Research Radar

Academic Publication • Published Mar 23, 2024

Black-winged kite algorithm: a nature-inspired meta-heuristic for solving benchmark functions and engineering problems

AbstractThis paper innovatively proposes the Black Kite Algorithm (BKA), a meta-heuristic optimization algorithm inspired by the migratory and predatory behavior of the black kite. The BKA integrates the Cauchy mutation strategy and the Leader str...

Academic Publication • Published Mar 18, 2024

Predicting the Performance and Adaptation of Artificial Elbow Due to Effective Forces using Deep Learning

Measuring power transmission in organs poses a significant challenge for researchers in the field, with various methods being explored, including the use of artificial intelligence algorithms. This study focused on developing a new neural network ...

Academic Publication • Published Mar 15, 2024

MADDPG-Based Joint Service Placement and Task Offloading in MEC Empowered Air–Ground Integrated Networks

Academic Publication • Published Mar 13, 2024

Evaluation metrics and statistical tests for machine learning

AbstractResearch on different machine learning (ML) has become incredibly popular during the past few decades. However, for some researchers not familiar with statistics, it might be difficult to understand how to evaluate the performance of ML mo...

Academic Publication • Published Unknown Date

Telomere-to-Telomere Phased Genome Assembly Using HERRO-Corrected Simplex Nanopore Reads

Telomere-to-telomere phased assemblies have become the norm in genomics. To achieve these for diploid and even polyploid genomes, the contemporary approach involves a combination of two long-read sequencing technologies: high-accuracy long reads, ...

Academic Publication • Published Unknown Date

Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

Abstract The breadth of life’s diversity is unfathomable, but public nucleic acid sequencing data offers a window into the dispersion and evolution of genetic diversity across Earth. However the rapid growth and ...

Academic Publication • Published Unknown Date

Multiple Protein Structure Alignment at Scale with FoldMason

Abstract Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended our r...

Academic Publication • Published Unknown Date

Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear baselines

Abstract Advanced deep-learning methods, such as foundation models, promise to learn representations of biology that can be employed to predict in silico the outcome of unseen ...

Academic Publication • Published Unknown Date

BindCraft: one-shot design of functional protein binders

Abstract Protein–protein interactions (PPIs) are at the core of all key biological processes. However, the complexity of the structural features that determine PPIs makes their design challenging. We present Bind...

Academic Publication • Published Unknown Date

Boltz-1 Democratizing Biomolecular Interaction Modeling

Abstract Understanding biomolecular interactions is fundamental to advancing fields like drug discovery and protein design. In this paper, we introduce B oltz -1, an open-sourc...

Academic Publication • Published Unknown Date

Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction

In this technical report, we present Protenix, a comprehensive reproduction of AlphaFold3 (AF3), aimed at advancing the field of biomolecular structure prediction. Protenix tackles the challenges of predicting complex interactions involving protei...

Academic Publication • Published Unknown Date

Have protein-ligand cofolding methods moved beyond memorisation?

Abstract Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with small molecule ligands, to enable real-...

Academic Publication • Published Unknown Date

Rēs ipSAE loquuntur : What’s wrong with AlphaFold’s ipTM score and how to fix it

Abstract AlphaFold’s ipTM metric is used to predict the accuracy of structural predictions of protein-protein interactions (PPIs) and the probability that two proteins interact...

Academic Publication • Published Unknown Date

Cellpose-SAM: superhuman generalization for cellular segmentation

Modern algorithms for biological segmentation can match inter-human agreement in annotation quality. This however is not a performance bound: a hypothetical human-consensus segmentation could reduce error rates in half. To obtain a model that gene...

Academic Publication • Published Unknown Date

Biomni: A General-Purpose Biomedical AI Agent

Abstract Biomedical research underpins progress in our understanding of human health and disease, drug discovery, and clinical care. However, with the growth of complex lab experiments, large datasets, many analy...

Academic Publication • Published Unknown Date

Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction

Abstract Accurately modeling biomolecular interactions is a central challenge in modern biology. While recent advances, such as AlphaFold3 and Boltz-1, have substantially improved our ability to predict biomolecu...

Academic Publication • Published Unknown Date

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Deep learning models that predict functional genomic measurements from DNA sequence are powerful tools for deciphering the genetic regulatory code. Existing methods trade off between input sequence length and prediction resolution, thereby limitin...

Academic Publication • Published Unknown Date

Corrective Retrieval Augmented Generation

Academic Publication • Published Unknown Date

Self-organized Electrical Nanostructure of DND  in Multi  -Layered  Nanostructures Espatterning

Academic Publication • Published Unknown Date

Nano-optical wafers are produced using the nano-lithography process on wafers with a diameter of 100 or 150 mm. Nano-optical chips are created from small wafers