arXiv Machine Learning

MetaboLLM: a metabolomics-specialized large language model for biochemical knowledge integration and predictive metabolite graph construction

arXiv:2608. 06253v1 Announce Type: new Abstract: Metabolomics knowledge is distributed across heterogeneous resources and remains difficult to translate into predictive representations.

arXiv AI

Jul 3

MKGR: Multimodal Knowledge-Graph Representation Learning for Cold-Start Protein-Protein Interaction Prediction

arXiv:2607. 01627v1 Announce Type: cross Abstract: Accurate protein-protein interaction (PPI) prediction is central to functional genomics, disease mechanism discovery, and drug development.

By Wenbo Zhang

rag multimodal benchmarks

arXiv Machine Learning

Jul 8

Canopy: A Heterograph Foundation Model for Metabolic Engineering

arXiv:2607. 06224v1 Announce Type: new Abstract: Designing microbial strains that produce high-value chemicals at commercially viable titers remains a central challenge in metabolic engineering.

By Jake Bowden, Laurence Legon, Satnam Surae

llms rag multimodal

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 30

GLIP: Graph and LLM Joint Pretraining for Graph-Level Tasks

arXiv:2606. 29773v1 Announce Type: new Abstract: Graphs are widely used to model relational systems, with applications in domains such as social networks, finance, and biomedicine.

By Haoxin Sun, Yiqing Lin, Yajun Huang, Chenhui Dong, Mingjun Li, Zhongzhi Zhang

llms diffusion fine-tuning benchmarks 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

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 AI

Jun 24

T2D-Bench: Evidence-Gated Evaluation of LLM Outputs for Type 2 Diabetes Using a Multi-Layer Clinical-Lifestyle Knowledge Graph

arXiv:2606. 24145v1 Announce Type: new Abstract: Large language models (LLMs) can produce clinically fluent recommendations for type 2 diabetes while failing to satisfy guideline constraints or explicitly justify lifestyle-related glycemic claims.

By Saba A. Farahani, Hung Cao, Ramesh Jain, Amir M. Rahmani

llms benchmarks safety

arXiv AI

Jul 24

Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances

arXiv:2511. 03354v2 Announce Type: replace-cross Abstract: Generative artificial intelligence (GenAI) is transforming bioinformatics by advancing genomics, proteomics, transcriptomics, structural biology, and drug discovery.

By Wasimul Karim, Riasad Alvi, Sayeem Been Zaman, Arefin Ittesafun Abian, Mohaimenul Azam Khan Raiaan, Saddam Mukta, Md Rafi Ur Rashid, Md Rafiqul Islam, Yakub Sebastian, Sami Azam

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 AI

Aug 10

MolBioKG: Grounding Out-of-Graph Molecules in Biomedical Knowledge Graphs via Multi-Resolution Structural Anchoring

arXiv:2608. 06713v1 Announce Type: new Abstract: Biomedical knowledge graphs (KGs) accelerate drug discovery, but standard pipelines assume query molecules already exist as graph entities, leaving unregistered molecules disconnected.

By Yiming Zhang, Hikaru Shindo, Shuan Chen, Kaushalya Madhawa, Jun Jin Choong, Yuna Oikawa, Takashi Fujiwara, Keisuke Ozawa

llms

arXiv Machine Learning

Aug 5

Bi-semantic Chemical Embedder for Joint Representation Learning of SMILES and Natural Language

arXiv:2608. 03855v1 Announce Type: new Abstract: Transformer models have revolutionized natural language processing (NLP), and text-based molecular representations like SMILES have successfully extended these architectures to chemistry.

By David Ming Segura, Jeremy Goumaz, Joshua W. Sin, Bojana Rankovi\'c, Philippe Schwaller

llms rag nlp

arXiv Machine Learning

Jul 3

An Additive MLP-GNN Framework for Characterizing Chemical and Structural Contributions to Aqueous Solubility

arXiv:2607. 02212v1 Announce Type: cross Abstract: Aqueous solubility is a key property in early-stage drug discovery, but most predictive models merge physicochemical descriptors and molecular graph information into a single representation, obscuring whether a prediction is driven by global chemistry, molecular structure, or both.

By Sampreeti Bhattacharya, Arkaprava Roy

rag fine-tuning

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