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NED-Tree: Bridging the Semantic Gap with Nonlinear Element Decomposition Tree for LLM Nonlinear Optimization Modeling

arXiv:2604.01588v1 Announce Type: new Abstract: Automating the translation of Operations Research (OR) problems from natural language to executable models is a critical challenge. While Large Language Models (LLMs) have shown promise in linear tasks, they suffer from severe performance degradation in real-world nonlinear scenarios due to semantic misalignment between mathematical formulations and solver codes, as well as unstable information extraction. In this study, we introduce NED-Tree, a systematic framework designed to bridge the semantic gap. NED-Tree employs (a) a sentence-by-sentence extraction strategy to ensure robust parameter mapping and traceability; and (b) a recursive tree-based structure that adaptively decomposes complex nonlinear terms into solver-compatible sub-elements. Additionally, we present NEXTOR, a novel benchmark specifically designed for complex nonlinear, extensive-constraint OR problems. Experiments across 10 benchmarks demonstrate that NED-Tree establishes a new state-of-the-art with 72.51% average accuracy, NED-Tree is the first framework that drives LLMs to resolve nonlinear modeling difficulties through element decomposition, achieving alignment between modeling semantics and code semantics. The NED-Tree framework and benchmark are accessible in the anonymous repository https://anonymous.4open.science/r/NORA-NEXTOR.

Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response

Cancer Immunol Immunother. 2026 Apr 2;75(4):131. doi: 10.1007/s00262-026-04374-3.

ABSTRACT

Immunotherapy has revolutionized cancer treatment, yet characterizing the spatial complexity of the tumor immune microenvironment remains a challenge. In this study, we established a comprehensive computational framework integrating multi-omics profiling across 27 cancer types to decode immune-related non-coding RNA regulatory networks. Moving beyond traditional bulk analysis, we utilized spatial transcriptomics to dissect the spatial localization of these regulators. We identified the SNHG6-BIRC5 axis as a critical driver of the "immune-cold" phenotype in lung adenocarcinoma. We provide visual evidence that this axis localizes to tumor nests and negatively correlates with T- cell infiltration, elucidating a mechanism of spatial immune exclusion. Validating the clinical relevance of these findings, genome-scale CRISPR-Cas9 screening data confirmed the functional essentiality of these targets for cancer cell survival. Furthermore, pharmacogenomic analysis revealed that high expression of this axis correlates with sensitivity to chemotherapy agents like Vinblastine, suggesting a potential stratification strategy for patients with immune-excluded tumors. To expand the clinical utility to immunotherapy prediction, we developed a pan-cancer XGBoost machine learning model incorporating 14 high-performance regulatory features. This model achieved robust performance in distinguishing immunotherapy responders from non-responders with an AUC of 0.771, outperforming traditional markers such as PD-L1. Collectively, this study highlights spatial determinants of immune exclusion and chemotherapy sensitivity- and presents a generalized machine- learning tool for precision immunotherapy stratification. The developed online resource is freely available to facilitate community-wide biomarker discovery.

PMID:41925746 | DOI:10.1007/s00262-026-04374-3

Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response

2 April 2026 at 18:00

Cancer Immunol Immunother. 2026 Apr 2;75(4):131. doi: 10.1007/s00262-026-04374-3.

ABSTRACT

Immunotherapy has revolutionized cancer treatment, yet characterizing the spatial complexity of the tumor immune microenvironment remains a challenge. In this study, we established a comprehensive computational framework integrating multi-omics profiling across 27 cancer types to decode immune-related non-coding RNA regulatory networks. Moving beyond traditional bulk analysis, we utilized spatial transcriptomics to dissect the spatial localization of these regulators. We identified the SNHG6-BIRC5 axis as a critical driver of the "immune-cold" phenotype in lung adenocarcinoma. We provide visual evidence that this axis localizes to tumor nests and negatively correlates with T- cell infiltration, elucidating a mechanism of spatial immune exclusion. Validating the clinical relevance of these findings, genome-scale CRISPR-Cas9 screening data confirmed the functional essentiality of these targets for cancer cell survival. Furthermore, pharmacogenomic analysis revealed that high expression of this axis correlates with sensitivity to chemotherapy agents like Vinblastine, suggesting a potential stratification strategy for patients with immune-excluded tumors. To expand the clinical utility to immunotherapy prediction, we developed a pan-cancer XGBoost machine learning model incorporating 14 high-performance regulatory features. This model achieved robust performance in distinguishing immunotherapy responders from non-responders with an AUC of 0.771, outperforming traditional markers such as PD-L1. Collectively, this study highlights spatial determinants of immune exclusion and chemotherapy sensitivity- and presents a generalized machine- learning tool for precision immunotherapy stratification. The developed online resource is freely available to facilitate community-wide biomarker discovery.

PMID:41925746 | PMC:PMC13046951 | DOI:10.1007/s00262-026-04374-3

Excessive pyroptosis mediates the exacerbation of pneumonia caused by low-lethality influenza virus and secondary MRSA co-infection

Cell Death Discovery, Published online: 02 April 2026; doi:10.1038/s41420-026-03031-z

Excessive pyroptosis mediates the exacerbation of pneumonia caused by low-lethality influenza virus and secondary MRSA co-infection
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