Publications

Research contributions and academic publications

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PhD

PhD Dissertation

Reactive Probabilistic Programming for Scalable Bayesian Inference

Dmitry V. BagaevEindhoven 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.

Read DissertationDoctoral Research
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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), 1017-10192022

Read Paper176 citations

Citation Metrics

2,384
Total Citations
2,060
Since 2020
12
h-index
12
i10-index

An Interesting Observation About Citation Patterns

Ironically, my most impactful contributions turned out to be in biochemistry and immunology, despite never having studied biology or chemistry (and still not knowing them well). This is largely due to the significant differences in citation patterns between fields. My contributions in these areas are primarily software-based - developing tools and databases like VDJdb that enable other researchers to conduct their biological research more effectively. It's much harder to accumulate citations in pure mathematics, where papers are read by a smaller, specialized community, compared to biology fields where research involves many collaborators and reaches a broader audience. While my overall percentage contribution in biology papers is lower due to larger author lists, the visibility and impact of the software tools I've built are significantly higher, as they serve as essential infrastructure for the broader research community.

Publications (14)

VDJtools: unifying post-analysis of T cell receptor repertoires

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

PLoS computational biology 11 (11), e10045032015

654
citations

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-D4272018

577
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-D10622020

416
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. e52020

276
citations

MAGERI: Computational pipeline for molecular-barcoded targeted resequencing

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

PLoS computational biology 13 (5), e10054802017

61
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), 1-142018

48
citations

VDJviz: a versatile browser for immunogenomics data

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

BMC genomics 17 (1), 4532016

45
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), 8072021

33
citations

Reactive message passing for scalable Bayesian inference

D Bagaev, B de Vries

Scientific Programming 2023 (1), 66016902023

25
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), 51612023

21
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, 265-2772019

16
citations

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

D Bagaev, I Konshin, K Nikitin

Russian supercomputing days, 54-662017

9
citations

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

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

Software Impacts 12, 1002992022

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 Processing2021

6
citations