Publications

Research contributions and academic publications

See also Academia — research focus, teaching, and student supervision.

h-index

13

i10-index

14

Publications

30+

Citations

2933+

PhD downloads

1893+

PhD Dissertation

Reactive Probabilistic Programming for Scalable Bayesian Inference

Dmitry V. Bagaev • Eindhoven University of Technology

2023

Bayesian inference realizes optimal information processing through a full commitment to reasoning by probability theory. The Bayesian framework is a crucial technology at the core of modern AI with applications such as speech and image recognition and generation, biomedical analysis, robot navigation, and more. This dissertation focuses on the realization of efficient Bayesian inference in large-scale probabilistic models, targeting real-time signal processing and control applications under real-world conditions. We present a practical architecture based on reactive message passing-based inference in a factor graph representation of the probabilistic model under study.

Nature Publication

VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2

M Goncharov, D Bagaev, D Shcherbinin, I Zvyagin, D Bolotin, PG Thomas, ...

Nature methods 19 (9), 1017-1019 • 2022

Read Paper290+ citations

My publications

Note that this list might be outdated, I try to sync it once in a while. Check my Google Scholar for the most recent updates.

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

M Shugay, DV Bagaev, IV Zvyagin, RM Vroomans, JC Crawford, G Dolton, ...

Nucleic acids research 46 (D1), D419-D427 • 2018

755+
citations

VDJtools: unifying post-analysis of T cell receptor repertoires

M Shugay, DV Bagaev, MA Turchaninova, DA Bolotin, OV Britanova, ...

PLoS computational biology 11 (11), e1004503 • 2015

723+
citations

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium

DV Bagaev, RMA Vroomans, J Samir, U Stervbo, C Rius, G Dolton, ...

Nucleic acids research 48 (D1), D1057-D1062 • 2020

502+
citations

SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T cell receptors

AS Shomuradova, MS Vagida, SA Sheetikov, KV Zornikova, D Kiryukhin, ...

Immunity 53 (6), 1245-1257. e5 • 2020

303+
citations

MAGERI: Computational pipeline for molecular-barcoded targeted resequencing

M Shugay, AR Zaretsky, DA Shagin, IA Shagina, IA Volchenkov, ...

PLoS computational biology 13 (5), e1005480 • 2017

65+
citations

Exploring the pre-immune landscape of antigen-specific T cells

MV Pogorelyy, AD Fedorova, JE McLaren, K Ladell, DV Bagaev, ...

Genome medicine 10 (1), 1-14 • 2018

53+
citations

VDJviz: a versatile browser for immunogenomics data

DV Bagaev, IV Zvyagin, EV Putintseva, M Izraelson, OV Britanova, ...

BMC genomics 17 (1), 453 • 2016

51+
citations

Variational message passing and local constraint manipulation in factor graphs

İ Şenöz, T van de Laar, D Bagaev, B de Vries

Entropy 23 (7), 807 • 2021

42+
citations

RxInfer: A Julia package for reactive real-time Bayesian inference

D Bagaev, A Podusenko, B De Vries

Journal of Open Source Software 8 (84), 5161 • 2023

39+
citations

Reactive message passing for scalable Bayesian inference

D Bagaev, B de Vries

Scientific Programming 2023 (1), 6601690 • 2023

20+
citations

Improving parallel efficiency of a complex hydrogeological problem simulation in GeRa

D Bagaev, F Grigoriev, I Kapyrin, I Konshin, V Kramarenko, A Plenkin

Russian Supercomputing Days, 265-277 • 2019

16+
citations

Dynamic optimization of linear solver parameters in mathematical modelling of unsteady processes

D Bagaev, I Konshin, K Nikitin

Russian supercomputing days, 54-66 • 2017

10+
citations

Expected free energy-based planning as variational inference

B de Vries, W Nuijten, T van de Laar, W Kouw, S Adamiat, T Nisslbeck, ...

arXiv preprint • 2025

7+
citations

Multi-agent trajectory planning with NUV priors

B van Erp, D Bagaev, A Podusenko, İ Şenöz, B de Vries

2024 American Control Conference (ACC), 2766-2771 • 2024

7+
citations

ReactiveMP.jl: A Julia package for reactive variational Bayesian inference

D Bagaev, B van Erp, A Podusenko, B de Vries

Software Impacts 12, 100299 • 2022

6+
citations

Message passing-based inference in the Gamma mixture model

A Podusenko, B van Erp, D Bagaev, İ Şenöz, B de Vries

2021 IEEE 31st International Workshop on Machine Learning for Signal Processing • 2021

6+
citations

Gaussian Variational Inference with Non-Gaussian Factors for State Estimation: A UWB Localization Case Study

A Stirling, M Lukashchuk, D Bagaev, W Kouw, JR Forbes

IEEE Robotics and Automation Letters • 2026

3+
citations

ExponentialFamilyManifolds.jl: Representing exponential families as Riemannian manifolds

M Lukashchuk, D Bagaev, A Podusenko, İ Şenöz, B de Vries

Proceedings of the JuliaCon Conferences 7 (70) • 2025

2+
citations

GraphPPL.jl: A Probabilistic Programming Language for Graphical Models

WWL Nuijten, D Bagaev, B de Vries

Entropy 26 (11) • 2024

2+
citations

Riemannian black box variational inference

M Lukashchuk, WWL Nuijten, D Bagaev, İ Şenöz, B de Vries

NeurIPS 2024 Workshop on Bayesian Decision-making and Uncertainty • 2024

1+
citations

Message passing-based inference in switching autoregressive models

A Podusenko, B van Erp, D Bagaev, B de Vries

2022 30th European Signal Processing Conference (EUSIPCO) • 2022

1+
citations

Composing Non-Conjugate Factor Graphs with Closed-Form Variational Inference

M Lukashchuk, K Yemets, WM Kouw, D Bagaev, İ Şenöz, J Beck, ...

arXiv preprint • 2026

0+
citations
Note that this list might be outdated, I try to sync it once in a while. Check my Google Scholar for the most recent updates.