Related papers: Improving Protein Optimization with Smoothed Fitne…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
The goal of protein fitness optimization is to discover new protein variants with enhanced fitness for a given use. The vast search space and the sparsely populated fitness landscape, along with the discrete nature of protein sequences,…
Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates…
A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in…
Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent advances in steering protein generative models (e.g.,…
Proteins are complex molecules responsible for different functions in nature. Enhancing the functionality of proteins and cellular fitness can significantly impact various industries. However, protein optimization using computational…
Training neural networks with high certified accuracy against adversarial examples remains an open challenge despite significant efforts. While certification methods can effectively leverage tight convex relaxations for bound computation,…
The evolutionary fitness landscape of biological molecules is extremely sparse and heterogeneous, with functional sequences forming isolated dense ``islands'' within a vast combinatorial space of largely non-functional variants. Protein…
Fitness landscapes are a useful concept to study the dynamics of meta-heuristics. In the last two decades, they have been applied with success to estimate the optimization power of several types of evolutionary algorithms, including genetic…
We propose an automated protocol for designing the energy landscape of a protein energy function by optimizing its parameters. The parameters are optimized so that not only the global minimum energy conformation becomes native-like, but…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
Recent advances in 3D Gaussian Splatting (3DGS) have focused on accelerating optimization while preserving reconstruction quality. However, many proposed methods entangle implementation-level improvements with fundamental algorithmic…
A significant challenge in nature-inspired algorithmics is the identification of specific characteristics of problems that make them harder (or easier) to solve using specific methods. The hope is that, by identifying these characteristics,…
Most real-world optimization problems are difficult to solve with traditional statistical techniques or with metaheuristics. The main difficulty is related to the existence of a considerable number of local optima, which may result in the…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Understanding the relationship between protein sequences and their functions is fundamental to protein engineering, but this task is hindered by the combinatorially vast sequence space and the experimental noise inherent in fitness…
Grasping has been a long-standing challenge in facilitating the final interface between a robot and the environment. As environments and tasks become complicated, the need to embed higher intelligence to infer from the surroundings and act…
The ability to engineer optimized protein variants has transformative potential for biotechnology and medicine. Prior sequence-based optimization methods struggle with the high-dimensional complexities due to the epistasis effect and the…
Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness…