High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

As machine learning (ML) algorithms are increasingly used in medical image analysis, concerns have emerged about their potential biases against certain social groups. Although many approaches have been proposed to ensure the fairness of ML models, most existing works focus only on medical image diagnosis tasks, such as image classification and segmentation, and overlooked prognosis scenarios, which involve predicting the likely outcome or progression of a medical condition over time. To address this gap, we introduce FairTTE, the first comprehensive framework for assessing fairness in time-to-event (TTE) prediction in medical imaging. FairTTE encompasses a diverse range of imaging modalities and TTE outcomes, integrating cutting-edge TTE prediction and fairness algorithms to enable systematic and fine-grained analysis of fairness in medical image prognosis. Leveraging causal analysis techniques, FairTTE uncovers and quantifies distinct sources of bias embedded within medical imaging datasets. Our large-scale evaluation reveals that bias is pervasive across different imaging modalities and that current fairness methods offer limited mitigation. We further demonstrate a strong association between underlying bias sources and model disparities, emphasizing the need for holistic approaches that target all forms of bias. Notably, we find that fairness becomes increasingly difficult to maintain under distribution shifts, underscoring the limitations of existing solutions and the pressing need for more robust, equitable prognostic models.

Recently, smart contracts have played a vital role in automatic financial and business transactions. To help end users without programming background to better understand the logic of smart contracts, previous studies have proposed models for automatically translating smart contract source code into their corresponding code summaries. However, in practice, only 13% of smart contracts deployed on the Ethereum blockchain are associated with source code. The practical usage of these existing tools is significantly restricted. Considering that bytecode is always necessary when deploying smart contracts, in this article, we first introduce the task of automatically generating smart contract code summaries from bytecode. We propose a novel approach, named Smart Contract Bytecode Translator ( SmartBT ) for automatically translating smart contract bytecode into fine-grained natural language description directly. Two key challenges are posed for this task: structural code logic hidden in bytecode and the huge semantic gap between bytecode and natural language descriptions. To address the first challenge, we transform bytecode into Control-Flow Graph (CFG) to learn code structural and logic details. Regarding the second challenge, we introduce an information retrieval component to fetch similar comments for filling the semantic gap. Then, the structural input and semantic input are used to build an attentional sequence-to-sequence neural network model. The copy mechanism is employed to copy rare words directly from similar comments, and the coverage mechanism is employed to eliminate repetitive outputs. The automatic evaluation results show that SmartBT outperforms a set of baselines by a large margin, and the human evaluation results show the effectiveness and potential of SmartBT in producing meaningful and accurate comments for smart contract code from bytecode directly.

Predicting chemical reaction yields is pivotal for efficient chemical synthesis, an area that focuses on the creation of novel compounds for diverse uses. Yield prediction demands accurate representations of reactions for forecasting practical transformation rates. Yet, the uncertainty issues broadcasting in real-world situations prohibit current models to excel in this task owing to the high sensitivity of yield activities and the uncertainty in yield measurements. Existing models often utilize single-modal feature representations, such as molecular fingerprints, SMILES sequences, or molecular graphs, which is not sufficient to capture the complex interactions and dynamic behavior of molecules in reactions. In this paper, we present an advanced Uncertainty-Aware Multimodal model (UAM) to tackle these challenges. Our approach seamlessly integrates data sources from multiple modalities by encompassing sequence representations, molecular graphs, and expert-defined chemical reaction features for a comprehensive representation of reactions. Additionally, we address both the model and data-based uncertainty, refining the model's predictive capability. Extensive experiments on three datasets, including two high throughput experiment (HTE) datasets and one chemist-constructed Amide coupling reaction dataset, demonstrate that UAM outperforms the state-of-the-art methods. The code and used datasets are available at https://github.com/jychen229/Multimodal-reaction-yield-prediction.

Voxel grid representation of 3D scene properties has been widely used to improve the training or rendering speed of the Neural Radiance Fields (NeRF) while at the same time achieving high synthesis quality. However, these methods accelerate the original NeRF at the expense of extra storage demand, which hinders their applications in many scenarios. To solve this limitation, we present TinyNeRF, a three-stage pipeline: frequency domain transformation, pruning and quantization that work together to reduce the storage demand of the voxel grids with little to no effects on their speed and synthesis quality. Based on the prior knowledge of visual signals sparsity in the frequency domain, we convert the original voxel grids in the frequency domain via block-wise discrete cosine transformation (DCT). Next, we apply pruning and quantization to enforce the DCT coefficients to be sparse and low-bit. Our method can be optimized from scratch in an end-to-end manner, and can typically compress the original models by 2 orders of magnitude with minimal sacrifice on speed and synthesis quality.