arXiv AI
MADDIE: Multi-Agent Drug Discovery Engine
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From Benchmark to Bench: Can Agents Survive Real-World Drug Discovery?
The paper introduces MAGI, an open modular agent that orchestrates molecular‑design tools by setting objectives, launching optimization, interpreting structure–activity relationships, and adjusting strategy. In nine retrospective lead‑optimization campaigns from three pharmaceutical companies, MAGI produced valid molecules via either direct LLM generation or delegation to REINVENT 4; LLM proposals stayed closer to local chemistry and achieved comparable or higher activity with fewer operations, while REINVENT explored broader chemical space. The success of a campaign depended on the accuracy of predictive models rather than the generation route, and a blinded evaluation showed chemists could not distinguish MAGI’s outputs from expert‑generated compounds, though the SAR reasoning was deemed plausible yet incomplete. The study positions MAGI as a coordination layer that can be plugged into existing workflows, but notes that the current ceiling for real projects is set by scorer applicability rather than tool orchestration.
arXiv AI
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TxBench-PP: Analyzing AI Agent Performance on Small-Molecule Preclinical Pharmacology
arXiv:2606. 19245v1 Announce Type: new Abstract: Artificial intelligence (AI) agents promise to accelerate drug discovery by compressing interpretation and decision-making loops, but practical deployment requires trusted evaluation on realistic program decisions.
arXiv AI
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FRAGMENTA: Efficient End-to-end Fragmentation-based Generative Model with Agentic Tuning for Drug Lead Optimization in Small Data Regime
arXiv:2511.20510v3 Announce Type: replace Abstract: Molecule generation from extremely limited training data is a key challenge in drug discovery. Existing fragment-based methods are more suitable th...
arXiv AI
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DrugMCTS: a drug repurposing framework combining multi-agent, RAG and Monte Carlo Tree Search
arXiv:2507.07426v4 Announce Type: replace Abstract: Recent advances in large language models have demonstrated considerable potential in scientific domains such as drug repositioning. However, their...
arXiv AI
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CP-Agent: Context-Aware Multimodal Reasoning for Cellular Morphological Profiling under Chemical Perturbations
arXiv:2606. 03435v1 Announce Type: new Abstract: Cell Painting combines multiplexed fluorescent staining, high-content imaging, and quantitative analysis to generate high-dimensional phenotypic readouts to support diverse downstream tasks such as mechanism-of-action (MoA) inference, toxicity prediction, and construction of drug-disease atlases.
arXiv AI
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Strategy-first synthesis planning for complex natural products
arXiv:2608. 07454v1 Announce Type: cross Abstract: The total synthesis of a complex molecule is among the most demanding intellectual and experimental feats in chemistry: a chemist must plan many steps ahead for how to assemble simple building blocks into an intricate target, devise backup strategies, and anticipate procedural challenges.