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Journal Articles
- 2024
[j63]Frank Emmert-Streib
, Shailesh Tripathi, Amer Farea, Olli Yli-Harja:
Advanced Scientometric Analysis of Scientific Machine Learning and PINNs: Topic Modeling and Trend Analysis. IEEE Access 12: 153253-153272 (2024)- 2020
- [j62]Frank Emmert-Streib, Olli Yli-Harja, Matthias Dehmer:
Artificial Intelligence: A Clarification of Misconceptions, Myths and Desired Status. Frontiers Artif. Intell. 3: 524339 (2020) - [j61]Frank Emmert-Streib, Olli Yli-Harja, Matthias Dehmer:
Explainable artificial intelligence and machine learning: A reality rooted perspective. WIREs Data Mining Knowl. Discov. 10(6) (2020) - 2019
- [j60]Aliyu Musa, Matthias Dehmer, Olli Yli-Harja, Frank Emmert-Streib:
Exploiting Genomic Relations in Big Data Repositories by Graph-Based Search Methods. Mach. Learn. Knowl. Extr. 1(1): 205-210 (2019) - 2018
- [j59]Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina V. Glazko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib:
A review of connectivity map and computational approaches in pharmacogenomics. Briefings Bioinform. 19(3): 506-523 (2018) - [j58]Frank Emmert-Streib, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer:
Understanding the World Economy in Terms of Networks: A Survey of Data-Based Network Science Approaches on Economic Networks. Frontiers Appl. Math. Stat. 4: 37 (2018) - [j57]Frank Emmert-Streib, Olli P. Yli-Harja, Matthias Dehmer:
Data Analytics Applications for Streaming Data From Social Media: What to Predict? Frontiers Big Data 1: 2 (2018) - 2017
- [j56]Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina V. Glazko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib:
A review of connectivity map and computational approaches in pharmacogenomics. Briefings Bioinform. 18(5): 903 (2017) - [j55]Shailesh Tripathi, Jason Lloyd-Price, Andre S. Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib:
sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. BMC Bioinform. 18(1): 325 (2017) - 2016
- [j54]Olga Anufrieva, Adrien Sala, Olli Yli-Harja, Meenakshisundaram Kandhavelu:
Real-time observation of bacterial gene expression noise. Nano Commun. Networks 8: 68-75 (2016) - 2013
- [j53]Teppo Annila, Eero Lihavainen, Ines J. Marques, Darren R. Williams, Olli Yli-Harja, Andre S. Ribeiro:
ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis. BMC Bioinform. 14(S-10): S5 (2013) - [j52]Muhammad Farhan, Pekka Ruusuvuori, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Olli Yli-Harja:
Multi-scale Gaussian representation and outline-learning based cell image segmentation. BMC Bioinform. 14(S-10): S6 (2013) - [j51]Sharif Chowdhury, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro:
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE). BMC Bioinform. 14(S-10): S8 (2013) - [j50]Antti Ylipää, Olli Yli-Harja, Wei Zhang, Matti Nykter:
Characterization of aberrant pathways across human cancers. BMC Syst. Biol. 7(S-1): S1 (2013) - [j49]Antti Häkkinen, Huy Tran, Olli Yli-Harja, Brian P. Ingalls, Andre S. Ribeiro:
Effects of multimerization on the temporal variability of protein complex abundance. BMC Syst. Biol. 7(S-1): S3 (2013) - [j48]Muhammad Farhan, Olli Yli-Harja, Antti Niemistö:
A novel method for splitting clumps of convex objects incorporating image intensity and using rectangular window-based concavity point-pair search. Pattern Recognit. 46(3): 741-751 (2013) - 2012
- [j47]Meenakshisundaram Kandhavelu, Eero Lihavainen, Anantha Barathi Muthukrishnan, Olli Yli-Harja, Andre Sanches Ribeiro:
Effects of Mg2+ on in vivo transcriptional dynamics of the lar promoter. Biosyst. 107(3): 129-134 (2012) - 2011
- [j46]Jarno Mäkelä, Heikki Huttunen, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro:
Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli. Bioinform. 27(19): 2714-2720 (2011) - [j45]Andre S. Ribeiro, Jason Lloyd-Price, Sharif Chowdhury, Olli Yli-Harja:
Diversity of temporal correlations between genes in models of noisy and noiseless gene networks. Biosyst. 104(2-3): 136-144 (2011) - [j44]Jarno Mäkelä, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro:
Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC Bioinform. 12: 121 (2011) - [j43]Kirsti Laurila, Bodil Oster, Claus L. Andersen, Philippe Lamy, Torben F. Ørntoft, Olli Yli-Harja, Carsten Wiuf:
A Beta-Mixture Model for Dimensionality Reduction, Sample Classification and Analysis. BMC Bioinform. 12: 215 (2011) - [j42]Meenakshisundaram Kandhavelu, Henrik Mannerström, Abhishekh Gupta, Antti Häkkinen, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro:
In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. BMC Syst. Biol. 5: 149 (2011) - [j41]Henrik Mannerström, Olli Yli-Harja, Andre S. Ribeiro:
Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation. EURASIP J. Bioinform. Syst. Biol. 2011 (2011) - [j40]Tuomo Mäki-Marttunen, Jugoslava Acimovic, Matti Nykter, Juha Kesseli, Keijo Ruohonen, Olli Yli-Harja, Marja-Leena Linne:
Information Diversity in Structure and Dynamics of Simulated Neuronal Networks. Frontiers Comput. Neurosci. 5: 26 (2011) - [j39]Antti Häkkinen, Fred G. Biddle, Olli-Pekka Smolander, Olli Yli-Harja, Andre S. Ribeiro:
Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene. Trans. Comp. Sys. Biology 13: 1-12 (2011) - 2010
- [j38]Pekka Ruusuvuori, Tarmo Äijö, Sharif Chowdhury, Cecilia Garmendia-Torres, Jyrki Selinummi, Mirko Birbaumer, Aimée M. Dudley, Lucas Pelkmans, Olli Yli-Harja:
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC Bioinform. 11: 248 (2010) - [j37]Sharif Chowdhury, Jason Lloyd-Price, Olli-Pekka Smolander, Wayne C. V. Baici, Timothy R. Hughes, Olli Yli-Harja, Gordon Chua, Andre S. Ribeiro:
Information propagation within the Genetic Network of Saccharomyces cerevisiae. BMC Syst. Biol. 4: 143 (2010) - [j36]Andre S. Ribeiro, Antti Häkkinen, Shannon Healy, Olli Yli-Harja:
Dynamical effects of transcriptional pause-prone sites. Comput. Biol. Chem. 34(3): 143-148 (2010) - [j35]Xiaofeng Dai, Olli Yli-Harja, Harri Lähdesmäki:
Novel Data Fusion Method and Exploration of Multiple Information Sources for Transcription Factor Target Gene Prediction. EURASIP J. Adv. Signal Process. 2010 (2010) - [j34]Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro:
Effects of Transcriptional Pausing on Gene Expression Dynamics. PLoS Comput. Biol. 6(3) (2010) - 2009
- [j33]Xiaofeng Dai, Olli Yli-Harja, Andre S. Ribeiro:
Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources. Bioinform. 25(18): 2362-2368 (2009) - [j32]Xiaofeng Dai, Timo Erkkilä, Olli Yli-Harja, Harri Lähdesmäki:
A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data. BMC Bioinform. 10 (2009) - [j31]Andre S. Ribeiro, Olli-Pekka Smolander, Tiina Rajala, Antti Häkkinen, Olli Yli-Harja:
Delayed Stochastic Model of Transcription at the Single Nucleotide Level. J. Comput. Biol. 16(4): 539-553 (2009) - 2008
- [j30]Antti Lehmussola, Pekka Ruusuvuori, Jyrki Selinummi, Tiina Rajala, Olli Yli-Harja:
Synthetic Images of High-Throughput Microscopy for Validation of Image Analysis Methods. Proc. IEEE 96(8): 1348-1360 (2008) - [j29]Antti Saarinen, Marja-Leena Linne, Olli Yli-Harja:
Stochastic Differential Equation Model for Cerebellar Granule Cell Excitability. PLoS Comput. Biol. 4(2) (2008) - [j28]Alireza Akhbardeh, Nikhil, Perttu E. Koskinen, Olli Yli-Harja:
Towards the experimental evaluation of novel supervised fuzzy adaptive resonance theory for pattern classification. Pattern Recognit. Lett. 29(8): 1082-1093 (2008) - 2007
- [j27]Miika Ahdesmäki, Harri Lähdesmäki, Andrew Gracey, Ilya Shmulevich, Olli Yli-Harja:
Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinform. 8 (2007) - [j26]Tommi Aho, Olli-Pekka Smolander, Jari Niemi, Olli Yli-Harja:
RMBNToolbox: random models for biochemical networks. BMC Syst. Biol. 1: 22 (2007) - [j25]Antti Niemistö, Matti Nykter, Tommi Aho, Henna Jalovaara, Kalle Marjanen, Miika Ahdesmäki, Pekka Ruusuvuori, Mikko Tiainen, Marja-Leena Linne, Olli Yli-Harja:
Computational Methods for Estimation of Cell Cycle Phase Distributions of Yeast Cells. EURASIP J. Bioinform. Syst. Biol. 2007 (2007) - [j24]Antti Lehmussola, Pekka Ruusuvuori, Jyrki Selinummi, Heikki Huttunen, Olli Yli-Harja:
Computational Framework for Simulating Fluorescence Microscope Images With Cell Populations. IEEE Trans. Medical Imaging 26(7): 1010-1016 (2007) - 2006
- [j23]Antti Lehmussola, Pekka Ruusuvuori, Olli Yli-Harja:
Evaluating the performance of microarray segmentation algorithms. Bioinform. 22(23): 2910-2917 (2006) - [j22]Matti Nykter, Tommi Aho, Miika Ahdesmäki, Pekka Ruusuvuori, Antti Lehmussola, Olli Yli-Harja:
Simulation of microarray data with realistic characteristics. BMC Bioinform. 7: 349 (2006) - [j21]Antti Saarinen, Marja-Leena Linne, Olli Yli-Harja:
Modeling single neuron behavior using stochastic differential equations. Neurocomputing 69(10-12): 1091-1096 (2006) - [j20]Antti Pettinen, Olli Yli-Harja, Marja-Leena Linne:
Comparison of automated parameter estimation methods for neuronal signaling networks. Neurocomputing 69(10-12): 1371-1374 (2006) - [j19]Harri Lähdesmäki, Sampsa Hautaniemi, Ilya Shmulevich, Olli Yli-Harja:
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Process. 86(4): 814-834 (2006) - 2005
- [j18]Antti Pettinen, Tommi Aho, Olli-Pekka Smolander, Tiina Manninen, Antti Saarinen, Kaisa-Leena Taattola, Olli Yli-Harja, Marja-Leena Linne:
Simulation tools for biochemical networks: evaluation of performance and usability. Bioinform. 21(3): 357-363 (2005) - [j17]Harri Lähdesmäki, Ilya Shmulevich, Valerie Dunmire, Olli Yli-Harja, Wei Zhang:
In silico microdissection of microarray data from heterogeneous cell populations. BMC Bioinform. 6: 54 (2005) - [j16]Miika Ahdesmäki, Harri Lähdesmäki, Ronald K. Pearson, Heikki Huttunen, Olli Yli-Harja:
Robust detection of periodic time series measured from biological systems. BMC Bioinform. 6: 117 (2005) - [j15]Antti Niemistö, Valerie Dunmire, Olli Yli-Harja, Wei Zhang, Ilya Shmulevich:
Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans. Medical Imaging 24(4): 549-553 (2005) - 2004
- [j14]Antti Niemistö, Ilya Shmulevich, Vladimir Vasilyevich Lukin, Alexander N. Dolia, Olli Yli-Harja:
Correction of Misclassifications Using a Proximity-Based Estimation Method. EURASIP J. Adv. Signal Process. 2004(8): 1142-1155 (2004) - [j13]Sampsa Hautaniemi, Markus Ringnér, Päivikki Kauraniemi, Reija Autio, Henrik Edgren, Olli Yli-Harja, Jaakko Astola, Anne Kallioniemi, Olli-Pekka Kallioniemi:
A strategy for identifying putative causes of gene expression variation in human cancers. J. Frankl. Inst. 341(1-2): 77-88 (2004) - 2003
- [j12]Reija Autio, Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi:
CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinform. 19(13): 1714-1715 (2003) - [j11]Sampsa Hautaniemi, Henrik Edgren, Petri Vesanen, Maija Wolf, Anna-Kaarina Järvinen, Olli Yli-Harja, Jaakko Astola, Olli-P. Kallioniemi, Outi Monni:
A novel strategy for microarray quality control using Bayesian networks. Bioinform. 19(16): 2031-2038 (2003) - [j10]Sampsa Hautaniemi, Olli Yli-Harja, Jaakko Astola, Päivikki Kauraniemi, Anne Kallioniemi, Maija Wolf, Jimmy Ruiz, Spyro Mousses, Olli-P. Kallioniemi:
Analysis and Visualization of Gene Expression Microarray Data in Human Cancer Using Self-Organizing Maps. Mach. Learn. 52(1-2): 45-66 (2003) - [j9]Harri Lähdesmäki, Ilya Shmulevich, Olli Yli-Harja:
On Learning Gene Regulatory Networks Under the Boolean Network Model. Mach. Learn. 52(1-2): 147-167 (2003) - [j8]Harri Lähdesmäki, Heikki Huttunen, Tommi Aho, Marja-Leena Linne, Jari Niemi, Juha Kesseli, Ronald K. Pearson, Olli Yli-Harja:
Estimation and inversion of the effects of cell population asynchrony in gene expression time-series. Signal Process. 83(4): 835-858 (2003) - 2002
- [j7]Ilya Shmulevich, Olli Yli-Harja, Jaakko Astola, Aleksey D. Korshunov:
On the robustness of the class of stack filters. IEEE Trans. Signal Process. 50(7): 1640-1649 (2002) - 2001
- [j6]Ilya Shmulevich, Olli Yli-Harja, Edward J. Coyle, Dirk-Jan Povel, Kjell Lemström:
Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key Finding. Comput. Humanit. 35(1): 23-35 (2001) - [j5]Pertti Koivisto, Olli Yli-Harja, Antti Niemistö, Ilya Shmulevich:
Breakdown probabilities of recursive stack filters. Signal Process. 81(1): 227-231 (2001) - [j4]Olli Yli-Harja, Pertti Koivisto, J. Andrew Bangham, Gavin C. Cawley, Richard W. Harvey, Ilya Shmulevich:
Simplified implementation of the recursive median sieve. Signal Process. 81(7): 1565-1570 (2001) - 1999
- [j3]Ilya Shmulevich, Olli Yli-Harja, Karen O. Egiazarian, Jaakko Astola:
Output distributions of recursive stack filters. IEEE Signal Process. Lett. 6(7): 175-178 (1999) - 1994
- [j2]Olli Yli-Harja:
Formula for the joint distribution of stack filters. IEEE Signal Process. Lett. 1(9): 129-130 (1994) - 1991
- [j1]Olli Yli-Harja, Jaakko Astola, Yrjö Neuvo:
Analysis of the properties of median and weighted median filters using threshold logic and stack filter representation. IEEE Trans. Signal Process. 39(2): 395-410 (1991)
Conference and Workshop Papers
- 2016
- [c24]Olli Yli-Harja, Frank Emmert-Streib, Jari Yli-Hietanen:
Mathematical Modeling in Systems Biology. WIVACE 2016: 161-166 - 2015
- [c23]Septimia Sârbu, Ilya Shmulevich, Olli Yli-Harja, Matti Nykter, Juha Kesseli:
Mapping dynamical states to structural classes for Boolean networks using a classification algorithm. EUSIPCO 2015: 160-164 - 2013
- [c22]Muhammad Farhan, Pekka Ruusuvuori, Mario Emmenlauer, Pauli Rämö, Olli Yli-Harja, Christoph Dehio:
Graph cut and image intensity-based splitting improves nuclei segmentation in high-content screening. Image Processing: Algorithms and Systems 2013: 86550F - [c21]Muhammad Farhan, Antti Larjo, Olli Yli-Harja, Tommi Aho:
Modeling bioprocess scale-up utilizing regularized linear and logistic regression. MLSP 2013: 1-6 - 2012
- [c20]Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja, Andre S. Ribeiro:
Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks. CMSB 2012: 307-321 - 2010
- [c19]Hannu Oinonen, Heikki Forsvik, Pekka Ruusuvuori, Olli Yli-Harja, Ville Voipio, Heikki Huttunen:
Identity verification based on vessel matching from fundus images. ICIP 2010: 4089-4092 - 2008
- [c18]Xiaofeng Dai, Harri Lähdesmäki, Olli Yli-Harja:
sBGMM: A Stratified Beta-Gaussian Mixture Model for Clustering Genes with Multiple Data Sources. BIOTECHNO 2008: 94-99 - [c17]Pekka Ruusuvuori, Antti Lehmussola, Jyrki Selinummi, Tiina Rajala, Heikki Huttunen, Olli Yli-Harja:
Benchmark set of synthetic images for validating cell image analysis algorithms. EUSIPCO 2008: 1-5 - [c16]Pekka Ruusuvuori, Jenni Seppälä, Timo Erkkilä, Antti Lehmussola, Jaakko A. Puhakka, Olli Yli-Harja:
Efficient automated method for image-based classification of microbial cells. ICPR 2008: 1-4 - 2006
- [c15]Antti Niemistö, Jyrki Selinummi, Ramsey Saleem, Ilya Shmulevich, John D. Aitchison, Olli Yli-Harja:
Extraction of the Number of Peroxisomes in Yeast Cells by Automated Image Analysis. EMBC 2006: 2353-2356 - [c14]Jyrki Selinummi, Pekka Ruusuvuori, Antti Lehmussola, Heikki Huttunen, Olli Yli-Harja, Riitta Miettinen:
Three-Dimensional Digital Image Analysis of Immunostained Neurons in Thick Tissue Sections. EMBC 2006: 4783-4786 - [c13]Pekka Ruusuvuori, Antti Lehmussola, Olli Yli-Harja:
Learning-based method for spot addressing in microarray images. Image Processing: Algorithms and Systems 2006: 416-425 - 2005
- [c12]Antti Lehmussola, Pekka Ruusuvuori, Olli Yli-Harja:
Exploring subjective image quality through isopreference curves. ICIP (1) 2005: 413-416 - 2003
- [c11]Heikki Huttunen, Pertti T. Koivisto, Antti Niemistö, Olli Yli-Harja:
Statistical characterization of detail preservation. Image Processing: Algorithms and Systems 2003: 66-77 - [c10]Jari Niemi, Kalle Marjanen, Heimo Ihalainen, Olli Yli-Harja:
Estimation of the distribution type and parameters based on multimodal histograms. Image Processing: Algorithms and Systems 2003: 135-146 - [c9]Antti Niemistö, Tommi Aho, Henna Thesleff, Mikko Tiainen, Kalle Marjanen, Marja-Leena Linne, Olli Yli-Harja:
Estimation of population effects in synchronized budding yeast experiments. Image Processing: Algorithms and Systems 2003: 448-459 - [c8]John A. Berger, Sampsa Hautaniemi, Henrik Edgren, Outi Monni, Sanjit K. Mitra, Olli Yli-Harja, Jaakko Astola:
Identifying underlying factors in breast cancer using independent component analysis. NNSP 2003: 81-90 - [c7]Ronald K. Pearson, Harri Lähdesmäki, Heikki Huttunen, Olli Yli-Harja:
Detecting Periodicity in Nonideal Datasets. SDM 2003: 274-278 - 2002
- [c6]Petri Vesanen, Mikko Tiainen, Olli Yli-Harja:
Calibration-free methods in segmentation of cDNA microarray images. Image Processing: Algorithms and Systems 2002: 291-302 - [c5]Kalle Marjanen, Heimo Ihalainen, Heikki Huttunen, Olli Yli-Harja:
Local entropy estimation in particle velocity images using histogram deconvolution. Image Processing: Algorithms and Systems 2002: 429-439 - 2000
- [c4]Antti Niemistö, Olli Yli-Harja, Antti Valmari, Pertti Koivisto, Ilya Shmulevich:
Reduction factors in finite automata with application to nonlinear filters. EUSIPCO 2000: 1-4 - 1999
- [c3]Olli P. Yli-Harja, J. Andrew Bangham, Richard W. Harvey:
State reduction of recursive median filters. Electronic Imaging: Nonlinear Image Processing 1999 - [c2]Olli Yli-Harja, Ilya Shmulevich, Kjell Lemström:
Graph-based smoothing of class data with applications in musical key finding. NSIP 1999: 311-315 - [c1]Olli Yli-Harja, J. Andrew Bangham, Richard W. Harvey, Richard V. Aldridge:
Correlation properties of cascaded recursive median filters. NSIP 1999: 491-495
Informal and Other Publications
- 2022
- [i3]Syeda Sakira Hassan, Rahul Mangayil, Tommi Aho, Olli Yli-Harja, Matti Karp:
Identification of feasible pathway information for c-di-GMP binding proteins in cellulose production. CoRR abs/2204.12526 (2022) - 2020
- [i2]Frank Emmert-Streib, Olli Yli-Harja, Matthias Dehmer:
Explainable Artificial Intelligence and Machine Learning: A reality rooted perspective. CoRR abs/2001.09464 (2020) - [i1]Frank Emmert-Streib, Olli Yli-Harja, Matthias Dehmer:
A clarification of misconceptions, myths and desired status of artificial intelligence. CoRR abs/2008.05607 (2020)
Coauthor Index
Andre S. Ribeiro
aka: Andre Sanches Ribeiro
aka: Andre Sanches Ribeiro
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