Machine Learning
Papers:
(Available as .pdf
unless otherwise specified) -
Ensemble
machine methods for DNA binding (with Y. Fan, and C. DeLisi), Machine
Learning and Applications 7,
M. Wani, et al., eds. IEEE,
Regulatory analysis for exploring human disease progression (with D. Holloway and C. DeLisi), Biology Direct 3:24,
2008. Algorithm available here.
Building
transcription factor classifiers and discovering relevant biological features, (with D. Holloway
and C. DeLisi), BiologyDirect 3:22, 30 May
2008. Algorithm available
here.
SVMMotif: A machine
learning motif algorithm (with Y. Fan, D.Holloway
and C. DeLisi), International Conference on Machine Learning and
Applications 6, 573-580, IEEE, Washington, 2007. Algorithm
available here.
Learning methods for DNA binding in computational biology (with D. Holloway, et al.) International Joint Conference
on Neural Networks, 20, IEEE, Los
Alamitos 1605, 2007.
Machine learning for regulatory analysis and
transcription factor target prediction in yeast
(with D. Holloway and C. DeLisi), Systems and Synthetic Biology 1 (2006),
25-46.
Approximating
functions in reproducing kernel Hilbert spaces via statistical learning theory
(with L. Raphael), in Splines and Wavelets,
G. Chen and M.J. Lai, eds,
(2006) 270-286
Machine learning methods for transcription data integration
(with D. Holloway and C.DeLisi),IBM
Journal of Research and Development 50(2006), 631-644 (Abstract only -
Journal link is here)
Information-based nonlinear approximation: An average case setting (with L. Plaskota), J. Complexity 21 (2005),211-228.
Extending
Girosi's approximation estimates for functions in Sobolev spaces via statistical learning theory (with L. Raphael and D. Williams), J. Analysis and Applications
3 No. 2 (2005), 67-90.
Statistical
likelihood representations of prior knowledge in machine learning (with L, Plaskota and A. Przybyszewski), Artificial Intelligence and Applications,
M.H. Hamza, Ed.,
Integrating genomic data to predict transcription factor binding
(with D. Holloway and C. DeLisi), Genome
Informatics 16 (2005), 83-94.
Machine
learning and statistical MAP methods (with L. Plaskota and A. Przybyszewski),
Intelligent Information Processing, Springer,
On some integrated
approaches to inference (with L. Plaskota),
technical report, (2005).
Complexity of predictive neural networks (with L. Plaskota) Proceedings of International Conference on
Complexity, Y.
Bar-Yam, Ed.,
Complexity of neural network approximation with limited
information: a worst-case approach
(with L. Plaskota), J. Complexity 17
(2001), 345-365.
Complexity of regularization RBF networks (with L. Plaskota), in Proceedings of International Joint
Congress on Neural Networks,INNS,
Review
of Complexity and Information, (by J.F. Traub and A.G. Werschulz), Bull.
Amer. Math Soc. 37 (2000), 199-204.
Information complexity of neural networks (with L. Plaskota), Neural Networks 13 (2000),365-376.
Neural networks, radial basis functions,
and complexity (with L. Plaskota),
Proceedings of Bialowieza Conference on Statistical
Physics, 1997, 122-145.
Journal of Machine Learning Research
Cambridge (UK) Machine Learning
Group
Princeton
Machine Learning Group
CMU Machine Learning Department
Resources:
General Machine Learning (ML):
I. Elementary Resources (definitions, tutorials,
basics):
ML:
http://en.wikipedia.org/wiki/Machine_learning
http://old-site.clsp.jhu.edu/workshops/ws09/documents/machine-learning-overview.pdf
http://mlthirst.wordpress.com/2013/01/08/machine-learning-guidance-for-beginners/
http://machinelearningmastery.com/self-study-guide-to-machine-learning/
http://www.werc.tu-darmstadt.de/fileadmin/user_upload/GROUP_WERC/LKE/tutorials/ML-tutorial-1-2.pdf
http://homes.cs.washington.edu/~pedrod/papers/cacm12.pdf
SVM:
http://en.wikipedia.org/wiki/Support_vector_machine
SVM
Lecture Notes – MA 770 (Kon)
II. Mid-level
Resources:
ML:
http://alex.smola.org/teaching/cmu2013-10-701x/
http://dimacs.rutgers.edu/Workshops/MachineLearning/slides/schapire.pdf
http://www.cs.uvm.edu/~icdm/algorithms/10Algorithms-08.pdf
Stanford course:
https://www.coursera.org/course/ml
http://see.stanford.edu/see/lecturelist.aspx?coll=348ca38a-3a6d-4052-937d-cb017338d7b1
SVM:
http://videolectures.net/epsrcws08_campbell_isvm/
http://www.cs.columbia.edu/~kathy/cs4701/documents/jason_svm_tutorial.pdf
http://pyml.sourceforge.net/doc/howto.pdf
Random Forests (RF):
RF
Lecture Notes – MA 770 (Kon)
k-nearest neighbors (kNN):
III.
Advanced Resources
ML:
http://alex.smola.org/teaching/cmu2013-10-701x/
http://ai.stanford.edu/~nilsson/MLBOOK.pdf
http://www-stat.stanford.edu/~tibs/ElemStatLearn/
SVM:
http://www.support-vector-machines.org
http://webee.technion.ac.il/people/rmeir/SVMReview.pdf
http://www.support-vector.net/LeuvenKerMet-2.pdf
http://www.mit.edu/~9.520/spring11/slides/class06-svm.pdf
http://www.stanford.edu/class/cs229/notes/cs229-notes3.pdf
RF:
http://stat-www.berkeley.edu/users/breiman/RandomForests/cc_home.htm#workings