Related papers: Bridging the Gaps in Statistical Models of Protein…

Bounding chains are a technique that offers three benefits to Markov chain practitioners: a theoretical bound on the mixing time of the chain under restricted conditions, experimental bounds on the mixing time of the chain that are provably…

Markov state models (MSMs) are a widely used method for approximating the eigenspectrum of the molecular dynamics propagator, yielding insight into the long-timescale statistical kinetics and slow dynamical modes of biomolecular systems.…

Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…

Protein language models (pLMs) have shown strong potential for zero-shot prediction of missense variant effects, yet systematic benchmarking on viral proteins remains limited, a critical gap given the need for proactive tools that can…

We propose an optimized parameter set for protein secondary structure prediction using three layer feed forward back propagation neural network. The methodology uses four parameters viz. encoding scheme, window size, number of neurons in…

Optimal designs minimize the number of experimental runs (samples) needed to accurately estimate model parameters, resulting in algorithms that, for instance, efficiently minimize parameter estimate variance. Governed by knowledge of past…

By virtue of its great utility in solving real-world problems, optimization modeling has been widely employed for optimal decision-making across various sectors, but it requires substantial expertise from operations research professionals.…

Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…

Benchmarks are the de facto standard for tracking progress in large language models (LLMs), yet static test sets can rapidly saturate, become vulnerable to contamination, and are costly to refresh. Scalable evaluation of open-ended items…

The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…

This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling…

Pre-trained models have been successful in many protein engineering tasks. Most notably, sequence-based models have achieved state-of-the-art performance on protein fitness prediction while structure-based models have been used…

Hidden Markov Models (HMM) model a sequence of observations that are dependent on a hidden (or latent) state that follow a Markov chain. These models are widely used in diverse fields including ecology, speech recognition, and…

In this study, we expand upon the FLIP benchmark-designed for evaluating protein fitness prediction models in small, specialized prediction tasks-by assessing the performance of state-of-the-art large protein language models, including…

Machine Learning (ML) has transformed many scientific fields, yet key applications still lack standardized benchmarks. Raman spectroscopy, a widely used technique for non-invasive molecular analysis, is one such field where progress is…

We propose a two-stage estimation method of variance components in time series models known as FDSLRMs, whose observations can be described by a linear mixed model (LMM). We based estimating variances, fundamental quantities in a time…

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research.…

State-space models (SSM) with Markov switching offer a powerful framework for detecting multiple regimes in time series, analyzing mutual dependence and dynamics within regimes, and asserting transitions between regimes. These models…

Motivated by disease progression-related studies, we propose an estimation method for fitting general non-homogeneous multi-state Markov models. The proposal can handle many types of multi-state processes, with several states and various…

Reward models (RMs) guide the alignment of large language models (LLMs), steering them toward behaviors preferred by humans. Evaluating RMs is the key to better aligning LLMs. However, the current evaluation of RMs may not directly…