Pekka Marttinen

122 papers A* 9A 6Journal 92Unranked 15

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	CBR-to-SQL: Rethinking Retrieval-based Text-to-SQL using Case-based Reasoning in the Healthcare Domain. CoRR Hung Nguyen, Hans Moen, Pekka Marttinen
2026	J	`jnl`	Edit Knowledge, Not Just Facts via Multi-Step Reasoning over Background Stories. CoRR Ya Gao, Kalle Kujanpää, Pekka Marttinen, Harri Valpola, Alexander Ilin
2025	J	`jnl`	Adaptive Residual-Update Steering for Low-Overhead Hallucination Mitigation in Large Vision Language Models. CoRR Zhengtao Zou, Ya Gao, Jiarui Guan, Bin Li, Pekka Marttinen
2025	J	`jnl`	Beyond the LUMIR challenge: The pathway to foundational registration models. CoRR Junyu Chen, Shuwen Wei, Joel Honkamaa, Pekka Marttinen, Hang Zhang, Min Liu, Yichao Zhou, Zuopeng Tan, Zhuoyuan Wang, Yi Wang, Hongchao Zhou, Shunbo Hu, Yi Zhang, Qian Tao, Lukas Förner, Thomas Wendler, Bailiang Jian, Benedikt Wiestler, Tim Hable, Jin Kim, Dan Ruan, Frederic Madesta, Thilo Sentker, Wiebke Heyer, Lianrui Zuo, Yuwei Dai, Jing Wu, Jerry L. Prince, Harrison X. Bai, Yong Du, Yihao Liu, Alessa Hering, Reuben Dorent, Lasse Hansen, Mattias P. Heinrich, Aaron Carass
2025	J	`jnl`	Efficient Knowledge Injection in LLMs via Self-Distillation. Trans. Mach. Learn. Res. Kalle Kujanpää, Pekka Marttinen, Harri Valpola, Alexander Ilin
2025	A*	`conf`	Identifying latent state transitions in non-linear dynamical systems. ICLR Çaglar Hizli, Çagatay Yildiz, Matthias Bethge, S. T. John, Pekka Marttinen
2025	J	`jnl`	Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges. CoRR Lasse Hansen, Wiebke Heyer, Christoph Großbröhmer, Frederic Madesta, Thilo Sentker, Jiazheng Wang, Yuxi Zhang, Hang Zhang, Min Liu, Junyi Wang, Xi Zhu, Yuhua Li, Liwen Wang, Daniil Morozov, Nazim Haouchine, Joel Honkamaa, Pekka Marttinen, Yichao Zhou, Zuopeng Tan, Zhuoyuan Wang, Yi Wang, Hongchao Zhou, Shunbo Hu, Yi Zhang, Qian Tao, Lukas Förner, Thomas Wendler, Bailiang Jian, Christian Wachinger, Jin Kim, Dan Ruan, Marek Wodzinski, Henning Müller, Tony C. W. Mok, Xi Jia, Jinming Duan, Mikael Brudfors, Seyed-Ahmad Ahmadi, Yunzheng Zhu, William Hsu, Tina Kapur, William M. Wells, Alexandra J. Golby, Aaron Carass, Harrison X. Bai, Yihao Liu, Perrine Paul-Gilloteaux, Joakim Lindblad, Natasa Sladoje, Andreas Walter, Junyu Chen, Reuben Dorent, Alessa Hering, Mattias P. Heinrich
2025	J	`jnl`	Memento No More: Coaching AI Agents to Master Multiple Tasks via Hints Internalization. CoRR Minttu Alakuijala, Ya Gao, Georgy Ananov, Samuel Kaski, Pekka Marttinen, Alexander Ilin, Harri Valpola
2025	J	`jnl`	MiniLingua: A Small Open-Source LLM for European Languages. CoRR Anna Aksenova, Boris Zverkov, Nicola Dainese, Alexander Nikitin, Pekka Marttinen
2025	—	`conf`	New Multimodal Similarity Measure for Image Registration via Modeling Local Functional Dependence with Linear Combination of Learned Basis Functions. MICCAI (2) Joel Honkamaa, Pekka Marttinen
2025	J	`jnl`	New multimodal similarity measure for image registration via modeling local functional dependence with linear combination of learned basis functions. CoRR Joel Honkamaa, Pekka Marttinen
2025	J	`jnl`	Object-level Self-Distillation for Vision Pretraining. CoRR Çaglar Hizli, Çagatay Yildiz, Pekka Marttinen
2025	J	`jnl`	POEMS: Product of Experts for Interpretable Multi-omic Integration using Sparse Decoding. CoRR Mihriban Kocak Balik, Pekka Marttinen, Negar Safinianaini
2025	J	`jnl`	Recursive Decomposition with Dependencies for Generic Divide-and-Conquer Reasoning. CoRR Sergio Hernández-Gutiérrez, Minttu Alakuijala, Alexander V. Nikitin, Pekka Marttinen
2025	J	`jnl`	Strategies for Robust Deep Learning Based Deformable Registration. CoRR Joel Honkamaa, Pekka Marttinen
2025	J	`jnl`	ViPlan: A Benchmark for Visual Planning with Symbolic Predicates and Vision-Language Models. CoRR Matteo Merler, Nicola Dainese, Minttu Alakuijala, Giovanni Bonetta, Pietro Ferrazzi, Yu Tian, Bernardo Magnini, Pekka Marttinen
2025	J	`jnl`	Video-Language Critic: Transferable Reward Functions for Language-Conditioned Robotics. Trans. Mach. Learn. Res. Minttu Alakuijala, Reginald McLean, Isaac Woungang, Nariman Farsad, Samuel Kaski, Pekka Marttinen, Kai Yuan
2024	J	`jnl`	A Unified Review of Deep Learning for Automated Medical Coding. ACM Comput. Surv. Shaoxiong Ji, Xiaobo Li, Wei Sun, Hang Dong, Ara Taalas, Yijia Zhang, Honghan Wu, Esa Pitkänen, Pekka Marttinen
2024	—	`conf`	Can docstring reformulation with an LLM improve code generation? EACL (Student Research Workshop) Nicola Dainese, Alexander Ilin, Pekka Marttinen
2024	—	`conf`	Diffusion Models as Probabilistic Neural Operators for Recovering Unobserved States of Dynamical Systems. MLSP Katsiaryna Haitsiukevich, Onur Poyraz, Pekka Marttinen, Alexander Ilin
2024	J	`jnl`	Diffusion models as probabilistic neural operators for recovering unobserved states of dynamical systems. CoRR Katsiaryna Haitsiukevich, Onur Poyraz, Pekka Marttinen, Alexander Ilin
2024	A*	`conf`	Generating Code World Models with Large Language Models Guided by Monte Carlo Tree Search. NeurIPS Nicola Dainese, Matteo Merler, Minttu Alakuijala, Pekka Marttinen
2024	J	`jnl`	Generating Code World Models with Large Language Models Guided by Monte Carlo Tree Search. CoRR Nicola Dainese, Matteo Merler, Minttu Alakuijala, Pekka Marttinen
2024	A*	`conf`	Generating Demonstrations for In-Context Compositional Generalization in Grounded Language Learning. EMNLP Sam Spilsbury, Pekka Marttinen, Alexander Ilin
2024	J	`jnl`	Identifiable Causal Inference with Noisy Treatment and No Side Information. Trans. Mach. Learn. Res. Antti Pöllänen, Pekka Marttinen
2024	J	`jnl`	Identifying latent state transition in non-linear dynamical systems. CoRR Çaglar Hizli, Çagatay Yildiz, Matthias Bethge, St John, Pekka Marttinen
2024	—	`conf`	Improving Medical Multi-modal Contrastive Learning with Expert Annotations. ECCV (20) Yogesh Kumar, Pekka Marttinen
2024	J	`jnl`	Improving Medical Multi-modal Contrastive Learning with Expert Annotations. CoRR Yogesh Kumar, Pekka Marttinen
2024	—	`conf`	In-Context Symbolic Regression: Leveraging Large Language Models for Function Discovery. ACL (Student Research Workshop) Matteo Merler, Katsiaryna Haitsiukevich, Nicola Dainese, Pekka Marttinen
2024	A*	`conf`	Kernel Language Entropy: Fine-grained Uncertainty Quantification for LLMs from Semantic Similarities. NeurIPS Alexander Nikitin, Jannik Kossen, Yarin Gal, Pekka Marttinen
2024	J	`jnl`	Kernel Language Entropy: Fine-grained Uncertainty Quantification for LLMs from Semantic Similarities. CoRR Alexander Nikitin, Jannik Kossen, Yarin Gal, Pekka Marttinen
2024	—	`conf`	Knowledge-augmented Graph Neural Networks with Concept-aware Attention for Adverse Drug Event Detection. LREC/COLING Ya Gao, Shaoxiong Ji, Pekka Marttinen
2024	—	`conf`	Query-Guided Self-Supervised Summarization of Nursing Notes. ML4H@NeurIPS Ya Gao, Hans Moen, Saila Koivusalo, Miika Koskinen, Pekka Marttinen
2024	J	`jnl`	Query-Guided Self-Supervised Summarization of Nursing Notes. CoRR Ya Gao, Hans Moen, Saila Koivusalo, Miika Koskinen, Pekka Marttinen
2024	J	`jnl`	Self-Supervised Forecasting in Electronic Health Records With Attention-Free Models. IEEE Trans. Artif. Intell. Yogesh Kumar, Alexander Ilin, Henri Salo, Sangita Kulathinal, Maarit K. Leinonen, Pekka Marttinen
2024	J	`jnl`	Towards modeling evolving longitudinal health trajectories with a transformer-based deep learning model. CoRR Hans Moen, Vishnu Raj, Andrius Vabalas, Markus Perola, Samuel Kaski, Andrea Ganna, Pekka Marttinen
2024	A	`conf`	VMS: Interactive Visualization to Support the Sensemaking and Selection of Predictive Models. IUI Chen He, Vishnu Raj, Hans Moen, Tommi Gröhn, Chen Wang, Laura-Maria Peltonen, Saila Koivusalo, Pekka Marttinen, Giulio Jacucci
2024	J	`jnl`	Video-Language Critic: Transferable Reward Functions for Language-Conditioned Robotics. CoRR Minttu Alakuijala, Reginald McLean, Isaac Woungang, Nariman Farsad, Samuel Kaski, Pekka Marttinen, Kai Yuan
2023	J	`jnl`	A Novel Deep Learning based Model for Erythrocytes Classification and Quantification in Sickle Cell Disease. CoRR Manish Bhatia, Balram Meena, Vipin Kumar Rathi, Prayag Tiwari, Amit Kumar Jaiswal, Shagaf M. Ansari, Ajay Kumar, Pekka Marttinen
2023	J	`jnl`	ASymReg: Robust symmetric image registration using anti-symmetric formulation and deformation inversion layers. CoRR Joel Honkamaa, Pekka Marttinen
2023	J	`jnl`	Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization. PLoS Comput. Biol. Fanni Ojala, Mohamad R. Abdul Sater, Loren G. Miller, James A. McKinnell, Mary K. Hayden, Susan S. Huang, Yonatan H. Grad, Pekka Marttinen
2023	A*	`conf`	Causal Modeling of Policy Interventions From Treatment-Outcome Sequences. ICML Caglar Hizli, S. T. John, Anne Tuulikki Juuti, Tuure Tapani Saarinen, Kirsi Hannele Pietiläinen, Pekka Marttinen
2023	J	`jnl`	Content Reduction, Surprisal and Information Density Estimation for Long Documents. CoRR Shaoxiong Ji, Wei Sun, Pekka Marttinen
2023	J	`jnl`	Deformation equivariant cross-modality image synthesis with paired non-aligned training data. Medical Image Anal. Joel Honkamaa, Umair Khan, Sonja Koivukoski, Mira Valkonen, Leena Latonen, Pekka Ruusuvuori, Pekka Marttinen
2023	J	`jnl`	EEG Based Emotion Recognition: A Tutorial and Review. ACM Comput. Surv. Xiang Li, Yazhou Zhang, Prayag Tiwari, Dawei Song, Bin Hu, Meihong Yang, Zhigang Zhao, Neeraj Kumar, Pekka Marttinen
2023	J	`jnl`	HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes. Bioinform. Sophie Wharrie, Zhiyu Yang, Vishnu Raj, Remo Monti, Rahul Gupta, Ying Wang, Alicia Martin, Luke J. O'Connor, Samuel Kaski, Pekka Marttinen, Pier Francesco Palamara, Christoph Lippert, Andrea Ganna
2023	J	`jnl`	Identifiable causal inference with noisy treatment and no side information. CoRR Antti Pöllänen, Pekka Marttinen
2023	A	`conf`	Incorporating functional summary information in Bayesian neural networks using a Dirichlet process likelihood approach. AISTATS Vishnu Raj, Tianyu Cui, Markus Heinonen, Pekka Marttinen
2023	J	`jnl`	Knowledge-augmented Graph Neural Networks with Concept-aware Attention for Adverse Drug Event Detection. CoRR Shaoxiong Ji, Ya Gao, Pekka Marttinen
2023	—	`conf`	Mixture of Coupled HMMs for Robust Modeling of Multivariate Healthcare Time Series. ML4H@NeurIPS Onur Poyraz, Pekka Marttinen
2023	J	`jnl`	Mixture of Coupled HMMs for Robust Modeling of Multivariate Healthcare Time Series. CoRR Onur Poyraz, Pekka Marttinen
2023	J	`jnl`	Multitask Balanced and Recalibrated Network for Medical Code Prediction. ACM Trans. Intell. Syst. Technol. Wei Sun, Shaoxiong Ji, Erik Cambria, Pekka Marttinen
2023	—	`conf`	Nonparametric modeling of the composite effect of multiple nutrients on blood glucose dynamics. ML4H@NeurIPS Arina Odnoblyudova, Caglar Hizli, St John, Andrea Cognolato, Anne Juuti, Simo Särkkä, Kirsi Pietiläinen, Pekka Marttinen
2023	J	`jnl`	Nonparametric modeling of the composite effect of multiple nutrients on blood glucose dynamics. CoRR Arina Odnoblyudova, Çaglar Hizli, St John, Andrea Cognolato, Anne Juuti, Simo Särkkä, Kirsi Pietiläinen, Pekka Marttinen
2023	A	`conf`	Patient Outcome and Zero-shot Diagnosis Prediction with Hypernetwork-guided Multitask Learning. EACL Shaoxiong Ji, Pekka Marttinen
2023	J	`jnl`	Quantifying Movement Behavior of Chronic Low Back Pain Patients in Virtual Reality. ACM Trans. Comput. Heal. Tommi Gröhn, Sammeli Liikkanen, Teppo Huttunen, Mika Mäkinen, Pasi Liljeberg, Pekka Marttinen
2023	A*	`conf`	Reader: Model-based language-instructed reinforcement learning. EMNLP Nicola Dainese, Pekka Marttinen, Alexander Ilin
2023	J	`jnl`	Supporting Management of Gestational Diabetes with Comprehensive Self-Tracking: Mixed-Method Study of Wearable Sensors. CoRR Mikko Kytö, Saila Koivusalo, Heli Tuomonen, Lisbeth Strömberg, Antti Ruonala, Pekka Marttinen, Seppo Heinonen, Giulio Jacucci
2023	A*	`conf`	Temporal Causal Mediation through a Point Process: Direct and Indirect Effects of Healthcare Interventions. NeurIPS Çaglar Hizli, St John, Anne Juuti, Tuure Saarinen, Kirsi Pietiläinen, Pekka Marttinen
2023	J	`jnl`	Temporal Causal Mediation through a Point Process: Direct and Indirect Effects of Healthcare Interventions. CoRR Çaglar Hizli, S. T. John, Anne Juuti, Tuure Saarinen, Kirsi Pietiläinen, Pekka Marttinen
2023	J	`jnl`	Unsupervised feature selection based on variance-covariance subspace distance. Neural Networks Saeed Karami, Farid Saberi-Movahed, Prayag Tiwari, Pekka Marttinen, Sahar Vahdati
2023	—	`conf`	Weak Supervision and Clustering-Based Sample Selection for Clinical Named Entity Recognition. ECML/PKDD (6) Wei Sun, Shaoxiong Ji, Tuulia Denti, Hans Moen, Oleg Kerro, Antti Rannikko, Pekka Marttinen, Miika Koskinen
2022	J	`jnl`	A Survey on Knowledge Graphs: Representation, Acquisition, and Applications. IEEE Trans. Neural Networks Learn. Syst. Shaoxiong Ji, Shirui Pan, Erik Cambria, Pekka Marttinen, Philip S. Yu
2022	J	`jnl`	A Unified Review of Deep Learning for Automated Medical Coding. CoRR Shaoxiong Ji, Wei Sun, Hang Dong, Honghan Wu, Pekka Marttinen
2022	J	`jnl`	COVIDNet: An Automatic Architecture for COVID-19 Detection With Deep Learning From Chest X-Ray Images. IEEE Internet Things J. Lang He, Prayag Tiwari, Rui Su, Xiuying Shi, Pekka Marttinen, Neeraj Kumar
2022	—	`conf`	Contextualized Graph Embeddings for Adverse Drug Event Detection. ECML/PKDD (2) Ya Gao, Shaoxiong Ji, Tongxuan Zhang, Prayag Tiwari, Pekka Marttinen
2022	A*	`conf`	Deconfounded Representation Similarity for Comparison of Neural Networks. NeurIPS Tianyu Cui, Yogesh Kumar, Pekka Marttinen, Samuel Kaski
2022	J	`jnl`	Deconfounded Representation Similarity for Comparison of Neural Networks. CoRR Tianyu Cui, Yogesh Kumar, Pekka Marttinen, Samuel Kaski
2022	J	`jnl`	Deep learning for depression recognition with audiovisual cues: A review. Inf. Fusion Lang He, Mingyue Niu, Prayag Tiwari, Pekka Marttinen, Rui Su, Jiewei Jiang, Chenguang Guo, Hongyu Wang, Songtao Ding, Zhongmin Wang, Xiaoying Pan, Wei Dang
2022	J	`jnl`	Deformation equivariant cross-modality image synthesis with paired non-aligned training data. CoRR Joel Honkamaa, Umair Khan, Sonja Koivukoski, Leena Latonen, Pekka Ruusuvuori, Pekka Marttinen
2022	J	`jnl`	EEG based Emotion Recognition: A Tutorial and Review. CoRR Xiang Li, Yazhou Zhang, Prayag Tiwari, Dawei Song, Bin Hu, Meihong Yang, Zhigang Zhao, Neeraj Kumar, Pekka Marttinen
2022	J	`jnl`	Joint Non-parametric Point Process model for Treatments and Outcomes: Counterfactual Time-series Prediction Under Policy Interventions. CoRR Çaglar Hizli, S. T. John, Anne Juuti, Tuure Saarinen, Kirsi Pietiläinen, Pekka Marttinen
2022	J	`jnl`	Look beyond labels: Incorporating functional summary information in Bayesian neural networks. CoRR Vishnu Raj, Tianyu Cui, Markus Heinonen, Pekka Marttinen
2021	J	`jnl`	A Critical Look At The Identifiability of Causal Effects with Deep Latent Variable Models. CoRR Severi Rissanen, Pekka Marttinen
2021	A*	`conf`	A Critical Look at the Consistency of Causal Estimation with Deep Latent Variable Models. NeurIPS Severi Rissanen, Pekka Marttinen
2021	J	`jnl`	Deep Learning for Depression Recognition with Audiovisual Cues: A Review. CoRR Lang He, Mingyue Niu, Prayag Tiwari, Pekka Marttinen, Rui Su, Jiewei Jiang, Chenguang Guo, Hongyu Wang, Songtao Ding, Zhongmin Wang, Wei Dang, Xiaoying Pan
2021	J	`jnl`	Does the Magic of BERT Apply to Medical Code Assignment? A Quantitative Study. CoRR Shaoxiong Ji, Matti Hölttä, Pekka Marttinen
2021	J	`jnl`	Does the magic of BERT apply to medical code assignment? A quantitative study. Comput. Biol. Medicine Shaoxiong Ji, Matti Hölttä, Pekka Marttinen
2021	J	`jnl`	Errors-in-Variables Modeling of Personalized Treatment-Response Trajectories. IEEE J. Biomed. Health Informatics Guangyi Zhang, Reza A. Ashrafi, Anne Juuti, Kirsi Pietiläinen, Pekka Marttinen
2021	—	`conf`	Medical Code Assignment with Gated Convolution and Note-Code Interaction. ACL/IJCNLP (Findings) Shaoxiong Ji, Shirui Pan, Pekka Marttinen
2021	J	`jnl`	Medical SANSformers: Training self-supervised transformers without attention for Electronic Medical Records. CoRR Yogesh Kumar, Alexander Ilin, Henri Salo, Sangita Kulathinal, Maarit K. Leinonen, Pekka Marttinen
2021	J	`jnl`	Multi-task Balanced and Recalibrated Network for Medical Code Prediction. CoRR Wei Sun, Shaoxiong Ji, Erik Cambria, Pekka Marttinen
2021	—	`conf`	Multitask Recalibrated Aggregation Network for Medical Code Prediction. ECML/PKDD (4) Wei Sun, Shaoxiong Ji, Erik Cambria, Pekka Marttinen
2021	J	`jnl`	Multitask Recalibrated Aggregation Network for Medical Code Prediction. CoRR Wei Sun, Shaoxiong Ji, Erik Cambria, Pekka Marttinen
2021	J	`jnl`	Patient Outcome and Zero-shot Diagnosis Prediction with Hypernetwork-guided Multitask Learning. CoRR Shaoxiong Ji, Pekka Marttinen
2020	J	`jnl`	A Survey on Knowledge Graphs: Representation, Acquisition and Applications. CoRR Shaoxiong Ji, Shirui Pan, Erik Cambria, Pekka Marttinen, Philip S. Yu
2020	A	`conf`	Batch simulations and uncertainty quantification in Gaussian process surrogate approximate Bayesian computation. UAI Marko Järvenpää, Aki Vehtari, Pekka Marttinen
2020	—	`conf`	Dilated Convolutional Attention Network for Medical Code Assignment from Clinical Text. ClinicalNLP@EMNLP Shaoxiong Ji, Erik Cambria, Pekka Marttinen
2020	J	`jnl`	Dilated Convolutional Attention Network for Medical Code Assignment from Clinical Text. CoRR Shaoxiong Ji, Erik Cambria, Pekka Marttinen
2020	J	`jnl`	Informative Gaussian Scale Mixture Priors for Bayesian Neural Networks. CoRR Tianyu Cui, Aki S. Havulinna, Pekka Marttinen, Samuel Kaski
2020	A	`conf`	Learning Global Pairwise Interactions with Bayesian Neural Networks. ECAI Tianyu Cui, Pekka Marttinen, Samuel Kaski
2020	J	`jnl`	Medical Code Assignment with Gated Convolution and Note-Code Interaction. CoRR Shaoxiong Ji, Shirui Pan, Pekka Marttinen
2019	J	`jnl`	A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation. PLoS Comput. Biol. Marko Järvenpää, Mohamad R. Abdul Sater, Georgia K. Lagoudas, Paul C. Blainey, Loren G. Miller, James A. McKinnell, Susan S. Huang, Yonatan H. Grad, Pekka Marttinen
2019	J	`jnl`	Batch simulations and uncertainty quantification in Gaussian process surrogate-based approximate Bayesian computation. CoRR Marko Järvenpää, Aki Vehtari, Pekka Marttinen
2019	J	`jnl`	Errors-in-variables Modeling of Personalized Treatment-Response Trajectories. CoRR Guangyi Zhang, Reza A. Ashrafi, Anne Juuti, Kirsi Pietiläinen, Pekka Marttinen
2019	J	`jnl`	Modelling G×E with historical weather information improves genomic prediction in new environments. Bioinform. Jussi Gillberg, Pekka Marttinen, Hiroshi Mamitsuka, Samuel Kaski
2019	J	`jnl`	Parallel Gaussian process surrogate method to accelerate likelihood-free inference. CoRR Marko Järvenpää, Michael U. Gutmann, Aki Vehtari, Pekka Marttinen
2019	—	`conf`	Predicting utilization of healthcare services from individual disease trajectories using RNNs with multi-headed attention. ML4H@NeurIPS Yogesh Kumar, Henri Salo, Tuomo Nieminen, Kristian Vepsalainen, Sangita Kulathinal, Pekka Marttinen
2019	J	`jnl`	Recovering Pairwise Interactions Using Neural Networks. CoRR Tianyu Cui, Pekka Marttinen, Samuel Kaski
2018	J	`jnl`	A Bayesian model of acquisition and clearance of bacterial colonization. CoRR Marko Järvenpää, Mohamad R. Abdul Sater, Georgia K. Lagoudas, Paul C. Blainey, Loren G. Miller, James A. McKinnell, Susan S. Huang, Yonatan H. Grad, Pekka Marttinen
2018	J	`jnl`	Bacmeta: simulator for genomic evolution in bacterial metapopulations. Bioinform. Aleksi Sipola, Pekka Marttinen, Jukka Corander
2018	J	`jnl`	ELFI: Engine for Likelihood-Free Inference. J. Mach. Learn. Res. Jarno Lintusaari, Henri Vuollekoski, Antti Kangasrääsiö, Kusti Skytén, Marko Järvenpää, Pekka Marttinen, Michael U. Gutmann, Aki Vehtari, Jukka Corander, Samuel Kaski
2018	J	`jnl`	Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge. Bioinform. Iiris Sundin, Tomi Peltola, Luana Micallef, Homayun Afrabandpey, Marta Soare, Muntasir Mamun Majumder, Pedram Daee, Chen He, Baris Serim, Aki S. Havulinna, Caroline Heckman, Giulio Jacucci, Pekka Marttinen, Samuel Kaski
2017	J	`jnl`	Improving drug sensitivity predictions in precision medicine through active expert knowledge elicitation. CoRR Iiris Sundin, Tomi Peltola, Muntasir Mamun Majumder, Pedram Daee, Marta Soare, Homayun Afrabandpey, Caroline Heckman, Samuel Kaski, Pekka Marttinen
2017	A	`conf`	Interactive Elicitation of Knowledge on Feature Relevance Improves Predictions in Small Data Sets. IUI Luana Micallef, Iiris Sundin, Pekka Marttinen, Muhammad Ammad-ud-din, Tomi Peltola, Marta Soare, Giulio Jacucci, Samuel Kaski
2017	J	`jnl`	Speciation trajectories in recombining bacterial species. PLoS Comput. Biol. Pekka Marttinen, William P. Hanage
2017	J	`jnl`	biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements. Bioinform. Matti Pirinen, Christian Benner, Pekka Marttinen, Marjo-Riitta Järvelin, Manuel A. Rivas, Samuli Ripatti
2016	J	`jnl`	Interactive Elicitation of Knowledge on Feature Relevance Improves Predictions in Small Data Sets. CoRR Luana Micallef, Iiris Sundin, Pekka Marttinen, Muhammad Ammad-ud-din, Tomi Peltola, Marta Soare, Giulio Jacucci, Samuel Kaski
2016	J	`jnl`	Multiple Output Regression with Latent Noise. J. Mach. Learn. Res. Jussi Gillberg, Pekka Marttinen, Matti Pirinen, Antti J. Kangas, Pasi Soininen, Mehreen Ali, Aki S. Havulinna, Marjo-Riitta Järvelin, Mika Ala-Korpela, Samuel Kaski
2016	J	`jnl`	metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis. Bioinform. Anna Cichonska, Juho Rousu, Pekka Marttinen, Antti J. Kangas, Pasi Soininen, Terho Lehtimäki, Olli T. Raitakari, Marjo-Riitta Järvelin, Veikko Salomaa, Mika Ala-Korpela, Samuli Ripatti, Matti Pirinen
2014	J	`jnl`	Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression. Bioinform. Pekka Marttinen, Matti Pirinen, Antti-Pekka Sarin, Jussi Gillberg, Johannes Kettunen, Ida Surakka, Antti J. Kangas, Pasi Soininen, Paul F. O'Reilly, Marika Kaakinen, Mika Kähönen, Terho Lehtimäki, Mika Ala-Korpela, Olli T. Raitakari, Veikko Salomaa, Marjo-Riitta Järvelin, Samuli Ripatti, Samuel Kaski
2013	J	`jnl`	Bayesian Information Sharing Between Noise And Regression Models Improves Prediction of Weak Effects. CoRR Jussi Gillberg, Pekka Marttinen, Matti Pirinen, Antti J. Kangas, Pasi Soininen, Marjo-Riitta Järvelin, Mika Ala-Korpela, Samuel Kaski
2010	J	`jnl`	Efficient Bayesian approach for multilocus association mapping including gene-gene interactions. BMC Bioinform. Pekka Marttinen, Jukka Corander
2009	J	`jnl`	Bayesian Clustering of Fuzzy Feature Vectors Using a Quasi-Likelihood Approach. IEEE Trans. Pattern Anal. Mach. Intell. Pekka Marttinen, Jing Tang, Bernard De Baets, Peter Dawyndt, Jukka Corander
2009	J	`jnl`	Bayesian clustering and feature selection for cancer tissue samples. BMC Bioinform. Pekka Marttinen, Samuel Myllykangas, Jukka Corander
2009	J	`jnl`	Bayesian learning of graphical vector autoregressions with unequal lag-lengths. Mach. Learn. Pekka Marttinen, Jukka Corander
2009	J	`jnl`	Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. BMC Bioinform. Petri Törönen, Pauli J. Ojala, Pekka Marttinen, Liisa Holm
2008	J	`jnl`	Bayesian modeling of recombination events in bacterial populations. BMC Bioinform. Pekka Marttinen, Adam Baldwin, William P. Hanage, Chris Dowson, Eshwar Mahenthiralingam, Jukka Corander
2008	J	`jnl`	Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinform. Jukka Corander, Pekka Marttinen, Jukka Sirén, Jing Tang
2006	J	`jnl`	Bayesian Model Learning Based on Predictive Entropy. J. Log. Lang. Inf. Jukka Corander, Pekka Marttinen
2006	J	`jnl`	Bayesian search of functionally divergent protein subgroups and their function specific residues. Bioinform. Pekka Marttinen, Jukka Corander, Petri Törönen, Liisa Holm
2004	J	`jnl`	BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinform. Jukka Corander, Patrik Waldmann, Pekka Marttinen, Mikko J. Sillanpää