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In the acceleration of deep neural network training, the GPU has become the mainstream platform. GPUs face substantial challenges on GNNs, such as workload imbalance and memory access irregularities, leading to underutilized hardware.…

We have recently used genetic programming to automatically generate an improved version of Langmead's DNA read alignment tool Bowtie2 Sect.5.3 RN/12/09. We find it runs more than four times faster than the Bioinformatics sequencing tool…

Parameter-efficient fine-tuning methods such as LoRA enable efficient adaptation of large pretrained models but often fall short of full fine-tuning performance. Existing approaches focus on aligning parameter updates, which only indirectly…

Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…

Solving quantifier-free non-linear real arithmetic (NRA) problems is a computationally hard task. To tackle this problem, prior work proposed a promising approach based on gradient descent. In this work, we extend their ideas and combine…

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…

Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic…

Nowadays, GPU accelerators are commonly used to speed up general-purpose computing tasks on a variety of hardware. However, due to the diversity of GPU architectures and processed data, optimization of codes for a particular type of…

Aim/Introduction: Distance-encoding biomorphic-informational neural network (DEBI-NN) is a recently proposed architecture in which connection weights are defined by the distances between neurons positioned in a Euclidian space. This…

Range minimum queries are frequently used in string processing and database applications including biological sequence analysis, document retrieval, and web search. Hence, various data structures have been proposed for improving their…

Loopy Belief Propagation (LBP) is a widely used approximate inference algorithm in probabilistic graphical models, with applications in computer vision, error correction codes, protein folding, program analysis, etc. However, LBP faces…

As recurrent neural networks become larger and deeper, training times for single networks are rising into weeks or even months. As such there is a significant incentive to improve the performance and scalability of these networks. While…

Designing novel proteins with desired characteristics remains a significant challenge due to the large sequence space and the complexity of sequence-function relationships. Efficient exploration of this space to identify sequences that meet…

We study optimization algorithms based on variance reduction for stochastic gradient descent (SGD). Remarkable recent progress has been made in this direction through development of algorithms like SAG, SVRG, SAGA. These algorithms have…

As the size of models and datasets grows, it has become increasingly common to train models in parallel. However, existing distributed stochastic gradient descent (SGD) algorithms suffer from insufficient utilization of computational…

In the context of the genome-wide association studies (GWAS), one has to solve long sequences of generalized least-squares problems; such a task has two limiting factors: execution time --often in the range of days or weeks-- and data…

In recent years, deep learning methods applying unsupervised learning to train deep layers of neural networks have achieved remarkable results in numerous fields. In the past, many genetic algorithms based methods have been successfully…

Dynamic Graph Neural Networks (DGNNs) are becoming increasingly popular due to their effectiveness in analyzing and predicting the evolution of complex interconnected graph-based systems. However, hardware deployment of DGNNs still remains…

Training on edge devices poses several challenges as these devices are generally resource-constrained, especially in terms of power. State-of-the-art techniques at the device level reduce the GPU frequency to enforce power constraints,…

Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…