Related papers: COCACOLA: binning metagenomic contigs using sequen…
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Improving charge carrier mobilities in organic semiconductors is a challenging task that has hitherto primarily been tackled by empirical structural tuning of promising core compounds. Knowledge-based methods can greatly accelerate such…
Effective training of today's large language models (LLMs) depends on large batches and long sequences for throughput and accuracy. To handle variable-length sequences on hardware accelerators, it is common practice to introduce padding…
We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach we combine two dimensionality reduction…
The rapid emergence of single-cell data has facilitated the study of many different biological conditions at the cellular level. Cluster analysis has been widely applied to identify cell types, capturing the essential patterns of the…
Instruction tuning is a supervised fine-tuning approach that significantly improves the ability of large language models (LLMs) to follow human instructions. We propose SelfCodeAlign, the first fully transparent and permissive pipeline for…
Ontologies are the prime way of organizing data in the Semantic Web. Often, it is necessary to combine several, independently developed ontologies to obtain a knowledge graph fully representing a domain of interest. The complementarity of…
Deep neural networks often degrade under distribution shifts. Although domain adaptation offers a solution, privacy constraints often prevent access to source data, making Test-Time Adaptation (TTA, which adapts using only unlabeled test…
Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us…
As code completion task from function-level to repository-level, leveraging contextual information from large-scale codebases becomes a core challenge. However, existing retrieval-augmented generation (RAG) methods typically treat code as…
Generating high-performance CUDA kernels remains challenging due to the need to navigate a combinatorial space of low-level transformations under noisy and expensive hardware feedback. Although large language models can synthesize…
To help address the occlusion problem in panoptic segmentation and image understanding, this paper proposes a new large-scale dataset named COCO-OLAC (COCO Occlusion Labels for All Computer Vision Tasks), which is derived from the COCO…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be…
How can we perform concolic execution to generate highly structured test inputs for systematically testing parsing programs? Existing concolic execution engines are significantly restricted by (1) input structure-agnostic path constraint…
Rapid growth of genetic databases means huge savings from improvements in their data compression, what requires better inexpensive statistical models. This article proposes automatized optimizations e.g. of Markov-like models, especially…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…