disable commenting for all posts, you can either set disqusShortname = "" or disable_comments = true in config.toml.

Create a project

To create a project:

hugo new project/my-project-name.md

Then edit the newly created file content/project/my-project-name.md. Either you can link the project to an external project website by setting the external_link = "http://external-project.com" variable at the top of the file, or you can add content (below the final +++) in order to render a project page on your website.

Create a talk

To create a talk:

hugo new talk/my-talk-name.md

Then edit the newly created file content/talk/my-talk-name.md with your full talk title and details. Note that many of the talk parameters are similar to the publication parameters.

So you would like to create a page which utilizes Academic’s widget system, similar to the homepage?

Create a new folder in your content folder, naming it with your new page name. In this example, we will create a courses page by creating a content/courses/ folder.

Within your new content/courses/ folder, create a file named _index.md containing the following parameters:

+++
title = "Courses"
date = 2017-01-01
widgets = true
+++

Install widgets into your content/courses/ folder. To achieve this, widgets can be copied from your content/home/ folder or downloaded from Github.

Create other pages (e.g. CV)

For other types of content, it is possible to create your own custom pages. For example, let’s create a cv.md page for your Curriculum Vitae in your content folder. Copy across the frontmatter from the top of one of your post files, adapting it as necessary, and editing your Markdown content below. You can then link to your new page by adding the code [My CV]{{< ref "cv.md" >}} to any of your existing content.

Alternatively, for the above example, we could use a PDF of your Curriculum Vitae. For this purpose, create a folder called files within your static folder and move a PDF file named cv.pdf to that location, so we have a static/files/cv.pdf file path. The PDF can then be linked to from any content by using the code: {{% staticref "files/cv.pdf" %}}Download my CV{{% /staticref %}}.

Manage archive pages

The archive (or node index) pages (e.g. /post/) are the special pages which list all of your content. They can exist for blog posts, publications, and talks. The homepage widgets will automatically link to the archive pages when you have more items of content than can be displayed in the widget. Therefore, if you don’t have much content, you may not see the automatic links yet - but you can also manually link to them using a normal Markdown formatted link in your content.

You can edit the title and add your own content, such as an introduction, by copying the following content _index.md files from the example site to the same structure within your content/ folder:

/themes/academic/exampleSite/content/post/_index.md
/themes/academic/exampleSite/content/publication/_index.md
/themes/academic/exampleSite/content/talk/_index.md

Then edit the title parameter in each _index.md as desired and add any content after the +++ preamble/frontmatter ends. You will notice that the _index.md files differ slightly, with some having special options available for the associated content type. For example, publication/_index.md contains an option for setting the citation style of the listings which appear on the publication archive page.

Removing content

Generally, to remove content, simply delete the relevant file from your content/post, content/publication, content/project, or content/talk folder.

View your updated site

After you have made changes to your site, you can view it by running the hugo server command and then opening localhost:1313 in your web browser.

Deploy your site

Finally, you can build the static website to a public/ folder ready for deployment using the hugo command.

You may then deploy your site by copying the public/ directory (by FTP, SFTP, WebDAV, Rsync, git push, etc.) to your production web server.

Note that running hugo does not remove any previously generated files before building. Therefore, it’s best practice to delete your public/ directory prior to running hugo to ensure no old or interim files are deployed to your server.

Writing content with Markdown, LaTeX, and Shortcodes

Sun, 17 Apr 2016 00:00:00 +1000

Content can be written using Markdown, LaTeX math, and Hugo Shortcodes. Additionally, HTML may be used for advanced formatting. This article gives an overview of the most common formatting options.

Sub-headings

## Heading 2
### Heading 3
#### Heading 4
##### Heading 5
###### Heading 6

Emphasis

Italics with *asterisks* or _underscores_.

Bold with **asterisks** or __underscores__.

Combined emphasis with **asterisks and _underscores_**.

Strikethrough with ~~two tildes~~.

Ordered lists

1. First item
2. Another item

Unordered lists

* First item
* Another item

Images

Images may be added to a page by placing them in your static/img/ folder and referencing them using one of the following two notations:

A general image:

![alternative text for search engines](/img/screenshot.png)

A numbered figure with caption:

{{< figure src="/img/screenshot.png" title="Figure Caption" >}}

Links

[I'm a link](https://www.google.com)
[A post]({{< ref "post/hi.md" >}})
[A publication]({{< ref "publication/hi.md" >}})
[A project]({{< ref "project/hi.md" >}})
[Another section]({{< relref "hi.md#who" >}})

To enable linking to a file, such as a PDF, first place the file in your static/files/ folder and then link to it using the following form:

{{% staticref "files/cv.pdf" "newtab" %}}Download my CV{{% /staticref %}}

The optional "newtab" argument for staticref will cause the link to be opened in a new tab.

Emojis

See the Emoji cheat sheet for available emoticons. The following serves as an example, but you should remove the spaces between each emoji name and pair of semicolons:

I : heart : Academic : smile :

I ❤️ Academic 😄

Blockquote

> This is a blockquote.

This is a blockquote.

Footnotes

I have more [^1] to say.

[^1]: Footnote example.

I have more ¹ to say.

Code highlighting

Pass the language of the code, such as python, as a parameter after three backticks:

```python
# Example of code highlighting
input_string_var = input("Enter some data: ")
print("You entered: {}".format(input_string_var))
```

Result:

# Example of code highlighting
input_string_var = input("Enter some data: ")
print("You entered: {}".format(input_string_var))

Highlighting options

The Academic theme uses highlight.js for source code highlighting, and highlighting is enabled by default for all pages. However, several configuration options are supported that allow finer-grained control over highlight.js.

The following table lists the supported options for configuring highlight.js, along with their expected type and a short description. A “yes” in the config.toml column means the value can be set globally in config.toml, and a “yes” in the preamble column means that the value can be set locally in a particular page’s preamble.

option	type	description	config.toml	preamble
`highlight`	boolean	enable/disable highlighting	yes	yes
`highlight_languages`	slice	choose additional languages	yes	yes
`highlight_style`	string	choose a highlighting style	yes	no

Option `highlight`

The highlight option allows enabling or disabling the inclusion of highlight.js, either globally or for a particular page. If the option is unset, it has the same effect as if you had specified highlight = true. That is, the highlight.js javascript and css files will be included in every page. If you’d like to only include highlight.js files on pages that actually require source code highlighting, you can set highlight = false in config.toml, and then override it by setting highlight = true in the preamble of any pages that require source code highlighting. Conversely, you could enable highlighting globally, and disable it locally for pages that do not require it. Here is a table that shows whether highlighting will be enabled for a page, based on the values of highlight set in config.toml and/or the page’s preamble.

config.toml	page preamble	highlighting enabled for page?
unset or true	unset or true	yes
unset or true	false	no
false	unset or false	no
false	true	yes

Option `highlight_languages`

The highlight_languages option allows you to specify additional languages that are supported by highlight.js, but are not considered “common” and therefore are not supported by default. For example, if you want source code highlighting for Go and clojure in all pages, set highlight_languages = ["go", "clojure"] in config.toml. If, on the other hand, you want to enable a language only for a specific page, you can set highlight_languages in that page’s preamble.

The highlight_languages options specified in config.toml and in a page’s preamble are additive. That is, if config.toml contains, highlight_languages = ["go"] and the page’s preamble contains highlight_languages = ["ocaml"], then javascript files for both go and ocaml will be included for that page.

If the highlight_languages option is set, then the corresponding javascript files will be served from the cdnjs server. To see a list of available languages, visit the cdnjs page and search for links with the word “languages”.

The highlight_languages option provides an easy and convenient way to include support for additional languages to be severed from a CDN. If serving unmodified files from cdnjs doesn’t meet your needs, you can include javascript files for additional language support via one of the methods described in the getting started guide.

Option `highlight_style`

The highlight_style option allows you to select an alternate css style for highlighted code. For example, if you wanted to use the solarized-dark style, you could set highlight_style = "solarized-dark" in config.toml.

If the highlight_style option is unset, the default is to use the file /css/highlight.min.css, either the one provided by the Academic theme, or else the one in your local static directory. The /css/highlight.min.css file provided by Academic is equivalent to the github style from highlight.js.

If the highlight_style option is set, then /css/highlight.min.css is ignored, and the corresponding css file will be served from the cdnjs server. To see a list of available styles, visit the cdnjs page and search for links with the word “styles”.

See the highlight.js demo page for examples of available styles.

Not all styles listed on the highlight.js demo page are available from the cdnjs server. If you want to use a style that is not served by cdnjs, just leave highlight_style unset, and place the corresponding css file in /static/css/highlight.min.css.

If you don’t want to change the default style that ships with Academic but you do want the style file served from the cdnjs server, set highlight_style = "github" in config.toml.

The highlight_style option is only recognized when set in config.toml. Setting highlight_style in your page’s preamble has no effect.

Twitter tweet

To include a single tweet, pass the tweet’s ID from the tweet’s URL as parameter to the shortcode:

{{< tweet 666616452582129664 >}}

Youtube

{{< youtube w7Ft2ymGmfc >}}

Vimeo

{{< vimeo 146022717 >}}

GitHub gist

{{< gist USERNAME GIST-ID  >}}

Speaker Deck

{{< speakerdeck 4e8126e72d853c0060001f97 >}}

$\rm \LaTeX$ math

$$\left [ – \frac{\hbar^2}{2 m} \frac{\partial^2}{\partial x^2} + V \right ] \Psi = i \hbar \frac{\partial}{\partial t} \Psi$$

$$\left [ – \frac{\hbar^2}{2 m} \frac{\partial^2}{\partial x^2} + V \right ] \Psi = i \hbar \frac{\partial}{\partial t} \Psi$$

Alternatively, inline math can be written by wrapping the formula with only a single $:

This is inline: $\mathbf{y} = \mathbf{X}\boldsymbol\beta + \boldsymbol\varepsilon$

This is inline: $\mathbf{y} = \mathbf{X}\boldsymbol\beta + \boldsymbol\varepsilon$

Note that Markdown special characters need to be escaped with a backslash so they are treated as math rather than Markdown. For example, * and _ become \* and \_ respectively.

Multiline equations

The standard LaTeX line break consisting of 2 backslashes needs to be replaced with 6 backslashes:

$$f(k;p\_0^\*) = \begin{cases} p\_0^\* & \text{if }k=1, \\\\\\
1-p\_0^\* & \text {if }k=0.\end{cases}$$

$$f(k;p_0^*) = \begin{cases} p_0^* & \text{if }k=1, \\
1-p_0^* & \text {if }k=0.\end{cases}$$

Publication abstracts

As Hugo and Academic attempt to parse TOML, Markdown, and LaTeX content in the abstract, the following guidelines should be followed just for the publication abstract and abstract_short fields:

escape each LaTeX backslash (\) with an extra backslash, yielding \\
escape each LaTeX underscore (_) with two backslashes, yielding \\_

Hence, abstract = "${O(d_{\max})}$" becomes abstract = "${O(d\\_{\\max})}$".

Table

Code:

| Command           | Description                    |
| ------------------| ------------------------------ |
| `hugo`            | Build your website.            |
| `hugo serve -w`   | View your website.             |

Result:

Command	Description
`hugo`	Build your website.
`hugo serve -w`	View your website.

Alerts

Alerts are a useful feature that add side content such as tips, notes, or warnings to your articles. They are especially handy when writing educational tutorial-style articles. Use the corresponding shortcodes to enable alerts inside your content:

{{% alert note %}}
Here's a tip or note...
{{% /alert %}}

This will display the following note block:

Here’s a tip or note…

{{% alert warning %}}
Here's some important information...
{{% /alert %}}

This will display the following warning block:

Here’s some important information…

A table of contents may be particularly useful for long posts or tutorial/documentation type content. Use the {{% toc %}} shortcode anywhere you wish within your Markdown content to automatically generate a table of contents.

Footnote example. ^{^}

Frequently Asked Questions (FAQ)

Sun, 10 Apr 2016 00:00:00 +1000

Common questions and answers will be listed here.

I cloned/downloaded Academic but Hugo produces errors when using it with my existing Hugo site

Academic is a website framework rather than just a theme. Therefore, you must follow the full installation guide found on the Demo/Documentation website or in the Github Readme. If you still have problems, first try running Hugo on the Academic Example Site found in the themes/academic/exampleSite folder and then compare the configuration parameters in the Example Site’s config.toml and content files with the files in your existing site.

Hosting your site with Netlify or Cloudflare and experience strange behavior such as filters not working?

Disable post-processing steps such as minification in your Netlify/Cloudflare admin panel.

Publications and other content are not sorted by newest first

Hugo/TOML require that the value for the date field should be in TOML format, as per frontmatter of the content/publication/ files in the example site. If you want to use a partial date, such as year, you should still complete a full date to make a valid TOML date format.

Issue parsing LaTeX in publication abstract

Let’s consider the following LaTeX which fails to parse correctly:

abstract = "${O(d_{\max})}$"

This is a side effect of Academic and Hugo attempting to parse TOML, Markdown and LaTeX content in the abstract. The solution is to:

escape each LaTeX backslash (\) with an extra backslash, yielding \\
escape each LaTeX underscore (_) with two backslashes, yielding \\_.

Hence, editing the above example, we get:

abstract = "${O(d\\_{\\max})}$"

Cannot achieve line break in multiline equation (LaTeX/Mathjax)

\\ usually achieves a line break in a multiline LaTeX/Mathjax equation, but due to Hugo’s Markdown parser it doesn’t.

Solution: use 6 backslashes for a line break, for example:

$$\begin{eqnarray} 
y &=& 1+1   \\\\\\
&=& 2
\end{eqnarray}$$

Bayesian nonparametric multilevel clustering with group-level contexts

Tue, 01 Jul 2014 00:00:00 +0000

Risk stratification using data from electronic medical records better predicts suicide risks than clinician assessments

Tue, 01 Jul 2014 00:00:00 +0000

Migrate from Jekyll to Hugo

Mon, 10 Mar 2014 00:00:00 +1100

Here are a few tips for migrating an existing website from Jekyll to Hugo. These tips can be applied in conjunction with following Hugo Academic’s getting started guide.

Move static content to `static`

Jekyll has a rule that any directory not starting with _ will be copied as-is to the _site output. Hugo keeps all static content under static. You should therefore move it all there. With Jekyll, something that looked like

▾ <root>/
    ▾ images/
        logo.png

should become

▾ <root>/
    ▾ static/
        ▾ images/
            logo.png

Additionally, you’ll want any files that should reside at the root (such as CNAME) to be moved to static.

Fix content

Depending on the amount of customization that was done for each post in Jekyll, this step will require more or less effort. There are no hard and fast rules here except that hugo server --watch and the Hugo Academic example site are your friends. Test your changes and fix errors as needed.

Publish

The default is for Jekyll to publish the website to a _site directory, whereas Hugo publishes to a public directory.

A practical example

Alexandre Normand migrated his website from Jekyll to Hugo in less than a day. You can see all his changes by looking at this GitHub diff. However, bear in mind that this example is not specific to the Academic theme nor does it use the latest version of Hugo.

TOBY: Early intervention in autism through technology

Mon, 01 Jul 2013 00:00:00 +0000

Svetha Venkatesh on Svetha Venkatesh

Example Talk

Adaptive Experimental Design using Bayesian Optimisation

Early Intervention for Autism

Health Analytics

Large Scale Surveillance

Social Media Analysis

Getting started with the Academic framework for Hugo

Table of Contents

Installation

Getting Started

Core parameters

Introduce yourself

Customize the homepage

Add your content

Remove unused widgets and pages

Themes

Customization & updating

Advanced customization

Navigation menu

Website icon

Analytics

Third party and local scripts (JS)

Language and translation

Permalinks

Advanced style customization (CSS)

Updating

Feedback & Contributing

License

Customizing the homepage with widgets

Add a widget to the homepage

Using the custom widget

Remove a widget from the homepage

Ordering widgets

Managing content

Table of Contents

Create a publication

Create a blog post

Create a project

Create a talk

Create a widget page

Create other pages (e.g. CV)

Manage archive pages

Removing content

View your updated site

Deploy your site

Writing content with Markdown, LaTeX, and Shortcodes

Table of Contents

Sub-headings

Emphasis

Ordered lists

Unordered lists

Images

Links

Emojis

Blockquote

Footnotes

Code highlighting

Highlighting options

Option highlight

Option highlight_languages

Option highlight_style

Twitter tweet

Youtube

Vimeo

GitHub gist

Speaker Deck

$\rm \LaTeX$ math

Multiline equations

Publication abstracts

Table

Alerts

Table of Contents

Frequently Asked Questions (FAQ)

Bayesian nonparametric multilevel clustering with group-level contexts

Risk stratification using data from electronic medical records better predicts suicide risks than clinician assessments

Migrate from Jekyll to Hugo

Move static content to static

Fix content

Publish

Option `highlight`

Option `highlight_languages`

Option `highlight_style`

Move static content to `static`