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We present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The…
Across a wide range of hardware scenarios, the computational efficiency and physical size of the arithmetic units significantly influence the speed and footprint of the overall hardware system. Nevertheless, the effectiveness of prior…
We present linear-time algorithms for partitioning a path or a tree with weights on the vertices by removing $k$ edges to maximize the minimum-weight component. We also use the same framework to partition a path with weight on the vertices,…
Decision trees are highly famous in machine learning and usually acquire state-of-the-art performance. Despite that, well-known variants like CART, ID3, random forest, and boosted trees miss a probabilistic version that encodes prior…
The aim of this paper is to check feasibility of using the maximal-entropy random walk in algorithms finding communities in complex networks. A number of such algorithms exploit an ordinary or a biased random walk for this purpose. Their…
The quality of mesh generation has long been considered a vital aspect in providing engineers with reliable simulation results throughout the history of the Finite Element Method (FEM). The element extraction method, which is currently the…
Recent research has shown that optimal picker tours in rectangular warehouses exhibit deterministic travel patterns within each aisle, and that certain previously considered traversals are unnecessary. Using these insights, this paper…
We develop a new Markov chain on graph partitions that makes relatively global moves yet is computationally feasible to be used as the proposal in the Metropolis-Hastings method. Our resulting algorithm can be made reversible and able to…
Contemporary accelerator designs exhibit a high degree of spatial localization, wherein two-dimensional physical distance determines communication costs between processing elements. This situation presents considerable algorithmic…
Gravitational $N$-body simulations calculate numerous interactions between particles. The tree algorithm reduces these calculations by constructing a hierarchical oct-tree structure and approximating gravitational forces on particles. Over…
Large Language Models (LLMs) have achieved significant advances in reasoning tasks. A key approach is tree-based search with verifiers, which expand candidate reasoning paths and use reward models to guide pruning and selection. Although…
Embedded systems have proliferated in various consumer and industrial applications with the evolution of Cyber-Physical Systems and the Internet of Things. These systems are subjected to stringent constraints so that embedded software must…
The present work attempts to integrate the independent efforts in the fast N-body community to create the fastest N-body library for many-core and heterogenous architectures. Focus is placed on low accuracy optimizations, in response to the…
As the demand for computational power grows, optimizing code through compilers becomes increasingly crucial. In this context, we focus on fully automatic code optimization techniques that automate the process of selecting and applying code…
Decision trees have been a very popular class of predictive models for decades due to their interpretability and good performance on categorical features. However, they are not always robust and tend to overfit the data. Additionally, if…
Treemaps have been used in information visualisation for over two decades. They make use of nested filled areas to represent information hierarchies such as file systems, library catalogues, etc. Recent years have witnessed the emergence of…
Tree-structured LSTM is promising way to consider long-distance interaction over hierarchies. However, there have been few research efforts on the hyperparameter tuning of the construction and traversal of tree-structured LSTM. To name a…
Data intensive applications on clusters often require requests quickly be sent to the node managing the desired data. In many applications, one must look through a sorted tree structure to determine the responsible node for accessing or…
While modern biotechnologies allow synthesizing new proteins and function measurements at scale, efficiently exploring a protein sequence space and engineering it remains a daunting task due to the vast sequence space of any given protein.…
The rapid technological evolution has accelerated software development for various domains and use cases, contributing to a growing share of global carbon emissions. While recent large language models (LLMs) claim to assist developers in…