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Evolutionary computing, particularly genetic algorithm (GA), is a combinatorial optimization method inspired by natural selection and the transmission of genetic information, which is widely used to identify optimal solutions to complex…
Graph Convolutional Networks (GCNs), particularly for large-scale graphs, are crucial across numerous domains. However, training distributed full-batch GCNs on large-scale graphs suffers from inefficient memory access patterns and high…
Motif discovery in DNA sequences is a challenging task in molecular biology. In computational motif discovery, Planted (l, d) motif finding is a widely studied problem and numerous algorithms are available to solve it. Both hardware and…
By exploiting discrete signal processing and simulating brain neuron communication, Spiking Neural Networks (SNNs) offer a low-energy alternative to Artificial Neural Networks (ANNs). However, existing SNN models, still face high…
For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs have been two significant challenges for developing a programmable high-performance graph library.…
We describe the multi-GPU gradient boosting algorithm implemented in the XGBoost library (https://github.com/dmlc/xgboost). Our algorithm allows fast, scalable training on multi-GPU systems with all of the features of the XGBoost library.…
We present a gravitational hierarchical N-body code that is designed to run efficiently on Graphics Processing Units (GPUs). All parts of the algorithm are executed on the GPU which eliminates the need for data transfer between the Central…
As large language models move toward million-token context windows, CPU tokenizers become a major slowdown because they process text one step at a time while powerful GPUs sit unused. We built a GPU-based byte-level BPE tokenizer that…
In a connected world, spare CPU cycles are up for grabs, if you only make its obtention easy enough. In this paper we present a distributed evolutionary computation system that uses the computational capabilities of the ubiquituous web…
We present results of the implementation of one MILC lattice QCD application-simulation with dynamical clover fermions using the hybrid-molecular dynamics R algorithm-on the Cell Broadband Engine processor. Fifty-four individual…
Graph Convolutional Networks (GCNs) have emerged as the state-of-the-art deep learning model for representation learning on graphs. It is challenging to accelerate training of GCNs, due to (1) substantial and irregular data communication to…
The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…
We introduce a fusion of GPU accelerated primal heuristics for Mixed Integer Programming. Leveraging GPU acceleration enables exploration of larger search regions and faster iterations. A GPU-accelerated PDLP serves as an approximate LP…
In a Gray-Box Optimization (GBO) setting that allows for partial evaluations, the fitness of an individual can be updated efficiently after a subset of its variables has been modified. This enables more efficient evolutionary optimization…
Current GP frameworks are highly effective on a range of real and simulated benchmarks. However, due to the high dimensionality of the genotypes for GP, the task of visualising the fitness landscape for GP search can be difficult. This…
A bottleneck for multi-timescale dynamics is the computation of the potential energy surface (PES). We explore the use of genetic programming (GP) to symbolically regress a mapping of the saddle-point barriers from only a few calculated…
In this work, we present an extension of Gaussian process (GP) models with sophisticated parallelization and GPU acceleration. The parallelization scheme arises naturally from the modular computational structure w.r.t. datapoints in the…
This paper proposes Genetic Algorithm with Border Trades (GAB), a novel modification of the standard genetic algorithm that enhances exploration by incorporating new chromosome patterns in the breeding process. This approach significantly…
Biological machine learning is often bottlenecked by a lack of scaled data. One promising route to relieving data bottlenecks is through high throughput screens, which can experimentally test the activity of $10^6-10^{12}$ protein sequences…
This work proposes a novel approach to evaluate and analyze the behavior of multi-population parallel genetic algorithms (PGAs) when running on a cluster of multi-core processors. In particular, we deeply study their numerical and…