arXiv Machine Learning

Asymmetric Focal Loss Improves Graph Neural Network Prediction of Drug-Drug Interactions

arXiv:2607. 07611v1 Announce Type: new Abstract: Background: Graph neural networks improve computational prediction of polypharmacy side effects, but standard binary cross-entropy training allocates equal capacity to well-classified and difficult examples, potentially missing clinically significant interactions.

arXiv AI

Jun 9

Pharmacogenomic Knowledge Graph Augmentation for Graph Neural Network-Based Drug-Drug Interaction Prediction

arXiv:2606. 07698v1 Announce Type: cross Abstract: Graph neural networks (GNNs) applied to drug-drug interaction (DDI) prediction rely exclusively on molecular structure encoded as SMILES-derived graphs.

By Juergen Dietrich

rag multimodal benchmarks safety

arXiv Machine Learning

Jun 16

A polarity-aware multi-relational model for the signed interaction prediction in biological networks

arXiv:2407. 07357v3 Announce Type: replace Abstract: Predicting signed interactions in biological networks is crucial for understanding drug mechanisms and facilitating drug repurposing.

By Ziye Zhou, Meijie Wang, Lun Yu

arXiv Machine Learning

Jul 7

CoFEND: A Cross-Modal Fusion End-to-End Network for Cold-Start Drug-Drug Interaction Prediction

arXiv:2607. 02928v1 Announce Type: new Abstract: Cold-start drug-drug interaction (DDI) prediction for new drugs is critical for minimizing unexpected adverse drug reactions.

By Di Wu, Hongyi Sun, Haichao Xu, Jia Chen, Zhong Chen, Jie Yang

multimodal safety

arXiv AI

Jul 7

Predicting Therapeutic Outcome via Aligning Patient-Specific Knowledge Graph and Gene-Level Perturbation Representations

arXiv:2607. 04557v1 Announce Type: cross Abstract: 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.

By Dongmin Bang, Sugyun An, Inyoung Sung, Ilho Yun, Sun Kim, Sangseon Lee

rag diffusion benchmarks

arXiv Machine Learning

Jul 28

MEGA-CL: A Molecular Foundation Model for Generalizable ADMET Prediction through Graph External Attention and Contrastive Learning

arXiv:2607. 24314v1 Announce Type: new Abstract: Predicting the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small molecules remains a major challenge in drug discovery.

By Tinghui Jin, Kedu Jin, Ying Li, Guanghui Ren, Jingzhi Xue, Shiyu Zhou, Xiaoli Dai, Li-bin Wei, Xijing Chen, Di Zhao, Jinfeng Liu

benchmarks safety

Hugging Face Trending Papers

Jul 6

Predicting Therapeutic Outcome via Aligning Patient-Specific Knowledge Graph and Gene-Level Perturbation Representations

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.

rag diffusion benchmarks

arXiv Machine Learning

Jun 15

Where Black-box Drug-Target Interaction Prediction Models Look: Cross-Method Explainability

arXiv:2606. 14245v1 Announce Type: new Abstract: Drug-target interaction (DTI) and affinity (DTA) predictors increasingly achieve strong benchmark scores, yet their internal use of sequence, fingerprint, and graph features often remains opaque.

By Ali Vefghi, Zahed Rahmati, Mohammad Akbari

benchmarks safety

arXiv Machine Learning

6d ago

Large-scale AI-Ready Data for Anti-Cancer Drug Response Modeling

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.

By Vincent Lavelle, Yitan Zhu, Kaitlyn Marlor, Thomas Brettin, Rick Stevens

benchmarks

arXiv Machine Learning

Jun 10

TRAPS: Therapeutic Response Analysis via Pathway-informed Stratification

arXiv:2606. 09898v1 Announce Type: new Abstract: Cancer treatment planning requires decisions across multiple clinical dimensions at once.

By Sujoy Banik, Sayantan Chakraborty, Boishakhi Das Toma, Zainab Ghafoor, Ushashi Bhattacharjee, Koushik Howlader, Tirtho Roy

benchmarks

arXiv Machine Learning

Aug 6

Geometry-Informed Parameter-Efficient Fine-Tuning of Pre-trained Molecular GNNs for Blood-Brain Barrier Permeability Prediction

arXiv:2608. 04257v1 Announce Type: new Abstract: Blood-brain barrier permeability (BBBP) prediction is a critical screening task in central nervous system drug discovery, where candidate molecules must be assessed for whether they can cross, or should be prevented from crossing, the blood-brain barrier.

By Marco Vieto Vega, Long D. Nguyen, Binh P. Nguyen

fine-tuning

arXiv Machine Learning

Jun 9

Do Larger Models Really Win in Drug Discovery? A Benchmark Assessment of Model Scaling in AI-Driven Molecular Property and Activity Prediction

arXiv:2604. 26498v3 Announce Type: replace Abstract: The rapid growth of molecular foundation models and large language models (LLMs) has encouraged a scale centred view of AI in drug discovery, in which larger pretrained models are expected to supersede compact cheminformatics models.

By Jinjiang Guo, Sheng Ding

llms benchmarks safety

arXiv AI

Jul 29

From Cellular Responses to Pharmacological Domains: Multimodal Zero-Shot Drug Representation Learning

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.

By Jintao Huang, Lu Leng, Ziyuan Yang

multimodal safety

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