Fetal ultrasound screening is a uniquely complex diagnostic task involving the simultaneous assessment of multiple fetal organs—each with its own anatomical and clinical context—within a single examination. Automating report generation for such cases poses a significant challenge: unlike existing methods that focus on single-organ radiology tasks (e.g., chest X-rays), fetal ultrasound requires reasoning over a structured, multiple-to-multiple setting, i.e., multi-organ images corresponding to a multi-section report. In this paper, we introduce FetusR, the first large-scale dataset for multi-organ fetal ultrasound reporting, containing 15,594 real-world cases with rich organ-wise annotations. To address the intrinsic image-report alignment, we propose Organ-Aware Routing Mixture-of-Retrieval Augmented Generation (ORM-RAG) inspired by the Mixture-of-Experts paradigm. Our method decomposes the complex alignment problem into multiple one-to-one sub-retrieval tasks. Specifically, ORM-RAG integrates (1) an organ-aware mixture-of-retrieval module that partitions the retrieval space into organ-specific corpora for independent retrieval, and (2) a dynamic routing mechanism that selectively aggregates high-confidence organ-specific reports while filtering uncertain ones. Extensive experiments demonstrate that our method significantly outperforms state-of-the-art baselines across both textual similarity and clinical accuracy metrics. Our work opens a new direction for long-form, structured report generation in real-world, multi-organ medical imaging scenarios.

MOTIVATION: Single-cell RNA sequencing (scRNA-Seq) technology enables detailed exploration of gene expression at the individual cell level, crucial for annotating cell types and understanding cellular diversity. Traditional methods for cell type annotation often rely on marker genes and manual labeling, posing challenges due to low data quality and incomplete reference datasets. RESULTS: We developed CeLLTra, a novel contrastive learning framework that leverages a Transformer-based model integrating biological pathway information to group genes into super tokens, effectively capturing comprehensive gene expression from scRNA-Seq data. By combining this pathway-informed Transformer with a pretrained domain-specific language model, CeLLTra accurately aligns cell-type annotations with gene expression profiles. Evaluations on a large-scale human scRNA-Seq dataset showed that CeLLTra significantly outperformed state-of-the-art methods in supervised and zero-shot cell-type prediction. Additionally, CeLLTra generalized well to external datasets, improving clustering performance and enabling better characterization of cancerous cell states in tumor-infiltrating myeloid cells from non-small cell lung cancer patients. AVAILABILITY AND IMPLEMENTATION: CeLLTra is freely available on GitHub (https://github.com/WJZheng-group/CeLLTra) and Zenodo (https://doi.org/10.5281/zenodo.17666735). The datasets underlying this article are the following: GSE201333 and GSE127465. All these datasets are publicly available and can be freely accessed on the Gene Expression Omnibus repository.

BACKGROUND: The potential benefits of drug combination synergy in cancer medicine are significant, yet the risks must be carefully managed due to the possibility of increased toxicity. Although artificial intelligence applications have demonstrated notable success in predicting drug combination synergy, several key challenges persist: (1) Existing models often predict average synergy values across a restricted range of testing dosages, neglecting crucial dose amounts and the mechanisms of action of the drugs involved. (2) Many graph-based models rely on static protein-protein interactions, failing to adapt to dynamic and higher-order relationships. These limitations constrain the applicability of current methods. RESULTS: We introduce SAFER, a Sub-hypergraph Attention-based graph model, addressing these issues by incorporating complex relationships among biological knowledge networks and considering dosing effects on subject-specific networks. SAFER outperformed previous models on the benchmark and the independent test set. The analysis of subgraph attention weight for the lung cancer cell line highlighted JAK-STAT signaling pathway, PRDM12, ZNF781, and CDC5L that have been implicated in lung fibrosis. CONCLUSIONS: SAFER presents an interpretable framework designed to identify drug-responsive signals. Tailored for comprehending dose effects on subject-specific molecular contexts, our model uniquely captures dose-level drug combination responses. This capability unlocks previously inaccessible avenues of investigation compared to earlier models. Furthermore, the SAFER framework can be leveraged by future inquiries to investigate molecular networks that uniquely characterize individual patients and can be applied to prioritize personalized effective treatment based on safe dose combinations.

We address security issues in a cloud database system which employs the DBaaS model --- a data owner (DO) exports data to a cloud database service provider (SP). To provide data security, sensitive data is encrypted by the DO before it is uploaded to the SP. Compared to existing secure query processing systems like CryptDB [7] and MONOMI [8], in which data operations (e.g., comparison or addition) are supported by specialized encryption schemes, our demo system, SDB, is implemented based on a set of data-interoperable secure operators, i.e., the output of an operator can be used as input of another operator. As a result, SDB can support a wide range of complex queries (e.g., all TPC-H queries) efficiently. In this demonstration, we show how our SDB prototype supports secure query processing on complex workload like TPC-H. We also demonstrate how our system protects sensitive information from malicious attackers.

We address security issues in a cloud database system which employs the DBaaS model. In such a model, a data owner (DO) exports its data to a cloud database service provider (SP). To provide data security, sensitive data is encrypted by the DO before it is uploaded to the SP. Existing encryption schemes, however, are only partially homomorphic in the sense that each of them was designed to allow one specific type of computation to be done on encrypted data. These existing schemes cannot be integrated to answer real practical queries that involve operations of different kinds. We propose and analyze a secure query processing system (SDB) on relational tables and a set of elementary operators on encrypted data that allow data interoperability, which allows a wide range of SQL queries to be processed by the SP on encrypted information. We prove that our encryption scheme is secure against two types of threats and that it is practically efficient.