arXiv subjects

Jan Obdržálek

Publications and source records attributed to Jan Obdržálek.

15 recordsLinked to original sources

arXiv2026

Explaining Digital Pathology Models via Clustering Activations

We present a clustering-based explainability technique for digital pathology models based on convolutional neural networks. Unlike commonly used methods based on saliency maps, such as occlusion, GradCAM, or relevance propagation, which highlight regions that contribute the most to the prediction for a single slide, our method shows the global behaviour of the model under consideration, while also providing more fine-grained information. The result clusters can be visualised not only to understand the model, but also to increase confidence in its operation, leading to faster adoption in clinical practice. We also evaluate the performance of our technique on an existing model for detecting prostate cancer, demonstrating its usefulness.

cs.CV↗

arXiv2025

Beyond Occlusion: In Search for Near Real-Time Explainability of CNN-Based Prostate Cancer Classification

Deep neural networks are starting to show their worth in critical applications such as assisted cancer diagnosis. However, for their outputs to get accepted in practice, the results they provide should be explainable in a way easily understood by pathologists. A well-known and widely used explanation technique is occlusion, which, however, can take a long time to compute, thus slowing the development and interaction with pathologists. In this work, we set out to find a faster replacement for occlusion in a successful system for detecting prostate cancer. Since there is no established framework for comparing the performance of various explanation methods, we first identified suitable comparison criteria and selected corresponding metrics. Based on the results, we were able to choose a different explanation method, which cut the previously required explanation time at least by a factor of 10, without any negative impact on the quality of outputs. This speedup enables rapid iteration in model development and debugging and brings us closer to adopting AI-assisted prostate cancer detection in clinical settings. We propose that our approach to finding the replacement for occlusion can be used to evaluate candidate methods in other related applications.

cs.CV↗

arXiv2024

Minuska: Towards a Formally Verified Programming Language Framework

Programming language frameworks allow us to generate language tools (e.g., interpreters) just from a formal description of the syntax and semantics of a programming language. As these frameworks tend to be quite complex, an issue arises whether we can trust the generated tools. To address this issue, we introduce a practical formal programming language framework called Minuska, which always generates a provably correct interpreter given a valid language definition. This is achieved by (1) defining a language MinusLang for expressing programming language definitions and giving it formal semantics and (2) using the Coq proof assistant to implement an interpreter parametric in a MinusLang definition and to prove it correct. Minuska provides strong correctness guarantees and can support nontrivial languages while performing well. This is the extended version of the SEFM24 paper of the same name.

cs.PL↗

arXiv2019

Shrub-depth: Capturing Height of Dense Graphs

The recent increase of interest in the graph invariant called tree-depth and in its applications in algorithms and logic on graphs led to a natural question: is there an analogously useful "depth" notion also for dense graphs (say; one which is stable under graph complementation)? To this end, in a 2012 conference paper, a new notion of shrub-depth has been introduced, such that it is related to the established notion of clique-width in a similar way as tree-depth is related to tree-width. Since then shrub-depth has been successfully used in several research papers. Here we provide an in-depth review of the definition and basic properties of shrub-depth, and we focus on its logical aspects which turned out to be most useful. In particular, we use shrub-depth to give a characterization of the lower $ω$ levels of the MSO1 transduction hierarchy of simple graphs.

cs.LO↗

arXiv2018

A New Perspective on FO Model Checking of Dense Graph Classes

We study the first-order (FO) model checking problem of dense graphs, namely those which have FO interpretations in (or are FO transductions of) some sparse graph classes. We give a structural characterization of the graph classes which are FO interpretable in graphs of bounded degree. This characterization allows us to efficiently compute such an FO interpretation for an input graph. As a consequence, we obtain an FPT algorithm for successor-invariant FO model checking of any graph class which is FO interpretable in (or an FO transduction of) a graph class of bounded degree. The approach we use to obtain these results may also be of independent interest.

cs.LO↗

arXiv2015

Faster Existential FO Model Checking on Posets

We prove that the model checking problem for the existential fragment of first-order (FO) logic on partially ordered sets is fixed-parameter tractable (FPT) with respect to the formula and the width of a poset (the maximum size of an antichain). While there is a long line of research into FO model checking on graphs, the study of this problem on posets has been initiated just recently by Bova, Ganian and Szeider (CSL-LICS 2014), who proved that the existential fragment of FO has an FPT algorithm for a poset of fixed width. We improve upon their result in two ways: (1) the runtime of our algorithm is O(f(|ϕ|,w).n^2) on n-element posets of width w, compared to O(g(|ϕ|). n^{h(w)}) of Bova et al., and (2) our proofs are simpler and easier to follow. We complement this result by showing that, under a certain complexity-theoretical assumption, the existential FO model checking problem does not have a polynomial kernel.

cs.LO↗

arXiv2015

FO Model Checking on Posets of Bounded Width

Over the past two decades the main focus of research into first-order (FO) model checking algorithms have been sparse relational structures-culminating in the FPT-algorithm by Grohe, Kreutzer and Siebertz for FO model checking of nowhere dense classes of graphs [STOC'14], with dense structures starting to attract attention only recently. Bova, Ganian and Szeider [LICS'14] initiated the study of the complexity of FO model checking on partially ordered sets (posets). Bova, Ganian and Szeider showed that model checking existential FO logic is fixed-parameter tractable (FPT) on posets of bounded width, where the width of a poset is the size of the largest antichain in the poset. The existence of an FPT algorithm for general FO model checking on posets of bounded width, however, remained open. We resolve this question in the positive by giving an algorithm that takes as its input an $n$-element poset $\cal P$ of width $w$ and an FO logic formula $ϕ$, and determines whether $ϕ$ holds on $\cal P$ in time $f(ϕ,w)\cdot n^2$.

cs.LO↗

arXiv2015

Kernelization Using Structural Parameters on Sparse Graph Classes

Meta-theorems for polynomial (linear) kernels have been the subject of intensive research in parameterized complexity. Heretofore, meta-theorems for linear kernels exist on graphs of bounded genus, $H$-minor-free graphs, and $H$-topological-minor-free graphs. To the best of our knowledge, no meta-theorems for polynomial kernels are known for any larger sparse graph classes; e.g., for classes of bounded expansion or for nowhere dense ones. In this paper we prove such meta-theorems for the two latter cases. More specifically, we show that graph problems that have finite integer index (FII) have linear kernels on graphs of bounded expansion when parameterized by the size of a modulator to constant-treedepth graphs. For nowhere dense graph classes, our result yields almost-linear kernels. While our parameter may seem rather strong, we argue that a linear kernelization result on graphs of bounded expansion with a weaker parameter (than treedepth modulator) would fail to include some of the problems covered by our framework. Moreover, we only require the problems to have FII on graphs of constant treedepth. This allows us to prove linear kernels for problems such as Longest Path/Cycle, Exact $s,t$-Path, Treewidth, and Pathwidth, which do not have FII on general graphs (and the first two not even on bounded treewidth graphs).

cs.DS↗

arXiv2014

Tree-depth and Vertex-minors

In a recent paper, Kwon and Oum claim that every graph of bounded rank-width is a pivot-minor of a graph of bounded tree-width (while the converse has been known true already before). We study the analogous questions for "depth" parameters of graphs, namely for the tree-depth and related new shrub-depth. We show that shrub-depth is monotone under taking vertex-minors, and that every graph class of bounded shrub-depth can be obtained via vertex-minors of graphs of bounded tree-depth. We also consider the same questions for bipartite graphs and pivot-minors.

cs.DM↗

arXiv2013

Expanding the expressive power of Monadic Second-Order logic on restricted graph classes

We combine integer linear programming and recent advances in Monadic Second-Order model checking to obtain two new algorithmic meta-theorems for graphs of bounded vertex-cover. The first shows that cardMSO1, an extension of the well-known Monadic Second-Order logic by the addition of cardinality constraints, can be solved in FPT time parameterized by vertex cover. The second meta-theorem shows that the MSO partitioning problems introduced by Rao can also be solved in FPT time with the same parameter. The significance of our contribution stems from the fact that these formalisms can describe problems which are W[1]-hard and even NP-hard on graphs of bounded tree-width. Additionally, our algorithms have only an elementary dependence on the parameter and formula. We also show that both results are easily extended from vertex cover to neighborhood diversity.

cs.DS↗

arXiv2012

Lower Bounds on the Complexity of MSO1 Model-Checking

One of the most important algorithmic meta-theorems is a famous result by Courcelle, which states that any graph problem definable in monadic second-order logic with edge-set quantifications (i.e., MSO2 model-checking) is decidable in linear time on any class of graphs of bounded tree-width. Recently, Kreutzer and Tazari proved a corresponding complexity lower-bound - that MSO2 model-checking is not even in XP wrt. the formula size as parameter for graph classes that are subgraph-closed and whose tree-width is poly-logarithmically unbounded. Of course, this is not an unconditional result but holds modulo a certain complexity-theoretic assumption, namely, the Exponential Time Hypothesis (ETH). In this paper we present a closely related result. We show that even MSO1 model-checking with a fixed set of vertex labels, but without edge-set quantifications, is not in XP wrt. the formula size as parameter for graph classes which are subgraph-closed and whose tree-width is poly-logarithmically unbounded unless the non-uniform ETH fails. In comparison to Kreutzer and Tazari; $(1)$ we use a stronger prerequisite, namely non-uniform instead of uniform ETH, to avoid the effectiveness assumption and the construction of certain obstructions used in their proofs; and $(2)$ we assume a different set of problems to be efficiently decidable, namely MSO1-definable properties on vertex labeled graphs instead of MSO2-definable properties on unlabeled graphs. Our result has an interesting consequence in the realm of digraph width measures: Strengthening the recent result, we show that no subdigraph-monotone measure can be "algorithmically useful", unless it is within a poly-logarithmic factor of undirected tree-width.

cs.LO↗

arXiv2012

STANSE: Bug-finding Framework for C Programs

STANSE is a free (available under the GPLv2 license) modular framework for finding bugs in C programs using static analysis. Its two main design goals are 1) ability to process large software projects like the Linux kernel and 2) extensibility with new bug-finding techniques with a minimal effort. Currently there are four bug-finding algorithms implemented within STANSE: AutomatonChecker checks properties described in an automata-based formalism, ThreadChecker detects deadlocks among multiple threads, LockChecker finds locking errors based on statistics, and ReachabilityChecker looks for unreachable code. STANSE has been tested on the Linux kernel, where it has found dozens of previously undiscovered bugs.

cs.SE↗

arXiv2010

Better algorithms for satisfiability problems for formulas of bounded rank-width

We provide a parameterized polynomial algorithm for the propositional model counting problem #SAT, the runtime of which is single-exponential in the rank-width of a formula. Previously, analogous algorithms have been known -- e.g.~[Fischer, Makowsky, and Ravve] -- with a single-exponential dependency on the clique-width of a formula. Our algorithm thus presents an exponential runtime improvement (since clique-width reaches up to exponentially higher values than rank-width), and can be of practical interest for small values of rank-width. We also provide an algorithm for the MAX-SAT problem along the same lines.

cs.DM↗

arXiv2010

Are there any good digraph width measures?

Several different measures for digraph width have appeared in the last few years. However, none of them shares all the "nice" properties of treewidth: First, being \emph{algorithmically useful} i.e. admitting polynomial-time algorithms for all $\MS1$-definable problems on digraphs of bounded width. And, second, having nice \emph{structural properties} i.e. being monotone under taking subdigraphs and some form of arc contractions. As for the former, (undirected) $\MS1$ seems to be the least common denominator of all reasonably expressive logical languages on digraphs that can speak about the edge/arc relation on the vertex set.The latter property is a necessary condition for a width measure to be characterizable by some version of the cops-and-robber game characterizing the ordinary treewidth. Our main result is that \emph{any reasonable} algorithmically useful and structurally nice digraph measure cannot be substantially different from the treewidth of the underlying undirected graph. Moreover, we introduce \emph{directed topological minors} and argue that they are the weakest useful notion of minors for digraphs.

cs.DM↗

arXiv2010

Qualitative Reachability in Stochastic BPA Games

We consider a class of infinite-state stochastic games generated by stateless pushdown automata (or, equivalently, 1-exit recursive state machines), where the winning objective is specified by a regular set of target configurations and a qualitative probability constraint `>0' or `=1'. The goal of one player is to maximize the probability of reaching the target set so that the constraint is satisfied, while the other player aims at the opposite. We show that the winner in such games can be determined in PTIME for the `>0' constraint, and both in NP and coNP for the `=1' constraint. Further, we prove that the winning regions for both players are regular, and we design algorithms which compute the associated finite-state automata. Finally, we show that winning strategies can be synthesized effectively.

cs.GT↗