Related papers: iTreePack: Protein Complex Side-Chain Packing by D…
We consider the numerical irreducible decomposition of a positive dimensional solution set of a polynomial system into irreducible factors. Path tracking techniques computing loops around singularities connect points on the same irreducible…
Fixed parameter tractable algorithms for bounded treewidth are known to exist for a wide class of graph optimization problems. While most research in this area has been focused on exact algorithms, it is hard to find decompositions of…
Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based…
The direpack package aims to establish a set of modern statistical dimension reduction techniques into the Python universe as a single, consistent package. The dimension reduction methods included resort into three categories: projection…
Nonlinear dimensionality reduction methods have demonstrated top-notch performance in many pattern recognition and image classification tasks. Despite their popularity, they suffer from highly expensive time and memory requirements, which…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
We present a dual optimization concept of predicting optimal sequences as well as optimal folds of off-lattice protein models in the context of multi-scale modeling. We validate the utility of the recently introduced hidden-force Monte…
The problem of selecting small groups of itemsets that represent the data well has recently gained a lot of attention. We approach the problem by searching for the itemsets that compress the data efficiently. As a compression technique we…
Hypertree decompositions of hypergraphs are a generalization of tree decompositions of graphs. The corresponding hypertree-width is a measure for the cyclicity and therefore tractability of the encoded computation problem. Many NP-hard…
We consider a Bar Charts Packing Problem (BCPP), in which it is necessary to pack bar charts (BCs) in a strip of minimum length. The problem is, on the one hand, a generalization of the Bin Packing Problem (BPP), and, on the other hand, a…
Treewidth is a well-studied decompositional parameter to measure the tree-likeness of a graph. While the propositional satisfiability problem (SAT) is known to be tractable when parameterized by the treewidth of the underlying primal graph,…
Large deformations of soft materials are customarily associated with strong constitutive and geometrical nonlinearities that originate new modes of fracture. Some isotropic materials can develop strong fracture anisotropy, which manifests…
We develop a technique that we call Conflict Packing in the context of kernelization, obtaining (and improving) several polynomial kernels for editing problems on dense instances. We apply this technique on several well-studied problems:…
In the Distance-constrained Vehicle Routing Problem (DVRP), we are given a graph with integer edge weights, a depot, a set of $n$ terminals, and a distance constraint $D$. The goal is to find a minimum number of tours starting and ending at…
We study the parameterized complexity of the graph isomorphism problem when parameterized by width parameters related to tree decompositions. We apply the following technique to obtain fixed-parameter tractability for such parameters. We…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
Dynamic programming on various graph decompositions is one of the most fundamental techniques used in parameterized complexity. Unfortunately, even if we consider concepts as simple as path or tree decompositions, such dynamic programming…
Anomaly detection is a fundamental problem in domains such as healthcare, manufacturing, and cybersecurity. This thesis proposes new unsupervised methods for anomaly detection in both structured and streaming data settings. In the first…
The Minimum Quartet Tree Cost problem is to construct an optimal weight tree from the $3{n \choose 4}$ weighted quartet topologies on $n$ objects, where optimality means that the summed weight of the embedded quartet topologies is optimal…
Beyond achieving higher compression efficiency over classical image compression codecs, deep image compression is expected to be improved with additional side information, e.g., another image from a different perspective of the same scene.…