Transfer learning for genomic prediction in underrepresented populations
General Science
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Mapping global methane emissions from space with deep learning
Climate & Sustainability
GigaPath-Flash and GigaTIME-Flash: Toward population-scale discovery with efficient pathology foundation models
What if pathology foundation models could do more with less? GigaPath-Flash and GigaTIME-Flash cut computational demands while maintaining strong performance, opening the door to larger studies and broader exploration. The post GigaPath-Flash and GigaTIME-Flash: Toward population-scale discovery with efficient pathology foundation models appeared first on Microsoft Research.
Looking beyond natural sequences
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
Planetary prediction engine: Automating global models via Earth AI
Earth AI
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A Simultaneous, Multidisciplinary Development and Design Journey - Reflections on Prototyping
This paper proposes a wayfaring approach for the early concept creation stage of development projects that have a very high degree of intended innovation and thus uncertainty. The method is supported by a concrete game design example involving the development of a tangible programming interface for virtual car racing games. We focus onto projects that not only have high degrees of freedom, for example in terms of reframing the problem or iterating the final project vision, but are also complex in nature. For example, these can be projects that allow for the exploration and exploitation of unknown unknowns and serendipity findings. Process wise we are primarily focusing onto the early stage that precedes the requirement fixation, which we see as more dynamic and evolutionary in nature. The core conceptual elements that we have derived from the development experiences are: simultaneous prototyping in multiple disciplines (such as computer science, electronics and mechanics and engineering in general, abductive learning based on the outcome of rapid cycles of designing, building and testing prototypes (probing), and the importance of includingall the involved disciplines (knowledge domains) from the beginning of the project on.
PepPCBench is a Comprehensive Benchmarking Framework for Protein-Peptide Complex Structure Prediction
Accurate modeling of protein-peptide interactions is essential for understanding fundamental biological processes and designing peptide-based drugs. However, predicting the complex structures of these interactions remains challenging, primarily due to the high conformational flexibility of peptides. To support a fair and systematic evaluation of recent deep learning (DL) approaches, we introduce PepPCBench, a benchmarking framework tailored to assess protein folding neural networks (PFNNs) in protein-peptide complex prediction. As part of this framework, we curated PepPCSet, a data set of 261 experimentally resolved complexes with peptides ranging from 5 to 30 residues. We benchmark five full-atom PFNNs, including AlphaFold3 (AF3), AlphaFold-Multimer (AFM), Chai-1, HelixFold3 (HF3), and RoseTTAFold-All-Atom (RFAA), using comprehensive evaluation metrics. Our benchmarking reveals meaningful performance differences among these methods and highlights the influence of peptide length, conformational flexibility, and training set similarity on prediction accuracy. While AF3 shows strong performance in structure prediction, further analysis indicates that confidence metrics correlate poorly with experimental binding affinities, underscoring the need for improved scoring strategies and generalizability. By providing a reproducible and extensible framework, PepPCBench enables a robust evaluation of PFNN-based methods and supports their continued development for peptide-protein structure prediction.
Engineering RAG Systems for Real-World Applications: Design, Development, and Evaluation
Retrieval-Augmented Generation (RAG) systems are emerging as a key approach for grounding Large Language Models (LLMs) in external knowledge, addressing limitations in factual accuracy and contextual relevance. However, there is a lack of empirical studies that report on the development of RAG-based implementations grounded in real-world use cases, evaluated through general user involvement, and accompanied by systematic documentation of lessons learned. This paper presents five domain-specific RAG applications developed for real-world scenarios across governance, cybersecurity, agriculture, industrial research, and medical diagnostics. Each system incorporates multilingual OCR, semantic retrieval via vector embeddings, and domain-adapted LLMs, deployed through local servers or cloud APIs to meet distinct user needs. A web-based evaluation involving a total of 100 participants assessed the systems across six dimensions: (i) Ease of Use, (ii) Relevance, (iii) Transparency, (iv) Responsiveness, (v) Accuracy, and (vi) Likelihood of Recommendation. Based on user feedback and our development experience, we documented twelve key lessons learned, highlighting technical, operational, and ethical challenges affecting the reliability and usability of RAG systems in practice.
DRHIN: An Integrated and Interactive Web Server for Drug Repositioning
Drug repositioning (DR) identifies new therapeutic uses for approved drugs, reducing development burdens and offering safer treatment options for patients. While high-throughput technologies generate complex, large-scale multiomics data, existing DR tools struggle to comprehensively analyze the resulting biological networks. To address this challenge, we present DRHIN, an integrated, interactive web server for DR over heterogeneous information networks (HINs) using advanced deep learning techniques. DRHIN integrates transcriptomics, proteomics, and microbiome data, incorporating eight biological entities and 19 association types to build diverse HINs and elucidate the underlying molecular mechanisms. It includes 19 state-of-the-art graph representation algorithms, enabling flexible training, comparison, and evaluation of heterogeneous network data. The platform provides a code-free portal supporting three key predictive tasks: discovering drug-disease associations, repurposing existing drugs for new indications, and identifying potential therapies for specific diseases, making analyses accessible and reproducible. Leveraging high-performance computing, DRHIN efficiently processes million-scale networks, ensuring practical applicability in real-world scenarios. The web server is freely accessible at http://drhin.tianshanzw.cn.