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Gizem Caylak

dblp:263/2236 · also Gizem Çaylak · DBLP profile ↗
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3ranked-venue papers
2as first author
2since 2021 · last 2024
0000-0001-9703-6912ORCID · corroborated

Domains — the database's venue-derived domains; a paper can count in several

Software engineering, systems software and programming languages · 2 · 1 first-author · 2 since 2021Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › genomics › genome-wide association study
epistasis detection
0.412020
Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection · RECOMB 2020
Bioinformatics and computational biology › statistical genetics
genetic association study
0.412020
Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection · RECOMB 2020
Bioinformatics and computational biology › statistical genetics › single nucleotide polymorphism analysis
SNP selection
0.412020
Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection · RECOMB 2020

Methods — techniques the papers use, named apart from their topics

combinatorial optimization · 0.4
YearPublicationVenuePosition
2024 Statically and Dynamically Delayed Sampling for Typed Probabilistic Programming Languages
abstract
Probabilistic programming languages (PPLs) make it possible to separate the concerns between probabilistic models and Bayesian inference algorithms. However, to make such inference efficient is technically very challenging, both in terms of execution time performance and inference accuracy. One successful optimization approach is the previously published work on dynamically delayed sampling. This runtime method makes use of analytical relations between random variables to reduce inference variance; however, tracking these relations introduces runtime overhead. Furthermore, implementing the dynamic approach in a statically typed language introduces type problems because delaying the sampling of random variables changes their types. Our work advances the state-of-the-art in two aspects. Firstly, to reduce the runtime overhead, we develop a compile-time version of delayed sampling. By incorporating optimization procedures during compilation, we eliminate the need for runtime relation tracking and consequent overhead. However, the compile-time version may not always be effective due to the program's possible dynamic behavior, such as stochastic branches, or the complexity of handling recursion. Secondly, we introduce constructs to implement dynamically delayed sampling in a statically typed universal PPL. Dynamically delayed sampling in statically typed languages is a viable optimization for complex Bayesian models, whereas simple models ought to be statically optimized. We evaluate both statically and dynamically delayed sampling on real-world examples, such as latent Dirichlet allocation and an epidemiology model, and implement the methods in a statically typed PPL, Miking CorePPL.
Gizem Caylak, Daniel Lundén, Viktor Senderov, David Broman
SLE1
2023 Automatic Alignment in Higher-Order Probabilistic Programming Languages
abstract
Abstract Probabilistic Programming Languages (PPLs) allow users to encode statistical inference problems and automatically apply an inference algorithm to solve them. Popular inference algorithms for PPLs, such as sequential Monte Carlo (SMC) and Markov chain Monte Carlo (MCMC), are built around checkpoints—relevant events for the inference algorithm during the execution of a probabilistic program. Deciding the location of checkpoints is, in current PPLs, not done optimally. To solve this problem, we present a static analysis technique that automatically determines checkpoints in programs, relieving PPL users of this task. The analysis identifies a set of checkpoints that execute in the same order in every program run—they are aligned. We formalize alignment, prove the correctness of the analysis, and implement the analysis as part of the higher-order functional PPL Miking CorePPL. By utilizing the alignment analysis, we design two novel inference algorithm variants: aligned SMC and aligned lightweight MCMC. We show, through real-world experiments, that they significantly improve inference execution time and accuracy compared to standard PPL versions of SMC and MCMC.
Daniel Lundén, Gizem Caylak, Fredrik Ronquist, David Broman
ESOP2
2020 Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection
Gizem Caylak, A. Ercüment Çiçek
RECOMB1