Collaborating Authors

Understanding Objective Functions in Neural Networks


The main inspiration for this blog post is based on the work I did on Bayesian Neural Networks with my friend Brian Trippe at the Computational and Biological Learning Lab in Cambridge University. I highly recommend anyone to read Brian's thesis on variational inference in neural networks. Disclaimer: At the Computational and Biological Learning Lab Bayesian machine learning techniques are unapologetically taught as the way forward. As such, be aware of potential bias in this blog post. For example in image classification, x represents an image and y the corresponding image label.

Unsupervised Learning in Genome Informatics Machine Learning

With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this book chapter, we review the state-of-the-art unsupervised learning algorithms for genome informatics from DNA to MicroRNA. DNA (DeoxyriboNucleic Acid) is the basic component of genomes. A significant fraction of DNA regions (transcription factor binding sites) are bound by proteins (transcription factors) to regulate gene expression at different development stages in different tissues. To fully understand genetics, it is necessary of us to apply unsupervised learning algorithms to learn and infer those DNA regions. Here we review several unsupervised learning methods for deciphering the genome-wide patterns of those DNA regions. MicroRNA (miRNA), a class of small endogenous non-coding RNA (RiboNucleic acid) species, regulate gene expression post-transcriptionally by forming imperfect base-pair with the target sites primarily at the 3$'$ untranslated regions of the messenger RNAs. Since the 1993 discovery of the first miRNA \emph{let-7} in worms, a vast amount of studies have been dedicated to functionally characterizing the functional impacts of miRNA in a network context to understand complex diseases such as cancer. Here we review several representative unsupervised learning frameworks on inferring miRNA regulatory network by exploiting the static sequence-based information pertinent to the prior knowledge of miRNA targeting and the dynamic information of miRNA activities implicated by the recently available large data compendia, which interrogate genome-wide expression profiles of miRNAs and/or mRNAs across various cell conditions.

Decision analysis: a Bayesian approach


See also:Influence diagrams for Bayesian decision analysis, European Journal of Operational Research, Volume 40, Issue 3, 15 June 1989, Pages 363–376Bayesian Decision Analysis: Principles and Practice, Cambridge University Press, 2010. Chapman and Hall

A Revolution: Belief Propagation in Graphs with Cycles

Neural Information Processing Systems

Department of Physics, Cavendish Laboratory Cambridge University Abstract Until recently, artificial intelligence researchers have frowned upon the application of probability propagation in Bayesian belief networks thathave cycles. The probability propagation algorithm is only exact in networks that are cycle-free. Examples of real-world channels include twisted-pair telephone wires, shielded cable-TV wire, fiberoptic cable, deep-space radio, terrestrial radio, and indoor radio. Engineers attempt to correct the errors introduced by the noise in these channels through the use of channel coding which adds protection to the information source, so that some channel errors can be corrected. A popular model of a physical channel is shown in Figure 1.