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Received — 15 September 2026 ⏭

Multi-Modal Time Series Prediction via Mixture of Modulated Experts

✇cs.AI, q-bio.NC updates on arXiv.org
By: Lige Zhang · Ali Maatouk · Jialin Chen · Karthik Charan Konduri · Leandros Tassiulas · Rex Ying
14 September 2026 at 12:00
arXiv:2601.21547v3 Announce Type: replace-cross Abstract: Real-world time series exhibit complex and evolving dynamics, making accurate forecasting extremely challenging. Recent multi-modal forecasting methods leverage textual information such as news reports to improve prediction, but most rely on token-level fusion that mixes temporal patches with language tokens in a shared embedding space. However, such fusion can be ill-suited when high-quality time-text pairs are scarce and when time series exhibit substantial variation in characteristics, thus complicating cross-modal alignment. In parallel, mixture-of-experts (MoE) architectures have proven effective for both time series modeling and multi-modal learning, yet many existing MoE-based modality integration methods still depend on token-level fusion. To address this, we propose Expert Modulation, a new mechanism for multi-modal time series prediction that conditions both routing and expert computation on textual signals, enabling direct and efficient cross-modal control over expert behavior. Through theoretical analysis and experiments, our proposed method demonstrates strong improvements in multi-modal time series prediction. The current code implementation is available at https://github.com/BruceZhangReve/MoME
Received — 26 March 2026 ⏭

Fluid-Derived Organoids from Pleural Effusion and Ascites: Emerging Models for Drug Resistance and Personalized Oncology

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Yongyang Chen · Xiaoqing Xu · Jialin Chen · Miao Yin · Jinhui Chen · Zhanghua Qi · Ming Shi · Wenmei Su
23 March 2026 at 18:00

J Cancer. 2026 Mar 4;17(3):614-625. doi: 10.7150/jca.127511. eCollection 2026.

ABSTRACT

Malignant pleural effusion (MPE) and malignant ascites (MA) are common complications in advanced-stage cancers, often signifying disease progression and resistance to treatment. Compared to tissue biopsies or surgical specimens, materials derived from effusions offer advantages such as minimal invasiveness, ease of accessibility, and the feasibility of repeated collection during therapeutic interventions. Organoids generated from tumor cells in effusions, termed fluid-derived organoids (FDOs), have demonstrated the ability to maintain genetic heterogeneity and accurately replicate patient-specific tumor phenotypes. These characteristics position FDOs as promising models for investigating drug resistance mechanisms and informing personalized oncology strategies. In the context of lung cancer, organoids derived from pleural effusions have been employed to study acquired resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors and immunotherapy. Similarly, in ovarian and gastrointestinal cancers, organoids derived from ascites have proven to be valuable platforms for examining chemotherapy resistance and conducting drug sensitivity testing. FDOs have shown significant potential for translational applications by effectively correlating ex vivo drug responses with clinical outcomes, thus facilitating real-time monitoring of resistance evolution. However, several challenges remain, such as achieving culture standardization, maintaining the integrity of tumor microenvironment components, and integrating with multi-omics approaches. This review provides a comprehensive overview of recent advancements in the use of pleural effusion- and ascites-derived organoids for drug resistance research, underscores their applications in personalized oncology, and explores future research directions.

PMID:41869438 | PMC:PMC13003542 | DOI:10.7150/jca.127511

Fluid-Derived Organoids from Pleural Effusion and Ascites: Emerging Models for Drug Resistance and Personalized Oncology

✇Omics In Lung
By: Yongyang Chen · Xiaoqing Xu · Jialin Chen · Miao Yin · Jinhui Chen · Zhanghua Qi · Ming Shi · Wenmei Su
23 March 2026 at 18:00

J Cancer. 2026 Mar 4;17(3):614-625. doi: 10.7150/jca.127511. eCollection 2026.

ABSTRACT

Malignant pleural effusion (MPE) and malignant ascites (MA) are common complications in advanced-stage cancers, often signifying disease progression and resistance to treatment. Compared to tissue biopsies or surgical specimens, materials derived from effusions offer advantages such as minimal invasiveness, ease of accessibility, and the feasibility of repeated collection during therapeutic interventions. Organoids generated from tumor cells in effusions, termed fluid-derived organoids (FDOs), have demonstrated the ability to maintain genetic heterogeneity and accurately replicate patient-specific tumor phenotypes. These characteristics position FDOs as promising models for investigating drug resistance mechanisms and informing personalized oncology strategies. In the context of lung cancer, organoids derived from pleural effusions have been employed to study acquired resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors and immunotherapy. Similarly, in ovarian and gastrointestinal cancers, organoids derived from ascites have proven to be valuable platforms for examining chemotherapy resistance and conducting drug sensitivity testing. FDOs have shown significant potential for translational applications by effectively correlating ex vivo drug responses with clinical outcomes, thus facilitating real-time monitoring of resistance evolution. However, several challenges remain, such as achieving culture standardization, maintaining the integrity of tumor microenvironment components, and integrating with multi-omics approaches. This review provides a comprehensive overview of recent advancements in the use of pleural effusion- and ascites-derived organoids for drug resistance research, underscores their applications in personalized oncology, and explores future research directions.

PMID:41869438 | PMC:PMC13003542 | DOI:10.7150/jca.127511

Received — 25 February 2026 ⏭

Towards A Universal Graph Structural Encoder

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jialin Chen · Haolan Zuo · Haoyu Peter Wang · Siqi Miao · Pan Li · Rex Ying
24 February 2026 at 13:00
arXiv:2504.10917v2 Announce Type: replace-cross Abstract: Recent advancements in large-scale pre-training have shown the potential to learn generalizable representations for downstream tasks. In the graph domain, however, capturing and transferring structural information across different graph domains remains challenging, primarily due to the inherent differences in graph topological patterns across various contexts. For example, a social network's structure is fundamentally different from that of a product co-purchase graph. Additionally, most existing models struggle to capture the rich topological complexity of graph structures, leading to inadequate exploration of the graph embedding space. To address these challenges, we propose GFSE, a universal pre-trained graph encoder designed to capture transferable structural patterns across diverse domains such as the web graph, social networks, and citation networks. GFSE is the first cross-domain graph structural encoder pre-trained with multiple self-supervised learning objectives. Built on a Graph Transformer, GFSE incorporates attention mechanisms informed by graph structural information, enabling it to encode intricate multi-level and fine-grained topological features within complex graph structures. The pre-trained GFSE produces generic and theoretically expressive positional and structural encoding for graphs, which can be seamlessly integrated with various downstream graph feature encoders, including graph neural networks for vectorized features and Large Language Models (LLMs) for text-attributed graphs. Comprehensive experiments on synthetic and real-world datasets demonstrate GFSE's capability to significantly enhance the model's performance while requiring substantially less task-specific fine-tuning.
Received — 17 February 2026 ⏭

Fin-RATE: A Real-world Financial Analytics and Tracking Evaluation Benchmark for LLMs on SEC Filings

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yidong Jiang · Junrong Chen · Eftychia Makri · Jialin Chen · Peiwen Li · Ali Maatouk · Leandros Tassiulas · Eliot Brenner · Bing Xiang · Rex Ying
17 February 2026 at 13:00
arXiv:2602.07294v3 Announce Type: replace-cross Abstract: With the increasing deployment of Large Language Models (LLMs) in the finance domain, LLMs are increasingly expected to parse complex regulatory disclosures. However, existing benchmarks often focus on isolated details, failing to reflect the complexity of professional analysis that requires synthesizing information across multiple documents, reporting periods, and corporate entities. Furthermore, these benchmarks do not disentangle whether errors arise from retrieval failures, generation inaccuracies, domain-specific reasoning mistakes, or misinterpretation of the query or context, making it difficult to precisely diagnose performance bottlenecks. To bridge these gaps, we introduce Fin-RATE, a benchmark built on U.S. Securities and Exchange Commission (SEC) filings and mirroring financial analyst workflows through three pathways: detail-oriented reasoning within individual disclosures, cross-entity comparison under shared topics, and longitudinal tracking of the same firm across reporting periods. We benchmark 17 leading LLMs, spanning open-source, closed-source, and finance-specialized models, under both ground-truth context and retrieval-augmented settings. Results show substantial performance degradation, with accuracy dropping by 18.60\% and 14.35\% as tasks shift from single-document reasoning to longitudinal and cross-entity analysis. This degradation is driven by increased comparison hallucinations, temporal and entity mismatches, and is further reflected in declines in reasoning quality and factual consistency--limitations that existing benchmarks have yet to formally categorize or quantify.
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