Related papers: AlphaFold two years on: validation and impact
The brain is a powerful tool used to achieve amazing feats. There have been several significant advances in neuroscience and artificial brain research in the past two decades. This article is a review of such advances, ranging from the…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
The AlphaFold computer program predicted protein structures for the whole human genome, which has been considered as a remarkable breakthrough both in artificial intelligence (AI) application and structural biology. Despite the varying…
Determining the factors that have an influence on software systems development and deployment project outcomes has been the focus of extensive and ongoing research for more than 30 years. We provide here a survey of the research literature…
We present an overview of how certain computational tools currently interact with mathematical practice, and reflect on the implications for research mathematics in the short to medium term, as the field navigates the emerging age of AI and…
Validation is often defined as the process of determining the degree to which a model is an accurate representation of the real world from the perspective of its intended uses. Validation is crucial as industries and governments depend…
There are many dimensions of software complexity. In this article, we explore how structural complexity is measured and used to study and control evolving software systems. We also present the current research challenges and emerging trends…
Two-dimensional patterns are used in many research areas in computer science, ranging from image processing to specification and verification of complex software systems (via scenarios). The contribution of this paper is twofold. First, we…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
AI systems represented by AlphaFold are rapidly expanding the scale of protein structure modelling data, and the MineProt project provides an effective solution for custom curation of these novel high-throughput data. It enables researchers…
How do protein structure prediction models fold proteins? We investigate this question by tracing how ESMFold folds a beta hairpin, a prevalent structural motif. Through counterfactual interventions on model latents, we identify two…
Diffusion models have revolutionized generative tasks through high-fidelity outputs, yet flow matching (FM) offers faster inference and empirical performance gains. However, current foundation FM models are computationally prohibitive for…
Background: This invited paper is the result of an invitation to write a retrospective article on a "TSE most influential paper" as part of the journal's 50th anniversary. Objective: To reflect on the progress of software engineering…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
RecBole has recently attracted increasing attention from the research community. As the increase of the number of users, we have received a number of suggestions and update requests. This motivates us to make some significant improvements…
ACL2 has long supported user-defined simplifiers, so-called metafunctions and clause processors, which are installed when corresponding rules of class :meta or :clause-processor are proved. Historically, such simplifiers could access the…
Displaying confidence scores in human-AI interaction has been shown to help build trust between humans and AI systems. However, most existing research uses only the confidence score as a form of communication. As confidence scores are just…
AI-based decision-making tools are rapidly spreading across a range of real-world, complex domains like healthcare, criminal justice, and child welfare. A growing body of research has called for increased scrutiny around the validity of AI…
Protein structures and functions are determined by a contiguous arrangement of amino acid sequences. Designing novel protein sequences and structures with desired geometry and functions is a complex task with large state spaces. Here we…
We will discuss recent results for the spin structure functions, with an emphasis on g2 . High precision g2 data allows for tests of the Burkhardt-Cottingham sum rule, and is needed to consistently evaluate higher twist effects.