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Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
Sampling-based decoding underlies complex reasoning in large language models (LLMs), where decoding strategies critically shape model behavior. Temperature- and truncation-based methods reshape the next-token distribution through global…
To accelerate the HMC with field transformation, we consider a variant of the trivializing map, the decimation map, which can be regarded as a coarse-graining transformation. Using the 2D $U(1)$ pure gauge model, combined with the guided…
Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be…
Logically constrained rewrite systems (LCTRSs) are a versatile and efficient rewriting formalism that can be used to model programs from various programming paradigms, as well as simplification systems in compilers and SMT solvers. In this…
In this paper we propose an approach for computing multiple high-quality near-isometric dense correspondences between a pair of 3D shapes. Our method is fully automatic and does not rely on user-provided landmarks or descriptors. This…
In 2016, Chandrasekaran, V\'egh, and Vempala published a method to solve the minimum-cost perfect matching problem on an arbitrary graph by solving a strictly polynomial number of linear programs. However, their method requires a strong…
In connection with the needs of solving optimization problems, the development of conditional minimization methods with convenient numerical implementation continues to attract the attention of mathematicians. In this monograph we propose…
We present a new nonlinear dimensionality reduction method, MAPLE, that enhances UMAP by improving manifold modeling. MAPLE employs a self-supervised learning approach to more efficiently encode low-dimensional manifold geometry. Central to…
Improving renewable energy resource utilization efficiency is crucial to reducing carbon emissions, and multi-parametric programming has provided a systematic perspective in conducting analysis and optimization toward this goal in smart…
Subgraph matching is a fundamental problem in graph analysis with a wide range of applications. However, due to its inherent NP-hardness, enumerating subgraph matches efficiently on large real-world graphs remains highly challenging. Most…
Designing accelerators for resource- and power-constrained applications is a daunting task. High-level Synthesis (HLS) addresses these constraints through resource sharing, an optimization at the HLS binding stage that maps multiple…
Cooperative co-evolution (CC) algorithms, based on the divide-and-conquer strategy, have emerged as the predominant approach to solving large-scale global optimization (LSGO) problems. The efficiency and accuracy of the grouping stage…
Resource balancing has been effectively used to mitigate the long-term aging effects of Negative Bias Temperature Instability (NBTI) in multi-core and Graphics Processing Unit (GPU) architectures. In this work, we investigate this strategy…
In this paper, we consider tree decompositions, branch decompositions, and clique decompositions. We improve the running time of dynamic programming algorithms on these graph decompositions for a large number of problems as a function of…
Partitioning for load balancing is a crucial first step to parallelize any type of computation. In this work, we propose SGORP, a new spatial partitioning method based on Subgradient Optimization, to solve the $d$-dimensional Rectilinear…
Several variants of the Constraint Satisfaction Problem have been proposed and investigated in the literature for modelling those scenarios where solutions are associated with some given costs. Within these frameworks computing an optimal…
Coarse-graining (CG) accelerates molecular simulations of protein dynamics by simulating sets of atoms as singular beads. Backmapping is the opposite operation of bringing lost atomistic details back from the CG representation. While…
Packing optimization is a prevalent problem that necessitates robust and efficient algorithms that are also simple to implement. One group of approaches is the raster methods, which rely on approximating the objects with pixelated…
In a large-scale and distributed matrix multiplication problem $C=A^{\intercal}B$, where $C\in\mathbb{R}^{r\times t}$, the coded computation plays an important role to effectively deal with "stragglers" (distributed computations that may…