MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'clustering'. Sat, 03 Sep 2011 02:36:23 +0100 http://www.medworm.com/index.php?rid=4841734&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2Fwp-content%2Fuploads%2F2011%2F05%2Fnev2lkit.mov An example of a spike sorting task using ‘nev2lkit enhanced‘ tool. Nev2lkit acts as a preprocessor for the extracellularly recorded data, extracting neural waveforms (i.e. spikes) from the continuous time series. Nev2lkit enhanced features user-customized optimization of the time-window used during the spike extraction procedure. Consequently, Nev2lkit employs Principal Component Analysis (PCA) in the spike [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4841734 Thu, 19 May 2011 17:19:40 +0100 4841734 http://www.medworm.com/index.php?rid=4525080&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2011%2Fnass-an-empirical-approach-to-spike-sorting-with-overlap-resolution-based-on-a-hybrid-noise-assisted-methodology%2F Background noise and spike overlap pose problems in contemporary spike-sorting strategies. In this paper, both issues are addressed by a hybrid scheme that combines the robust representation of spike waveforms to facilitate the reliable identification of contributing neurons with efficient data learning to enable the precise decomposition of coactivations. A recently introduced manifold learning technique, [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4525080 Sat, 26 Feb 2011 07:39:05 +0100 4525080 http://www.medworm.com/index.php?rid=4304983&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2011%2Fan-expectation-maximization-tutorial-in-neural-signal-processing%2F In this tutorial by Dr. Liam Paninski, the Expectation-Maximization (EM) algorithm is discussed and illustrated in a variety of neural examples. Key topics addressed: Example: Mixture models and spike sorting The method of bound optimization via auxiliary functions provides a useful alternative optimization technique The EM algorithm for maximizing the likelihood given hidden data may be derived [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4304983 Mon, 03 Jan 2011 11:18:06 +0100 4304983 http://www.medworm.com/index.php?rid=4294824&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2010%2Ftutorial-on-geometrical-data-analysis-algorithms-for-vectorial-pattern-analysis%2F By Dr. Nikolaos A. Laskaris The term ‘‘pattern’’, currently, encompasses the notion of a variety of data-forms the machines have to tackle with. Despite the fact that in early days it was used mostly for pictorial information, i.e. 2D-signals, now the same term stands almost for any output from a data-source. For instance, any digital-signal can be [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4294824 Tue, 28 Dec 2010 12:10:14 +0100 4294824 http://www.medworm.com/index.php?rid=3212505&cid=t_103127_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F27%2Fclustering-geo-samples-by-title-briefly-revisited%2F So, we had a brief discussion regarding my previous post and clearly the statement: The longest key for which values exist classifies your titles does not hold true for all cases. Not that I ever said that it did! I remind you that this blog is a place for the half-formed ideas that spill out of my head, not an instruction manual. Let’s look, for example, at GSE19318. This GEO series comprises 2 platforms: one for dog (10 samples) and one for humans (1 sample), with these sample titles: ['Dog-tumor-81705', 'Dog-tumor-78709', 'Dog-tumor-88012', 'Dog-tumor-8888302', 'Dog-tumor-209439', 'Dog-tumor-212227', 'Dog-tumor-48', 'Dog-tumor-125', 'Dog-tumor-394', 'Dog-tumor-896', 'Human-tumor'] Run that through the Ruby code in my last post and we get: {"Dog-tumor-48"=>["... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3212505 Wed, 27 Jan 2010 01:29:56 +0100 3212505 http://www.medworm.com/index.php?rid=3201861&cid=t_103127_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F24%2Fthinking-algorithmically-clustering-geo-samples-by-title%2F Today’s challenge. Take a look at this array, which contains the “title” field for the 6 samples from GSE1323, a series in the GEO microarray database: ['SW-480-1','SW-480-2','SW-480-3','SW-620-1','SW-620-2','SW-620-3'] Humans are very good at classification. Almost instantly, you’ll see that there are 2 classes, “SW-480″ and “SW-620″, each with 3 samples. How can we write a program to do the same job? I’m sure that for those with formal training in computer science and algorithms, this is pretty trivial. The rest of us have to figure it out from first principles. Here’s what I did, in words: # Imagine that you have 2 titles: "abc1" and "abc2" # Take the first character - call it the key, call the remaining... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3201861 Sun, 24 Jan 2010 05:03:00 +0100 3201861 http://www.medworm.com/index.php?rid=4219983&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2009%2Fsigtool-a-matlab-based-environment-for-sharing-laboratory-developed-software-to-analyze-biological-signals%2F Developed to run within MATLAB, sigTOOL provides a programming and analysis environment for processing neuroscience data. A graphical-user interface to this environment provides the end-user with a self-contained application for waveform and spike-train analysis. User-written extensions to this application can be added to the interface on-the-fly without the need to modify any of the existing [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4219983 Sat, 16 May 2009 21:38:25 +0100 4219983 http://www.medworm.com/index.php?rid=4220068&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2008%2Fperformance-evaluation-of-pca-based-spike-sorting-algorithms%2F Adamos DA, Kosmidis EK and Theophilidis G Deciphering the electrical activity of individual neurons from multi-unit noisy recordings is critical for understanding complex neural systems. A widely used spike sorting algorithm is being evaluated for single-electrode nerve trunk recordings. The algorithm is based on principal component analysis (PCA) for spike feature extraction. In the neuroscience [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4220068 Tue, 09 Sep 2008 07:14:06 +0100 4220068 http://www.medworm.com/index.php?rid=4220078&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2008%2Ffind-toolbox-finding-information-in-neural-data%2F A Matlab-based, open-source analysis toolbox for multiple-neuron recordings and network simulations. Currently the FIND-Toolbox accommodates import of multiple proprietary data formats, based on the Neuroshare Project . Physiological data from different acquisition systems and Network simulations Environments can now be compared using identical analysis methods. This allows verifying of both results across experiments and laboratories [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4220078 Thu, 21 Aug 2008 07:17:44 +0100 4220078 http://www.medworm.com/index.php?rid=1147435&cid=t_103127_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fopen-source-tournament-rdkit-enters.html Egon is right! It is great that more and more open source tools are entering the drug design arena. On the other hand, we really need some benchmarking and feature comparisons for allowing to learn which tools should be used for which tasks.Noel dashed off an email to Greg Landrum, the main developer (who it turns out is also the developer of YAeHMOP (Yet Another extended Huckel Molecular Orbital Package) ), and he asked him what the story was. Two days ago, he returned from holidays and pointed Noel to the correct website and the documentation, and Noel couldn't believe what he was seeing...Some features that are cool:(1) Molecules based on the Boost Graph Library(2) All the Python stuff works for me on Windows!(3) 2D depiction!!!(4) 2D depiction that mimics 3D conformations!!!(5) 2D --> ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147435 Fri, 14 Sep 2007 18:40:00 +0100 1147435 http://www.medworm.com/index.php?rid=479203&cid=t_103127_87_f&fid=34866&url=http%3A%2F%2Fwww.thecardioblog.com%2F2007%2F02%2F23%2Fgrape-news-for-your-heart%2F Filed under: Diet, Prevention, NutritionA few days ago I mentioned how it is apparently just as healthy for your heart to drink white wine as it is red. But, what I probably should have stated at the time is that drinking grape juice (especially the not-as-easy-to-drink concentrate) is a non-alcoholic beverage that can also improve your circulation and reduce bad (LDL) cholesterol -- minus the fun of getting drunk and peeing in public. The flavonols found in red wine are found in equal abundance in Concord and other purple grape juice; which, let's face it, makes sense considering they are both made from grapes. And, just like wine, grape juice can help your heart in three ways: By reducing the oxidation of bad (LDL) cholesterol, improving elasticity of the arteries, and reducing platelet ... The Cardio Blog blogs http://www.medworm.com/rss/comments.php?id=479203 Fri, 23 Feb 2007 05:00:00 +0100 479203 http://www.medworm.com/index.php?rid=4220284&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2006%2Fautomatic-spike-detection-and-sorting-using-wavelets-and-super-paramagnetic-clustering%2F Wave_clus is a fast and unsupervised algorithm for spike detection and sorting. Although it gives a first unsupervised solution, this can be further modified according to the experimenter’s preference (semi-automatic sorting). By Rodrigo Quian Quiroga, Reader in Bioengineering, Dept. Engineering. University of Leicester, UK. The method combines the wavelet transform,which localizes distinctive spike features, with [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4220284 Wed, 02 Aug 2006 20:42:29 +0100 4220284 http://www.medworm.com/index.php?rid=4220295&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2006%2Fexpectation-maximization-theory%2F An article on Expectation Maximization Theory, taken from the book “Biometric Authentication: A Machine Learning Approach”. The article/book-chapter addresses a data-clustering algorithm, called the expectation-maximization (EM) algorithm, when complete or partial information of observed data is made available. The book is written by M.W. Mak, S.Y. Kung, S.H. Lin. and the sample chapter is provided [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4220295 Fri, 10 Mar 2006 13:15:02 +0100 4220295 http://www.medworm.com/index.php?rid=4220296&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2006%2Fa-cluster-analysis-tutorial%2F The term cluster analysis (first used by Tryon, 1939) encompasses a number of different algorithms and methods for grouping objects of similar kind into respective categories. A general question facing researchers in many areas of inquiry is how to organize observed data into meaningful structures, that is, to develop taxonomies. In other words cluster analysis [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4220296 Wed, 08 Mar 2006 18:52:10 +0100 4220296 http://www.medworm.com/index.php?rid=4220327&cid=t_103127_122_f&fid=35070&url=http%3A%2F%2Fneurobot.bio.auth.gr%2F2005%2Fhow-many-clusters-which-clustering-method%2F Answers Via Model-Based Cluster Analysis. C. Fraley and A. E. Raftery Technical Report No. 329 Department of Statistics University of Washington Box 354322 Seattle, WA 98195-4322 USA We consider the problem of determining the structure of clustered data, without prior knowledge of the number of clusters or any other [...] (Source: Neurobot) Neurobot blogs http://www.medworm.com/rss/comments.php?id=4220327 Tue, 01 Feb 2005 09:19:59 +0100 4220327