arXiv:2607. 07467v1 Announce Type: new Abstract: Spatial and Single-cell transcriptomics are transformative in deciphering cellular dynamics.
Spatial and Single-cell transcriptomics are transformative in deciphering cellular dynamics. As the fundamental paradigm for reconstructing cell developmental paths, trajectory inference (TI) is critical.
The paper introduces PACEvolve, a framework that improves self‑evolving agents powered by Large Language Models by addressing their tendency to become trapped in local contexts and repeat flawed hypotheses. It does so through three techniques: Hierarchical Context Management to prune memory, Momentum‑Based Backtracking to escape local minima, and a self‑adaptive Collaborative Evolution policy to balance refinement and knowledge transfer. These methods enable the agents to maintain a global view of search momentum and achieve state‑of‑the‑art results on complex evolutionary benchmarks.
arXiv:2608. 14710v1 Announce Type: cross Abstract: Predicting spatial gene expression from hematoxylin and eosin (H\&E)-stained images offers a cost-effective alternative to spatial transcriptomics (ST).
Scientific datasets are commonly organized as hierarchical repositories containing heterogeneous and interdependent files, making their inspection, integration, and analysis labor-intensive and reliant on domain expertise. Although large language model (LLM) agents have advanced substantially in planning, reasoning, and tool use, existing research has largely overlooked their ability to interact with real scientific data assets through executable environments.
arXiv:2606. 24235v1 Announce Type: new Abstract: Spatial proteomics enables single-cell-resolution characterization of protein expression within tissue architecture, playing a critical role in understanding tumor microenvironments and guiding precision medicine.
BaseCamp is an agentic AI framework that automates the decision layer of DNA sequencing pipelines by deploying six specialized AI agents for tasks such as sample intake, quality control, alignment, variant calling, annotation, cross‑stage monitoring, and reporting. The agents rely on established bioinformatics tools for actual sequence analysis, while using fine‑tuned, domain‑specialized large language models to select, configure, and interpret these tools’ outputs, ensuring reproducibility and local data privacy. Evaluation demonstrates that the agents’ configurations align with expert practice, provide an explicit filtering ledger for traceability, and detect anomalies that traditional monitoring may miss.
arXiv:2607. 26722v1 Announce Type: cross Abstract: Harness plays a critical role in large language model agent performance, and building a high-performing harness requires substantial expert effort.
NS-Copilot is a large‑language‑model driven multi‑agent system designed to automate neuroscience data analysis. It integrates domain‑specific pre‑trained models for modalities such as EEG and extracellular spike data, and uses a natural‑language interface to orchestrate agents that plan, generate code, and synthesize results. In benchmarks on Alzheimer’s, Parkinson’s, and working‑memory spike decoding, the system consistently outperformed strong baselines across multiple trials.
arXiv:2601. 21800v4 Announce Type: replace Abstract: We introduce BioAgent Bench, an evaluation suite designed for measuring the performance and robustness of AI agents in common bioinformatics tasks.
ContextPilot is a proactive context‑management framework designed to improve long‑horizon agentic reasoning with large language models. It expands the toolset to include planning, long‑term memory, and soft context offloading, and introduces a reinforcement‑learning strategy that focuses on critical editing decisions and assigns action‑level advantages. Experiments on long‑context QA and deep search tasks demonstrate that ContextPilot achieves stronger performance with a more compact working context, outperforming existing baselines across various base models and benchmarks.
Geographic Information System (GIS) professionals rely on multi-step spatial analysis workflows to support decision-making in urban planning, disaster response, and environmental monitoring. The process is tedious, time-consuming, and error-prone.
arXiv:2511.20109v2 Announce Type: replace Abstract: Climate science demands automated workflows to transform comprehensive questions into data-driven statements across massive, heterogeneous datasets...