arXiv:2608. 12219v1 Announce Type: new Abstract: Treating patients with combinations of drugs reduces the risk of resistance to any individual drug.
arXiv:2608. 11444v1 Announce Type: cross Abstract: Drug response prediction (DRP) models are an active area of research in pharmacogenomics, with growing potential to accelerate the identification of effective anticancer drugs.
arXiv:2608. 19906v1 Announce Type: new Abstract: Accurately ranking active ligands for a target protein pocket from massive chemical libraries remains a central challenge in virtual screening.
The paper introduces a framework to predict whether a compound’s potency can be quantified in dose‑response profiling, treating quantifiability as a separate triage goal from biological activity. It shows that features from low‑cost primary screens, rather than molecular structure, strongly predict quantifiability, and that this prediction holds across new chemical scaffolds and assay families. The authors argue that incorporating quantifiability predictions can better allocate expensive dose‑response resources.
arXiv:2608. 07609v1 Announce Type: cross Abstract: High-throughput screening (HTS) assays are central to early-stage drug discovery but are often limited by extreme data sparsity, as primary screens typically use only a single replicate per test substance.
arXiv:2603.03517v2 Announce Type: replace-cross Abstract: General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and perfor...
arXiv:2607. 25322v1 Announce Type: new Abstract: Multimodal drug discovery enables drug representation learning beyond chemical structure by incorporating cellular responses such as gene expression and cell morphology.
The paper introduces AssayBench-Loop, a large benchmark of 1,389 CRISPR screens across five phenotype categories, and builds on it to develop AssayLoop, a sequential experimental design framework that combines a transformer-based acquisition policy (AssayFormer) trained on historical data with LLM-derived biological priors. AssayLoop achieves a 5.67‑fold enrichment over random selection, recovering 27.7% of hits after testing only about 5% of the library, and outperforms existing adaptive-design methods and standalone LLMs. The authors also present AssayLLM, extending the approach directly to an LLM via task‑specific post‑training, and show that performance improves with more historical training data and transfers to unseen phenotype categories.
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.
Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles. Preclinical transfer-learning models can simulate drug-induced expression changes but are often hard to interpret and unstable, whereas knowledge-graph methods provide mechanistic context yet remain static and fail to capture drug-induced transcriptomic perturbation dynamics.
ProbeMatchDTI introduces a probe-driven framework for drug‑target interaction prediction that preserves weak biochemical signals by using IterProbe to retain contextual states and BindingProbe to model cross‑entity complementarity at multiple scales. The method improves AUC‑ROC by 2.0% on BindingDB and 0.5% on DrugBank compared to prior biochemical representation learning approaches. Feature‑level analyses confirm the effectiveness of the probe-driven pattern matching, and the predictions are linked to an evidence‑guided downstream drug‑discovery workflow for candidate refinement and validation planning.
arXiv:2606. 29949v1 Announce Type: cross Abstract: H&E-stained whole-slide images offer cohort-scale availability and rich spatial context but lack molecular specificity, whereas bulk RNA-seq provides transcriptome-wide resolution at high cost with limited archival availability.
The paper introduces LLM4CKD, a framework that uses large language models (LLMs) for early chronic kidney disease (CKD) screening without task‑specific training. By employing clinically selected tabular features and structured prompt templates, the authors evaluate LLMs in zero‑shot and few‑shot settings against traditional machine learning, deep learning, and tabular foundation models. Results show that LLMs can match or outperform conventional methods in low‑data scenarios, though their performance varies with model choice and input complexity, highlighting a trade‑off between data efficiency and stability.