In this talk I will first recall the basic concepts of property-based testing and then cover a couple of recent applications, while sharing some of the folklore and community know-how. I will then offer a personal perspective on the approach, both in terms of programming language theory and software engineering.

Speaker: Jan Midtgaard

The seminar will be held in google meet on Monday, December 21, at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

True concurrency semantics propose an alternative solution. In this framework it is possible to explicitly define the causality relations between atomic actions and avoid the reasoning in terms of all possible interleavings.

In this talk we will consider event structures — one of the classic domains in the theory of true concurrency. We will show how event structures can be used to define denotational (compositional) semantics on the example of Calculus of Communicating Systems (CCS).

Speaker: Evgenii Moiseenko

References:

Winskel G. Event structure semantics for CCS and related languages //International Colloquium on Automata, Languages, and Programming. – Springer, Berlin, Heidelberg, 1982. – С. 561-576.

Winskel G. Event structures //Advanced Course on Petri Nets. – Springer, Berlin, Heidelberg, 1986. – С. 325-392.

The seminar will be held in google meet on Monday, December 14, at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

Speaker: Egor Namakonov

The seminar will be held in google meet on Monday, November 30, at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

The talk was dedicated to the recent paper "Comprehensive profiling of an aging immune system reveals clonal GZMK^{+} CD8 T cells as conserved hallmark of inflammaging" where the authors described novel immune cell populated associated with inflammaging and identified potential targets to develop therapy for inflammation related disease in aging.

- Single Cell ATAC-seq protocol
- Assessment of existing computational methods
- Methods used in the paper for analysing multiple scATAC-seq experiments for different conditions

Speaker: Rustam Azimov

References:

1 Terekhov A. et al. Context-Free Path Querying with Single-Path Semantics by Matrix Multiplication //Proceedings of the 3rd Joint International Workshop on Graph Data Management Experiences & Systems (GRADES) and Network Data Analytics (NDA). – 2020. – С. 1-12.

2) Orachev E. et al. Context-Free Path Querying by Kronecker Product //European Conference on Advances in Databases and Information Systems. – Springer, Cham, 2020. – С. 49-59.

The seminar will be held in google meet on Monday, November 30, at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

]]>In the talk we consider a more declarative approach to evaluating relational programs which is insensitive to the order of conjuncts and does not introduce essential performance overhead.

The talk is based on a paper P.Lozov, D.Boulytchev "Efficient Fair Conjunction for Structurally-Recursive Relations", which is accepted for publication to the workshop PEPM 2021.

Speaker: Peter Lozov

References:

P.Lozov, D.Boulytchev "Efficient Fair Conjunction for Structurally-Recursive Relations"

The seminar will be held in google meet on Monday, November 23, at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

Speaker: Ekaterina Verbitskaia

References:

Choppella, Venkatesh, and Christopher T. Haynes. "Source-tracking unification." Information and Computation 201, no. 2 (2005): 121-159.The seminar will be held in google meet on Monday, November 16, at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

]]>Slides:

- Transcription regulation
- ChromHMM and DNA methylation
- ChIP-seq analysis 1
- ChIP-seq analysis 2
- Downstream analysis
- DNA methylation analysis 1
- DNA methylation analysis 2

The course consists of two major parts.

The first part was dedicated to the role of epigenetics in transcriptional regulation. The second part was dedicated to methods and computational pipelines for experimental data analysis.

The following topics were covered by the block Transcription regulation:

- Regulation
- Transcription Factors
- ChIP-seq
- Chromatin
- DNase, ATAC-seq
- Histone modifications
- Enhancers
- TAD, CTCF, 3C, 4C, 5C, HighC

The block ChromHMM and DNA methylation covered:

- ChromHMM
- ENCODE project
- DNA methylation
- Cytosine context CpG, CHH, etc.
- Methylation across genome
- Bisulfite conversion
- Protocols WGBS, RRBS
- Methylation clocks

Practical part was dedicated to computational approaches. This block was split into three almost independent parts: ChIP-seq analysis, genomic positional data downstream analysis and DNA methylation.

Pipeline for ChIP-seq analysis:

ChIP-seq analysis was divided into three blocks:

ChIP-seq 1-2 topics:

- Downloading datasets, ENCODE
- Useful Linux commands
- QC + MultiQC
- Alignment + QC / filtration
- Visualization for BAM file
- Peak calling MACS2, SICER, SPAN & JBR
- Peaks - confidence, statistics
- Differential peak calling

Downstream analysis topics:

- Genomic regions manipulation - BEDTools
- Associated/closest gene annotation, working with GTF files
- Coverage profile per TSS/Genes/etc - DeepTools
- Functional genome annotation - ChIPpeakAnno, ChIPSeekR
- Motif analysis TF - Homer + MEME
- Pathway enrichment analysis - GREAT / EnrichR
- Similar datasets - ChIP-Atlas

Pipeline for DNA methylation analysis:

DNA methylation analysis was split into two blocks:

Covered topics:

- Alignment + QC + Visualization
- Call Methylation + QC + Visualization
- Hyper-/Hypo-/Partially- Methylated Regions
- Partially Methylated Domains
- DMRs
- Bis-SNP approach
- Compare Methylation Micro Arrays with NGS data
- Methylation Clock
- Methylation @ Loci

The course took 5 hours of theory (Feb 13, 2020) and 23 hours of practice (Nov 2-7, 2020).

We thank ITMO University and Yandex for the provided cloud based computational infrastructure.

]]>The seminar will be held in google meet on Monday, November 9 at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

]]>The first act of the talk will introduce and explain the universes of the Coq proof assistant to set the scene for the second act. In the second act we'll get acquainted with a pretty recent experimental addition to the family of Coq's universes, low and behold, our major character -- SProp, a universe of strict propositions. I'll provide a number of examples to illustrate the applicability of SProp, its elimination principles over type, the difference between Sprop and Prop and how all the universes interact.

Speaker: Anton Trunov

References:

1. "Definitional proof-irrelevance without K" - G. Gilbert, J. Cockx, M. Sozeau, N. Tabareau (2019), https://dl.acm.org/doi/10.1145/3290316

2. The Coq Reference Manual: https://coq.github.io/doc/master/refman/addendum/s...

The seminar will be held in google meet on Monday November 2 at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

]]>D. Kondyrev, A. Lakhansky, D. Safenreiter "Zero-knowledge proof Algorithms in blockchain systems: principles of operation and examples of implementations".

To get access to zoom, write tokareva@math.nsc.ru

]]>In this talk, three different approaches to represent the inductive invariants of ADT-manipulating programs will be discussed: by first-order formulas, by tree automata, and by first-order formulas with size constraints.

The comparison of the expressive power of these representations based on simple examples will show us how state-of-art invariant inference tools often diverge because of invariant undefinability in the first-order language. We will also talk about the automatic inference of regular invariants of ADT-manipulating programs using finite model finders. An evaluation against state-of-art Horn-solvers will show us that the automata-based representation of invariants is more practical than the one based on first-order logic since invariants are capable of expressing more complex properties of the computation and their automatic construction is less expensive.

Speaker: Yurii Kostyukov

References:

1). Zhang T., Sipma H. B., Manna Z. Decision procedures for recursive data structures with integer constraints //International Joint Conference on Automated Reasoning. – Springer, Berlin, Heidelberg, 2004. – С. 152-167.

2). Reynolds A. J. Finite model finding in satisfiability modulo theories. – 2013.

The seminar will be held in google meet on Monday October 26 at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

]]>In this seminar we will discuss the benifits of using reactive stream (Flow) based approach in Monte-Carlo simulations. We will discuss two specific cases:

- Electron trapping in magnetic fields in the Troitsk nu-mass tritium source.
- Reactor-like gamma echancement mechanism in absolute chaotic case.

The seminar will be mostly dedicated to code discussion. Also we will briefly discusss the random-forging process which is an important part of the SimBa project.

]]>We are glad to inform you that the Review of AES proposed by NIST will be presented at the first time in the history! So, join us: <br>

https://www.youtube.com/channel/UCgPgiLl3WCqMLXU38tVYulw/.

The lecture starts an hour before the start of the first round of the Olympiad, namely on October, 18 at 3 p.m. NOVT (UTC+7).

Nicky Mouha is a researcher at the Computer Security Division of NIST (USA), a member of crypto standartization committees at NIST, ISO/IEC JTC1 SC27, and ASC X9F; a co-author of the Triple DES (3DES) standard, which is one of only two block ciphers that are approved for use by the U.S. government. Nicky is well known as the designer of the Chaskey algorithm and as the inventor of the MILP and SAT-based techniques that have now become the standard tools to analyze the security of cryptographic algorithms against statistical attacks.

Recall that the Olympiad starts tomorrow! Be registered on nsucrypto.nsu.ru.

]]>In the talk, we will look at the semantic approach for proving type safety and program equivalence by building step-indexing semantics for the lambda calculus with recursive types and (probably) a more realistic language of von Neumann machine instructions.

Speaker: Dmitry Rozplokhas

References:

Andrew W. Appel, David Allen McAllester. An indexed model of recursive types for foundational proof-carrying code. Transactions on Programming Languages and Systems, 2001. https://dl.acm.org/doi/10.1145/504709.504712

The seminar will be held in google meet on Monday October 19 at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

]]>I. Sutormin "Nonlinearity of balanced Boolean functions. Review"

]]>Speaker: Vladimir Gladstein

References:

Peter W. O’Hearn. 2020. Incorrectness Logic. Proc. ACM Program. Lang. 4, POPL, Article 10 (January 2020), 32 pages. https://doi.org/10.1145/3371078

The seminar will be held in google meet on Monday October 12 at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)

The talk proposes methods from the field of program synthesis for the implementation of machine-dependent compilation phases. The phases are based on a reduction to SMT problem which allows to get rid of heuristic and approximate approaches, that requires complex software implementation of a compiler. Practical applications of the developed methods and algorithms are illustrated by the example of a compiler for a specialized processor with an instruction set that accelerates the implementation of lightweight cryptography algorithms in the Internet of Things.

Speaker: Peter Sovietov

References:

1) Hennessy, John L., and David A. Patterson. "A new golden age for computer architecture." Communications of the ACM 62.2 (2019): 48-60. https://cacm.acm.org/magazines/2019/2/234352-a-new...

2) Lopes, Nuno P., and John Regehr. "Future Directions for Optimizing Compilers." arXiv preprint arXiv:1809.02161 (2018).
https://arxiv.org/abs/1809.02161

The seminar will be held in google meet on Monday October 5 at 17:30 (google meet room: https://meet.google.com/myu-dhmz-gvu)