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Clustering by Passing Messages Between Data Points
A method called “affinity propagation,” which takes as input measures of similarity between pairs of data points, which found clusters with much lower error than other methods, and it did so in less than one-hundredth the amount of time.
Factor graphs and the sum-product algorithm
A generic message-passing algorithm, the sum-product algorithm, that operates in a factor graph, that computes-either exactly or approximately-various marginal functions derived from the global function.
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
- B. Alipanahi, Andrew Delong, M. Weirauch, B. Frey
- Biology, MedicineNature Biotechnology
- 1 August 2015
This work shows that sequence specificities can be ascertained from experimental data with 'deep learning' techniques, which offer a scalable, flexible and unified computational approach for pattern discovery.
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
It is estimated that transcripts from ∼95% of multiexon genes undergoAlternative splicing and that there are ∼100,000 intermediate- to high-abundance alternative splicing events in major human tissues.
A compendium of RNA-binding motifs for decoding gene regulation
A systematic analysis of the RNA motifs recognized by RNA-binding proteins, encompassing 205 distinct genes from 24 diverse eukaryotes, provides an unprecedented overview of RNA- binding proteins and their targets, and constitute an invaluable resource for determining post-transcriptional regulatory mechanisms in eukARYotes.
The human splicing code reveals new insights into the genetic determinants of disease
A computational model is developed that scores how strongly genetic variants affect RNA splicing, a critical step in gene expression whose disruption contributes to many diseases, including cancers and neurological disorders, and provides insights into the role of aberrant splicing in disease.
Widespread intron retention in mammals functionally tunes transcriptomes.
- Ulrich Braunschweig, N. Barbosa-Morais, +6 authors B. Blencowe
- Biology, MedicineGenome research
- 1 November 2014
It is shown that intron retention acts widely to reduce the levels of transcripts that are less or not required for the physiology of the cell or tissue type in which they are detected, and this "transcriptome tuning" function of IR acts through both nonsense-mediated mRNA decay and nuclear sequestration and turnover of IR transcripts.
The "wake-sleep" algorithm for unsupervised neural networks.
An unsupervised learning algorithm for a multilayer network of stochastic neurons is described. Bottom-up "recognition" connections convert the input into representations in successive hidden layers,…
The Evolutionary Landscape of Alternative Splicing in Vertebrate Species
The findings suggest that the evolution of alternative splicing has for the most part been very rapid and thatAlternative splicing patterns of most organs more strongly reflect the identity of the species rather than the organ type, with the highest complexity in primates.
Graphical Models for Machine Learning and Digital Communication
- B. Frey
- Computer Science
- 26 June 1998
Probabilistic inference in graphical models pattern classification unsupervised learning data compression channel coding future research directions and how this affects research directions is investigated.