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Svetlana Poznanović

Publications and source records attributed to Svetlana Poznanović.

15 recordsLinked to original sources
arXiv2026

Unimodality and log-concavity of generalized Glasby-Paseman sequences

In this paper, we consider a two-parameter ($l$ and $a$) generalization of a sequence that Glasby and Paseman considered. Based on computer experiments, we conjecture its unimodality, log-concavity, peak positions, and the asymptotic behavior of the maximum values. Then we prove this conjecture for the case where $l=2$ and $a=1$. We finish the paper by making some comments about the conjecture on the generalized sequence.

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arXiv2025

An Efficient Algorithm for Exploring RNA Branching Conformations under the Nearest-Neighbor Thermodynamic Model

Background: In the Nearest-Neighbor Thermodynamic Model, a standard approach for RNA secondary structure prediction, the energy of the multiloops is modeled using a linear entropic penalty governed by three branching parameters. Although these parameters are typically fixed, recent work has shown that reparametrizing the multiloop score and considering alternative branching conformations can lead to significantly better structure predictions. However, prior approaches for exploring the alternative branching structures were computationally inefficient for long sequences. Results: We present a novel algorithm that partitions the parameter space, identifying all distinct branching structures (optimal under different branching parameters) for a given RNA sequence using the fewest possible minimum free energy computations. Our method efficiently computes the full parameter-space partition and the associated optimal structures, enabling a comprehensive evaluation of the structural landscape across parameter choices. We apply this algorithm to the Archive II benchmarking dataset, assessing the maximum attainable prediction accuracy for each sequence under the reparameterized multiloop model. We find that the potential for improvement over default predictions is substantial in many cases, and that the optimal prediction accuracy is highly sensitive to auxiliary modeling decisions, such as the treatment of lonely base pairs and dangling ends. Conclusion: Our results support the hypothesis that the conventional choice of multiloop parameters may limit prediction accuracy and that exploring alternative parameterizations is both tractable and worthwhile. The efficient partitioning algorithm we introduce makes this exploration feasible for longer sequences and larger datasets. Furthermore, we identify several open challenges in identifying the optimal structure.

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arXiv2025

Can geometric combinatorics improve RNA branching predictions?

Prior results for tRNA and 5S rRNA demonstrated that secondary structure prediction accuracy can be significantly improved by modifying the parameters in the multibranch loop entropic penalty function. However, for reasons not well understood at the time, the scale of improvement possible across both families was well below the level for each family when considered separately. We resolve this dichotomy here by showing that each family has a characteristic target region geometry, which is distinct from the other and significantly different from their own dinucleotide shuffles. This required a much more efficient approach to computing the necessary information from the branching parameter space, and a new theoretical characterization of the region geometries. The insights gained point strongly to considering multiple possible secondary structures generated by varying the multiloop parameters. We provide proof-of-principle results that this significantly improves prediction accuracy across all 8 additional families in the Archive II benchmarking dataset.

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arXiv2024

Toggleability Spaces of Fences

We completely describe the order ideal (resp. antichain) toggleability space for general fences: the space of statistics which are linear combinations of order ideal (antichain) indicator functions and equal to a constant plus a linear combination of toggleability statistics. This allows us to strengthen some homomesies under rowmotion on fences proven by Elizalde et al. and prove some new homomesy results for combinatorial, piecewise-linear, and birational rowmotion.

math.CO↗
arXiv2023

On the maximum of the weighted binomial sum $(1+a)^{-r}\sum_{i=0}^{r}\binom{m}{i}a^{i}$

Recently, Glasby and Paseman considered the following sequence of binomial sums $\{2^{-r}\sum_{i=0}^{r}\binom{m}{i}\}_{r=0}^{m}$ and showed that this sequence is unimodal and attains its maximum value at $r=\lfloor\frac{m}{3}\rfloor+1$ for $m\in\mathbb{Z}_{\geq0}\setminus\{0,3,6,9,12\}$. They also analyzed the asymptotic behavior of the maximum value of the sequence as $m$ approaches infinity. In the present work, we generalize their results by considering the sequence $\{(1+a)^{-r}\sum_{i=0}^{r}\binom{m}{i}a^{i}\}_{r=0}^{m}$ for integers $a \geq 1$. We also consider a family of discrete probability distributions that naturally arises from this sequence.

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arXiv2023

Homomesy via Toggleability Statistics

The rowmotion operator acting on the set of order ideals of a finite poset has been the focus of a significant amount of recent research. One of the major goals has been to exhibit homomesies: statistics that have the same average along every orbit of the action. We systematize a technique for proving that various statistics of interest are homomesic by writing these statistics as linear combinations of "toggleability statistics" (originally introduced by Striker) plus a constant. We show that this technique recaptures most of the known homomesies for the posets on which rowmotion has been most studied. We also show that the technique continues to work in modified contexts. For instance, this technique also yields homomesies for the piecewise-linear and birational extensions of rowmotion; furthermore, we introduce a $q$-analogue of rowmotion and show that the technique yields homomesies for "$q$-rowmotion" as well.

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arXiv2023

Descent polynomials for labeled tree

Motivated by the properties of the descent polynomials, which enumerate permutations of $S_n$ with a fixed descent set, we define descent polynomials for labeled rooted trees. We give recursive and explicit formulas for these polynomials and show when known properties of the descent polynomials carry over to the setting of trees.

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arXiv2019

Hecke insertion and maximal increasing and decreasing sequences in fillings of stack polyominoes

We prove that the number of 01-fillings of a given stack polyomino (a polyomino with justified rows whose lengths form a unimodal sequence) with at most one 1 per column which do not contain a fixed-size northeast chain and a fixed-size southeast chain, depends only on the set of row lengths of the polyomino. The proof is via a bijection between fillings of stack polyominoes which differ only in the position of one row and uses the Hecke insertion algorithm by Buch, Kresch, Shimozono, Tamvakis, and Yong and the jeu de taquin for increasing tableaux of Thomas and Yong. Moreover, our bijection gives another proof of the result by Chen, Guo, and Pang that the crossing number and the nesting number have a symmetric joint distribution over linked partitions.

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arXiv2019

Tree Descent Polynomials: Unimodality and Central Limit Theorem

For a poset whose Hasse diagram is a rooted plane forest $F$, we consider the corresponding tree descent polynomial $A_F(q)$, which is a generating function of the number of descents of the labelings of $F$. When the forest is a path, $A_F(q)$ specializes to the classical Eulerian polynomial. We prove that the coefficient sequence of $A_F(q)$ is unimodal and that if $\{T_{n}\}$ is a sequence of trees with $|T_{n}| = n$ and maximal down degree $D_{n} = O(n^{0.5-ε})$ then the number of descents in a labeling of $T_{n}$ is asymptotically normal.

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arXiv2019

Random shuffles on trees using extended promotion

The Tsetlin library is a very well studied model for the way an arrangement of books on a library shelf evolves over time. One of the most interesting properties of this Markov chain is that its spectrum can be computed exactly and that the eigenvalues are linear in the transition probabilities. In this paper we consider a generalization which can be interpreted as a self-organizing library in which the arrangements of books on each shelf are restricted to be linear extensions of a fixed poset. The moves on the books are given by the extended promotion operators of Ayyer, Klee, and Schilling while the shelves, bookcases, etc. evolve according to the move-to-back moves as in the the self-organizing library of Björner. We show that the eigenvalues of the transition matrix of this Markov chain are $\pm 1$ integer combinations of the transition probabilities if the posets that prescribe the restrictions on the book arrangements are rooted forests or more generally, if they consist of ordinal sums of a rooted forest and so called ladders. For some of the results we show that the monoids generated by the moves are either $\mathcal{R}$-trivial or, more generally, in $\textbf{DO(Ab)}$ and then we use the theory of left random walks on the minimal ideal of such monoids to find the eigenvalues. Moreover, in order to give a combinatorial description of the eigenvalues in the more general case, we relate the eigenvalues when the restrictions on the book arrangements change only by allowing for one additional transposition of two fixed books.

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arXiv2017

On Dantzig figures from graded lexicographic orders

We construct two families of Dantzig figures, which are $(d,2d)$-polytopes with an antipodal vertex pair, from convex hulls of initial subsets for the graded lexicographic (grlex) and graded reverse lexicographic (grevlex) orders on $\mathbb{Z}^{d}_{\geq 0}$. These two polytopes have the same number of vertices, $\mathcal{O}(d^{2})$, and the same number of edges, $\mathcal{O}(d^{3})$, but are not combinatorially equivalent. We provide an explicit description of the vertices and the facets for both families and describe their graphs along with analyzing their basic properties such as the radius, diameter, existence of Hamiltonian circuits, and chromatic number. Moreover, we also analyze the edge expansions of these graphs.

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arXiv2017

On the structure of RNA branching polytopes

The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy function assigned to the multibranch loops. Parametric analysis can be performed to elucidate the dependance of the prediction on the branching parameters used in the NNTM. Since the objective function is linear, this boils down to analyzing the normal fans of the branching polytopes. Here we show that because of the way the multibranch loops are scored under the NNTM, certain branching patterns are possible for all sequences. We do this by characterizing the dominant parts of the parameter space obtained by looking at the relevant section of the normal fan; therefore, we conclude that the structures that are normally found in nature are obtained for a relatively small set of parameters.

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arXiv2017

Properties of the Promotion Markov Chain on Linear Extensions

The Tsetlin library is a very well studied model for the way an arrangement of books on a library shelf evolves over time. One of the most interesting properties of this Markov chain is that its spectrum can be computed exactly and that the eigenvalues are linear in the transition probabilities. This result has been generalized in different ways by various people. In this work we investigate one of the generalizations given by the extended promotion Markov Chain on linear extensions of a poset $P$ introduced by Ayyer, Klee, and Schilling in 2014. They showed that if the poset $P$ is a rooted forest, the transition matrix of this Markov chain has eigenvalues that are linear in the transition probabilities and described their multiplicities. We show that the same property holds for a larger class of posets for which we also derive convergence to stationarity results.

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arXiv2016

Graphical Mahonian Statistics on Words

Foata and Zeilberger defined the graphical major index, $\mathrm{maj}'_U$, and the graphical inversion index, $\mathrm{inv}'_U$, for words. These statistics are a generalization of the classical permutation statistics $\mathrm{maj}$ and $\mathrm{inv}$ indexed by directed graphs $U$. They showed that $\mathrm{maj}'_U$ and $\mathrm{inv}'_U$ are equidistributed over all rearrangement classes if and only if $U$ is bipartitional. In this paper we strengthen their result by showing that if $\mathrm{maj}'_U$ and $\mathrm{inv}'_U$ are equidistributed on a single rearrangement class then $U$ is essentially bipartitional. Moreover, we define a graphical sorting index, $\mathrm{sor}'_U$, which generalizes the sorting index of a permutation. We then characterize the graphs $U$ for which $\mathrm{sor}'_U$ is equidistributed with $\mathrm{inv}'_U$ and $\mathrm{maj}'_U$ on a single rearrangement class.

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arXiv2016

Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences

Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the objective functions. The goal of a parametric analysis is to elucidate such dependencies, especially as they pertain to the accuracy and robustness of the optimal solutions. Techniques from geometric combinatorics, including polytopes and their normal fans, have been used previously to give parametric analyses of simple models for DNA sequence alignment and RNA branching configurations. Here, we present a new computational framework, and proof-of-principle results, which give the first complete parametric analysis of the branching portion of the nearest neighbor thermodynamic model for secondary structure prediction for real RNA sequences.

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