We introduce M$^2$Hub, a toolkit for advancing machine learning in materials discovery. Machine learning has achieved remarkable progress in modeling molecular structures, especially biomolecules for drug discovery. However, the development of machine learning approaches for modeling materials structures lag behind, which is partly due to the lack of an integrated platform that enables access to diverse tasks for materials discovery. To bridge this gap, M$^2$Hub will enable easy access to materials discovery tasks, datasets, machine learning methods, evaluations, and benchmark results that cover the entire workflow. Specifically, the first release of M$^2$Hub focuses on three key stages in materials discovery: virtual screening, inverse design, and molecular simulation, including 9 datasets that covers 6 types of materials with 56 tasks across 8 types of material properties. We further provide 2 synthetic datasets for the purpose of generative tasks on materials. In addition to random data splits, we also provide 3 additional data partitions to reflect the real-world materials discovery scenarios. State-of-the-art machine learning methods (including those are suitable for materials structures but never compared in the literature) are benchmarked on representative tasks. Our codes and library are publicly available at https://github.com/yuanqidu/M2Hub.
Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experiments, previous methods have primarily relied on self-supervised models trained on vast, unlabeled protein sequence or structure datasets. While initial protein representation learning studies solely focused on either sequence or structural features, recent hybrid architectures have sought to merge these modalities to harness their respective strengths. However, these sequence-structure models have so far achieved only incremental improvements when compared to the leading sequence-only approaches, highlighting unresolved challenges effectively leveraging these modalities together. Moreover, the function of certain proteins is highly dependent on the granular aspects of their surface topology, which have been overlooked by prior models. To address these limitations, we introduce the Sequence-Structure-Surface Fitness (S3F) model - a novel multimodal representation learning framework that integrates protein features across several scales. Our approach combines sequence representations from a protein language model with Geometric Vector Perceptron networks encoding protein backbone and detailed surface topology. The proposed method achieves state-of-the-art fitness prediction on the ProteinGym benchmark encompassing 217 substitution deep mutational scanning assays, and provides insights into the determinants of protein function. Our code is at https://github.com/DeepGraphLearning/S3F.
Felix Teufel, Aaron W. Kollasch, Yining Huang et al.
Accurately predicting protein fitness with minimal experimental data is a persistent challenge in protein engineering. We introduce PRIMO (PRotein In-context Mutation Oracle), a transformer-based framework that leverages in-context learning and test-time training to adapt rapidly to new proteins and assays without large task-specific datasets. By encoding sequence information, auxiliary zero-shot predictions, and sparse experimental labels from many assays as a unified token set in a pre-training masked-language modeling paradigm, PRIMO learns to prioritize promising variants through a preference-based loss function. Across diverse protein families and properties-including both substitution and indel mutations-PRIMO outperforms zero-shot and fully supervised baselines. This work underscores the power of combining large-scale pre-training with efficient test-time adaptation to tackle challenging protein design tasks where data collection is expensive and label availability is limited.
Emerging Large Language Models (LLMs) like GPT-4 have revolutionized Natural Language Processing (NLP), showing potential in traditional tasks such as Named Entity Recognition (NER). Our study explores a three-phase training strategy that harnesses GPT-4's capabilities to enhance the BERT model's performance on NER. Initially, GPT-4 annotates a subset of the CONLL2003 and additional BBC dataset without fine-tuning. We then train BERT using a mix of original and LLM-annotated data, analyzing the efficacy of LLM annotations against traditional methods. The second phase involves comparative experiments with different training regimens, assessing the synergy between distilled and original data. We observe that sequential strategies, particularly a simple mix of training first with distilled data followed by original data, significantly boost performance. In the third phase, we investigate various data blending techniques, including sigmoid and power decay functions, to optimize the training process further. Our results indicate that a strategic mix of distilled and original data markedly elevates the NER capabilities of BERT. Our approach presents a scalable methodology that reduces manual annotation costs and increases efficiency, making it especially pertinent in resource-limited and closed-network environments. The study concludes that while the 'Simple Mix' strategy yields the best results, understanding its underlying mechanisms requires further research. Future work will also focus on refining prompt designs and enhancing annotation selection processes, aiming to extend our methodology to diverse NLP tasks.
We propose a knowledge engine called Sinoledge mainly for doctors, physicians, and researchers in medical field to organize thoughts, manage reasoning process, test and deploy to production environments effortlessly. Our proposal can be related to rule engine usually used in business or medical fields. More importantly, our proposal provides a user-friendly interface, an easy-maintain way of organizing knowledge, an understandable testing functionality and a highly available and efficient back-end architecture.
We introduce a framework for AI-based medical consultation system with knowledge graph embedding and reinforcement learning components and its implement. Our implement of this framework leverages knowledge organized as a graph to have diagnosis according to evidence collected from patients recurrently and dynamically. According to experiment we designed for evaluating its performance, it archives a good result. More importantly, for getting better performance, researchers can implement it on this framework based on their innovative ideas, well designed experiments and even clinical trials.