Science based AI model certification for untrained operational environments with application in traffic state estimation

The expanding role of Artificial Intelligence (AI) in diverse engineering domains highlights the challenges associated with deploying AI models in new operational environments, involving substantial investments in data collection and model training. Rapid application of AI necessitates evaluating the feasibility of utilizing pre-trained models in unobserved operational settings with minimal or no additional data. However, interpreting the opaque nature of AI's black-box models remains a persistent challenge. Addressing this issue, this paper proposes a science-based certification methodology to assess the viability of employing pre-trained data-driven models in untrained operational environments. The methodology advocates a profound integration of domain knowledge, leveraging theoretical and analytical models from physics and related disciplines, with data-driven AI models. This novel approach introduces tools to facilitate the development of secure engineering systems, providing decision-makers with confidence in the trustworthiness and safety of AI-based models across diverse environments characterized by limited training data and dynamic, uncertain conditions. The paper demonstrates the efficacy of this methodology in real-world safety-critical scenarios, particularly in the context of traffic state estimation. Through simulation results, the study illustrates how the proposed methodology efficiently quantifies physical inconsistencies exhibited by pre-trained AI models. By utilizing analytical models, the methodology offers a means to gauge the applicability of pre-trained AI models in new operational environments. This research contributes to advancing the understanding and deployment of AI models, offering a robust certification framework that enhances confidence in their reliability and safety across a spectrum of operational conditions.

Empowering Healthcare through Privacy-Preserving MRI Analysis

In the healthcare domain, Magnetic Resonance Imaging (MRI) assumes a pivotal role, as it employs Artificial Intelligence (AI) and Machine Learning (ML) methodologies to extract invaluable insights from imaging data. Nonetheless, the imperative need for patient privacy poses significant challenges when collecting data from diverse healthcare sources. Consequently, the Deep Learning (DL) communities occasionally face difficulties detecting rare features. In this research endeavor, we introduce the Ensemble-Based Federated Learning (EBFL) Framework, an innovative solution tailored to address this challenge. The EBFL framework deviates from the conventional approach by emphasizing model features over sharing sensitive patient data. This unique methodology fosters a collaborative and privacy-conscious environment for healthcare institutions, empowering them to harness the capabilities of a centralized server for model refinement while upholding the utmost data privacy standards.Conversely, a robust ensemble architecture boasts potent feature extraction capabilities, distinguishing itself from a single DL model. This quality makes it remarkably dependable for MRI analysis. By harnessing our groundbreaking EBFL methodology, we have achieved remarkable precision in the classification of brain tumors, including glioma, meningioma, pituitary, and non-tumor instances, attaining a precision rate of 94% for the Global model and an impressive 96% for the Ensemble model. Our models underwent rigorous evaluation using conventional performance metrics such as Accuracy, Precision, Recall, and F1 Score. Integrating DL within the Federated Learning (FL) framework has yielded a methodology that offers precise and dependable diagnostics for detecting brain tumors.

Causal Prototype-inspired Contrast Adaptation for Unsupervised Domain Adaptive Semantic Segmentation of High-resolution Remote Sensing Imagery

Semantic segmentation of high-resolution remote sensing imagery (HRSI) suffers from the domain shift, resulting in poor performance of the model in another unseen domain. Unsupervised domain adaptive (UDA) semantic segmentation aims to adapt the semantic segmentation model trained on the labeled source domain to an unlabeled target domain. However, the existing UDA semantic segmentation models tend to align pixels or features based on statistical information related to labels in source and target domain data, and make predictions accordingly, which leads to uncertainty and fragility of prediction results. In this paper, we propose a causal prototype-inspired contrast adaptation (CPCA) method to explore the invariant causal mechanisms between different HRSIs domains and their semantic labels. It firstly disentangles causal features and bias features from the source and target domain images through a causal feature disentanglement module. Then, a causal prototypical contrast module is used to learn domain invariant causal features. To further de-correlate causal and bias features, a causal intervention module is introduced to intervene on the bias features to generate counterfactual unbiased samples. By forcing the causal features to meet the principles of separability, invariance and intervention, CPCA can simulate the causal factors of source and target domains, and make decisions on the target domain based on the causal features, which can observe improved generalization ability. Extensive experiments under three cross-domain tasks indicate that CPCA is remarkably superior to the state-of-the-art methods.

OpenMEDLab: An Open-source Platform for Multi-modality Foundation Models in Medicine

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

PETA: Evaluating the Impact of Protein Transfer Learning with Sub-word Tokenization on Downstream Applications

Large protein language models are adept at capturing the underlying evolutionary information in primary structures, offering significant practical value for protein engineering. Compared to natural language models, protein amino acid sequences have a smaller data volume and a limited combinatorial space. Choosing an appropriate vocabulary size to optimize the pre-trained model is a pivotal issue. Moreover, despite the wealth of benchmarks and studies in the natural language community, there remains a lack of a comprehensive benchmark for systematically evaluating protein language model quality. Given these challenges, PETA trained language models with 14 different vocabulary sizes under three tokenization methods. It conducted thousands of tests on 33 diverse downstream datasets to assess the models' transfer learning capabilities, incorporating two classification heads and three random seeds to mitigate potential biases. Extensive experiments indicate that vocabulary sizes between 50 and 200 optimize the model, whereas sizes exceeding 800 detrimentally affect the model's representational performance. Our code, model weights and datasets are available at https://github.com/ginnm/ProteinPretraining.

Multi-level Protein Representation Learning for Blind Mutational Effect Prediction

Directed evolution plays an indispensable role in protein engineering that revises existing protein sequences to attain new or enhanced functions. Accurately predicting the effects of protein variants necessitates an in-depth understanding of protein structure and function. Although large self-supervised language models have demonstrated remarkable performance in zero-shot inference using only protein sequences, these models inherently do not interpret the spatial characteristics of protein structures, which are crucial for comprehending protein folding stability and internal molecular interactions. This paper introduces a novel pre-training framework that cascades sequential and geometric analyzers for protein primary and tertiary structures. It guides mutational directions toward desired traits by simulating natural selection on wild-type proteins and evaluates the effects of variants based on their fitness to perform the function. We assess the proposed approach using a public database and two new databases for a variety of variant effect prediction tasks, which encompass a diverse set of proteins and assays from different taxa. The prediction results achieve state-of-the-art performance over other zero-shot learning methods for both single-site mutations and deep mutations.

Accurate and Definite Mutational Effect Prediction with Lightweight Equivariant Graph Neural Networks

Directed evolution as a widely-used engineering strategy faces obstacles in finding desired mutants from the massive size of candidate modifications. While deep learning methods learn protein contexts to establish feasible searching space, many existing models are computationally demanding and fail to predict how specific mutational tests will affect a protein's sequence or function. This research introduces a lightweight graph representation learning scheme that efficiently analyzes the microenvironment of wild-type proteins and recommends practical higher-order mutations exclusive to the user-specified protein and function of interest. Our method enables continuous improvement of the inference model by limited computational resources and a few hundred mutational training samples, resulting in accurate prediction of variant effects that exhibit near-perfect correlation with the ground truth across deep mutational scanning assays of 19 proteins. With its affordability and applicability to both computer scientists and biochemical laboratories, our solution offers a wide range of benefits that make it an ideal choice for the community.

SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

A Ligand-and-structure Dual-driven Deep Learning Method for the Discovery of Highly Potent GnRH1R Antagonist to treat Uterine Diseases

Gonadotrophin-releasing hormone receptor (GnRH1R) is a promising therapeutic target for the treatment of uterine diseases. To date, several GnRH1R antagonists are available in clinical investigation without satisfying multiple property constraints. To fill this gap, we aim to develop a deep learning-based framework to facilitate the effective and efficient discovery of a new orally active small-molecule drug targeting GnRH1R with desirable properties. In the present work, a ligand-and-structure combined model, namely LS-MolGen, was firstly proposed for molecular generation by fully utilizing the information on the known active compounds and the structure of the target protein, which was demonstrated by its superior performance than ligand- or structure-based methods separately. Then, a in silico screening including activity prediction, ADMET evaluation, molecular docking and FEP calculation was conducted, where ~30,000 generated novel molecules were narrowed down to 8 for experimental synthesis and validation. In vitro and in vivo experiments showed that three of them exhibited potent inhibition activities (compound 5 IC50 = 0.856 nM, compound 6 IC50 = 0.901 nM, compound 7 IC50 = 2.54 nM) against GnRH1R, and compound 5 performed well in fundamental PK properties, such as half-life, oral bioavailability, and PPB, etc. We believed that the proposed ligand-and-structure combined molecular generative model and the whole computer-aided workflow can potentially be extended to similar tasks for de novo drug design or lead optimization.