Related papers: ExpressInHost: A codon tuning tool for the express…
We consider the problem of customizing text-to-image diffusion models with user-supplied reference images. Given new prompts, the existing methods can capture the key concept from the reference images but fail to align the generated image…
Molecular evolution is the process of simulating the natural evolution of molecules in chemical space to explore potential molecular structures and properties. The relationships between similar molecules are often described through…
Accurately predicting gene mutations, mutation subtypes and their exons in lung cancer is critical for personalized treatment planning and prognostic assessment. Faced with regional disparities in medical resources and the high cost of…
Generating protein sequences that fold into a intended 3D structure is a fundamental step in de novo protein design. De facto methods utilize autoregressive generation, but this eschews higher order interactions that could be exploited to…
Generating as diverse molecules as possible with desired properties is crucial for drug discovery research, which invokes many approaches based on deep generative models today. Despite recent advancements in these models, particularly in…
Autotuning of performance-relevant source-code parameters allows to automatically tune applications without hard coding optimizations and thus helps with keeping the performance portable. In this paper, we introduce a benchmark set of ten…
To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning in the directed evolution workflow.…
Writing high-performance code requires significant expertise in the programming language, compiler optimizations, and hardware knowledge. This often leads to poor productivity and portability and is inconvenient for a non-programmer…
Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep…
Building a working mental model of a protein typically requires weeks of reading, cross-referencing crystal and predicted structures, and inspecting ligand complexes, an effort that is slow, unevenly accessible, and often requires…
We investigate the evolutionary processes behind the development and optimization of multiple threads of execution in digital organisms using the avida platform, a software package that implements Darwinian evolution on populations of…
Neural Machine Translation (NMT) has become a popular technology in recent years, and the encoder-decoder framework is the mainstream among all the methods. It's obvious that the quality of the semantic representations from encoding is very…
Cosmological hydrogen recombination has recently been the subject of renewed attention because of its importance for predicting the power spectrum of cosmic microwave background anisotropies. It has become clear that it is necessary to…
Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits.…
Detecting changepoints in a time series of length $N$ entails evaluating up to $2^{N-1}$ possible changepoint models, making exhaustive enumeration computationally infeasible. Genetic algorithms (GAs) provide a stochastic way to identify…
Computational antibody design seeks to automatically create an antibody that binds to an antigen. The binding affinity is governed by the 3D binding interface where antibody residues (paratope) closely interact with antigen residues…
Realizing the advantages of quantum computation requires access to the full Hilbert space of states of many quantum bits (qubits). Thus, large-scale quantum computation faces the challenge of efficiently generating entanglement between many…
During the software lifecycle, a program can evolve several times for different reasons such as the optimisation of a bottle-neck, the refactoring of an obscure function, etc. These code changes often involve several functions or modules,…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time…