Search Results for author: Michail Mamalakis

Found 8 papers, 6 papers with code

TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering

1 code implementation27 Aug 2024 Yiqing Shen, Zan Chen, Michail Mamalakis, Yungeng Liu, Tianbin Li, Yanzhou Su, Junjun He, Pietro Liò, Yu Guang Wang

While large language models (LLMs) have achieved much progress in the domain of natural language processing, their potential in protein engineering remains largely unexplored.

Multiple-choice Protein Folding

A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding

1 code implementation8 Jun 2024 Yiqing Shen, Zan Chen, Michail Mamalakis, Luhan He, Haiyang Xia, Tianbin Li, Yanzhou Su, Junjun He, Yu Guang Wang

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding.

Descriptive Language Modelling +2

Contrastive-Adversarial and Diffusion: Exploring pre-training and fine-tuning strategies for sulcal identification

no code implementations29 May 2024 Michail Mamalakis, Héloïse de Vareilles, Shun-Chin Jim Wu, Ingrid Agartz, Lynn Egeland Mørch-Johnsen, Jane Garrison, Jon Simons, Pietro Lio, John Suckling, Graham Murray

Techniques like adversarial learning, contrastive learning, diffusion denoising learning, and ordinary reconstruction learning have become standard, representing state-of-the-art methods extensively employed for fully training or pre-training networks across various vision tasks.

Contrastive Learning Denoising

Solving the enigma: Deriving optimal explanations of deep networks

1 code implementation16 May 2024 Michail Mamalakis, Antonios Mamalakis, Ingrid Agartz, Lynn Egeland Mørch-Johnsen, Graham Murray, John Suckling, Pietro Lio

In this study, for the first time, we propose a novel framework designed to enhance the explainability of deep networks, by maximizing both the accuracy and the comprehensibility of the explanations.

Binary Classification Decision Making

A novel framework employing deep multi-attention channels network for the autonomous detection of metastasizing cells through fluorescence microscopy

1 code implementation2 Sep 2023 Michail Mamalakis, Sarah C. Macfarlane, Scott V. Notley, Annica K. B Gad, George Panoutsos

The method relies on fluorescence microscopy images showing the spatial organization of actin and vimentin filaments in normal and metastasizing single cells, using a combination of multi-attention channels network and global explainable techniques.

Diagnostic

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