This tiling happens to be a solution that ensures that graph nodes are regularly spaced 1-, 2-, or 3- unit lengths apart.

If we re-orient all of the tiles in the same direction, the nodes then become two unit lengths apart — and the graph becomes homomorphic with a hexagonal tiling.

I’ll let you know if I find an application to the 1-, 2-, 3- hop pattern.

Egon’s suggestion in the comments works best. Loading the JARs distributed for a project almost always requires far less work. If you’re like me and haven’t used Java in a while, it should be noted that the Java SE6 compiler and runtime both allow you to specify wildcards when referring to directories containing JARs. For Java SE6 and up, something like the below commands would work.

javac -classpath .:jar/*:dist/jar/* MGNQSAR.java
java  -classpath .:jar/*:dist/jar/* MGNQSAR

The directory “dist/jar” contains CDK JARs, while the directory “jar” contains dependencies. Embarrassingly enough, I didn’t notice this directory hiding in plain sight, meaning that I didn’t have to go out and find the same log4j package distributed directly from Apache.

Oh well! Live and learn

Original Post

So today, I had to get some QSAR descriptors calculated from The Chemistry Development Kit (CDK) (Java) as a means to benchmark Chris’ MGN custom neural network architecture. While trying to compile CDK into my very simple main, I encountered a number of problems with LoggingToolFactory. Below is a simplified main that illustrates the problem…

import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.qsar.*;
import org.openscience.cdk.io.MDLV2000Reader;
import java.io.FileReader;
import java.io.FileNotFoundException;

public class MGNQSAR {

    public static void main(String[] args) {

        String path = "Molecules/Kidney/Mouse/1,3-Butadiene.sdf";

        FileReader fr = null;

        try {
            fr = new FileReader(path);
        } catch (FileNotFoundException fnfe) {
            System.err.println("FATAL: Couldn't find file ...");
            System.err.println(path);
            return;
        }

        MDLV2000Reader m2r = new MDLV2000Reader(fr); //Null pointer exception here.
        Molecule mol = null;

        try {
            mol = m2r.read(new Molecule());
        } catch (CDKException cdke) {
            System.err.println("FATAL: CDK became enraged ...");
            System.err.println(cdke.toString());
            return;
        }
        return;
    }
}

Logging is generally a good idea. In fact, it’s such a good idea — you should probably deploy some logging in every piece of medium- to large- scale software that you produce. The problem I encountered today was the absence of documentation of how to compile and run a main that calls code from CDK that calls LoggingToolFactory.createLoggingTool(.).

Here’s some context. All of the classes that I’ve encountered in CDK call this method statically to create a class-wide logger. This method provides the caller with a logging tool object that does some recording of debug information, or jots down a few notes about the path of execution in CDK, or saves some other informative alert for the end user. The logging tool is offered up to any class that implements the interface ILoggingTool (CDK allows you to implement your own). By default CDK offers two such tools — one that wraps Apache log4j (org.openscience.cdk.tools.LoggingTool), and stdout as a fallback (when log4j isn’t available) wrapped within (org.openscience.cdk.tools.SystemOutLoggingToolTest).

By design, the factory createLoggingTool(.) attempts to provide the user with an already instantiated copy of a logging tool — it’s the factory design pattern we all know. The problem is as follows. CDK has to be able to try and instantiate the wrapper for log4j first before trying to instantiate the stdout fallback. The notion of trying to instantiate is not something that one often does in Java. To perform this task, one has to use reflection — in this case, it looks like CDK’s LoggingToolFactory uses a few methods found in (java.lang.reflect.InvocationTargetException) and (java.lang.reflect.Method).

So how does reflection cause woe?

Well, when I compile my main, Javac visits the classes I’ve imported and the classes that they’ve imported (etc.) and compiles the Java sources into class bytecode files. That is, Javac does this for everything that’s been declared for import at compile time. That means that everything that requires reflection isn’t compiled since that code is only analyzed at runtime. Next, Java runs main and executes some code called by CDK — that code tries to createLoggingTool(.) but fails gracefully since Javac never compiled the corresponding classes (neither the log4j wrapper nor the stdout fallback wrapper). All is well until the uninstantiated logging tool is called to actually log anything — resulting in a null pointer exception.

It took me a while to track the problem down, but the solution is simple.

Manually compile (Javac) SystemOutLoggingTool — or better yet, get Apache log4j, then also manually compile LoggingTool.

The corresponding compile and run commands would look like this …

	javac MGNQSAR.java
	javac -classpath .:log4j-1.2.17.jar org/openscience/cdk/tools/LoggingTool.java
	javac org/openscience/cdk/tools/SystemOutLoggingTool.java
	java  -classpath .:log4j-1.2.17.jar MGNQSAR

Where I’ve symbolically linked CDK’s org directory as a subdirectory of my working directory; and I’ve also symbolically linked (Apache log4j)’s jar file as an entry in this working directory too.

I hope this helps you too!

>>> Download: A Network Security Spotlight on SSL/TLS and HTTPS (pdf) <<<

Figure $_: A Schematic of the SSL/TLS Handshaking Procedure.

This document is licensed under Creative Commons Attribution 3.0 Unported. The enclosed figures are further released into the public domain.

I think we’ll have an excellent turn out — Richard and I did advertise as much as humanly possible after all

This method should work with phpBB3 version 3.0.x.

This method results in a mandatory field to be completed by the registrant during registration time. You can assign it any question you like where the answer is a string of text that you decide. I’ve given a really simple question in this example. Use a more difficult question that a bot would have trouble with but that your typical registrants can answer.

We do this with a custom profile field in the registration screen as in the below screen capture.

The above is a screen capture of an example mandatory question (choose a more secure question).

There are two steps to setting this up.

First, set up a custom question that must be answered — you can find such a setting in the administrative control panel (ACP) as in the following screen capture.

Add a mandatory question in user and groups → custom profile fields → create new field.
Here, I’ve named mine guelph_question.

After you click Create new field, you will be presented with a screen where you can create the question of your choosing — be sure to make the field mandatory by using the radio button labelled Required field listed under Visibility options.

Second, add the following code indicated below in includes/ucp/ucp_register.php – Notice that I’ve placed my custom code after existing code to check for a valid password and e-mail. This is commented under validate custom profile fields ( — just checked — starts at line 247 in the 3.0.9 source code). Replace the simple question and answer I’ve placed there with your own question and answer. Notice that you also have full control over the error message that the registrant sees if they answer the question incorrectly.

// validate custom profile fields
$cp->submit_cp_field('register', $user->get_iso_lang_id(), $cp_data, $error);

if (!sizeof($error))
{
	if ($data['new_password'] != $data['password_confirm'])
	{
		$error[] = $user->lang['NEW_PASSWORD_ERROR'];
	}

	if ($data['email'] != $data['email_confirm'])
	{
		$error[] = $user->lang['NEW_EMAIL_ERROR'];
	}
}

// Anti-spam code below ...
if (!sizeof($error)) {
	if (!isset($_POST['pf_guelph_question']) ||
	$_POST['pf_guelph_question'] != 'Gryphon') {
		$error[] = 'Incorrect answer to Guelph question.';
	}
}
// ... EOAnti-spam code

And you’re done.

I hope this works for you! Enjoy

The code and course project paper are originally dated April 20th, 2011.

>>> Download: FCMProjectPaper.pdf | FCMProject.tgz <<<

( Requires pypng – Python PNG encoder/decoder )

Here are the examples included in the above archive. I like pictures.

Sunny in 8-bit greyscale, 3-bit greyscale, 2-bit greyscale.

Auryo in 8-bit greyscale, 3-bit greyscale, 2-bit greyscale.

Enjoy

The full name of the conference is Fourth International Barcode of Life Conference.

>>> Download: ( pdf: EddieMaBOL2011Adelaide.pdf | zip: EddieMaBOL2011Adelaide.pdf.zip ) <<<

Slides 6, 16, 24 from my presentation — The need for automation; Compositional bias and human edits [null hypothesis]; Where are human edits occurring [in Lepidoptera]?

This has been a very enjoyable conference

We needed to (1) remove page numbers, but (2) continue to include page headers that have the paper title and author names.

To do this, I mashed together the horrible block of markup below

% declarations for front matter

%%%%% hack -- remove page numbers
\pagestyle{empty}
\usepackage{fancyhdr}
\lhead{}
\chead{\emph{\footnotesize
Primary Author and Secondary Author / Procedia Computer Science 00 (2011)
}}
\cfoot{}
\renewcommand{\headrulewidth}{0pt}
\pagestyle{fancy}
%%%%%

\begin{document}

The above example requires the fancy header package (\usepackage{fancyhdr}), we get an italicized, small text header (\emph{\footnotesize{…}}) with arbitrary text. Since I don’t explicitly define page numbers, they won’t appear. We also don’t need footers (\cfoot{}).

Note that you can create your own arbitrary headers with this package, or — if you’re in a rush like I was — just use the above as is, and replace the arbitrary text

Hope this helps!

My slides introduce Tiny Encryption Algorithm (TEA) pretty well, along with Genetic Algorithm (GA) and Harmony Search (HS). The slides detailing the results aren’t quite as self-explanatory, but are bearable since the theme is fairly easy to establish: simpler keys are easier to break than more complicated ones.

>>> Download: CAS2011Chicago.pdf – my presentation from Chicago. <<<

I might look at cryptanalysis again in future — but I’ll certainly use Evolutionary Computation (EC) again. It’s just too readily available in my toolkit, and is far too easy to deploy. One of the major lessons of this project that became very clear through during discussion with the audience is that the operators that are part of an EC algorithm should reflect the kind of problem we’re trying to solve. This might seem obvious at first, but I think it’s more subtle than that. For this project, HS enabled the EC to probe a keyspace with many repetitions — something that GA operators alone didn’t provide us.

In general however, the solution space is lumpy enough that using ECs against stronger encryption schemes is just not viable — unless the EC had some magic to overcome the linearly inseparable lumps. I haven’t yet met such an operator and am not convinced one way or another about its existence. I’ll certainly introduce you if I ever do bump into it

The Gaussian Function is given by …

$$ f(x) = ae^{-\frac{(x-b)^2}{2c^2}} $$

• a, b, c are the curve parameters with respect to which we differentiate the residual function
• e is Euler’s number

Given a set of coordinates I’d like to fit (x_i, y_i), i ∈ [1, m], the residuals are given by …

$$ r_i = y_i – ae^{-\frac{(x_i-b)^2}{2c^2}} $$

We want to get …

$$ \frac{\partial{r}}{\partial{a}}, \frac{\partial{r}}{\partial{b}}, \frac{\partial{r}}{\partial{c}} $$

In each of these partials, we can omit the first term y_i because it drops to zero immediately when held constant.

Let’s start with r’(a) … (b, c, x, y ∈ k)

\begin{align}
r &= -ae^{-\frac{(x-b)^2}{2c^2}} \\
r &= -ae^{u}, (u \in k) \\
r’ &= -e^{u}u’ \\
\therefore \frac{\partial{r}}{\partial{a}} &= -e^{-\frac{(x-b)^2}{2c^2}}
\end{align}

Now let’s get r’(b) … (a, c, x, y ∈ k)

\begin{align}
r &= -ae^{-\frac{(x-b)^2}{2c^2}} \\
r &= -ae^{u} \\
u &= -\frac{(x-b)^2}{2c^2} \\
u &= -\frac{x^2-2bx+b^2}{2c^2} \\
u &= -\frac{x^2}{2c^2}-\frac{2bx+b^2}{2c^2}, (-\frac{x^2}{2c^2} \in k) \\
u’ &= -\frac{-2x + 2b}{2c^2} \\
u’ &= -\frac{b – x}{c^2} \\
r’ &= -ae^{u}(u’) \\
r’ &= -ae^{-\frac{(x-b)^2}{2c^2}}(-\frac{b – x}{c^2}) \\
\therefore \frac{\partial{r}}{\partial{b}} &= \frac{a(b – x)e^{-\frac{(x-b)^2}{2c^2}}}{c^2}
\end{align}

Finally, let’s get r’(c) … (a, b, x, y ∈ k)

\begin{align}
r &= -ae^{-\frac{(x-b)^2}{2c^2}} \\
r &= -ae^{u} \\
u &= -\frac{(x-b)^2}{2c^2} \\
u &= -{(x-b)^2}\frac{1}{2c^2}, (-{(x-b)^2} \in k) \\
(\frac{1}{v})’ &= \frac{-v’}{v^2} \\
(\frac{1}{2c^2})’ &= \frac{-(2c^2)’}{(2c^2)^2} \\
&= \frac{-4c}{4c^4} \\
&= \frac{-1}{c^3}, (c \neq 0) \\
u’ &= -(x-b)^2\frac{-1}{c^3} \\
u’ &= \frac{(x-b)^2}{c^3} \\
r’ &= -ae^{u}(u’) \\
r’ &= -ae^{-\frac{(x-b)^2}{2c^2}}(\frac{(x-b)^2}{c^3}) \\
\therefore \frac{\partial{r}}{\partial{c}} &= \frac{-a(x-b)^2e^{-\frac{(x-b)^2}{2c^2}}}{c^3}
\end{align}

That’s all three partials!

Here are Maxima’s answers for r’(b) and r’(c) …

dr/db = -a*(x-b)*%e^-((x-b)^2/(2*c^2))/c^2
dr/dc = -a*(x-b)^2*%e^-((x-b)^2/(2*c^2))/c^3