Machine Learning and Systems Biology Research Department
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120 repositories
polygraph-benchmark
PublicBenchmarking framework for graph generative models (ICLR 2026)Gelato
PublicCode and Data for the paper: "Gelato: Graph Edit Distance via Autoregressive Neural Combinatorial Optimization" (ICLR 2026)CellPick
PublicAn interactive cell selection tool for spatial omicsDeepEST
PublicHuman_scDVP_Analysis
Publicbioverse
Publicgraph-kernels
PublicRECOMB2026Cosmo
PublicCosmo
PublicAutoGraph
PublicOfficial code for "Flatten Graphs as Sequences: Transformers are scalable graph generators" (NeurIPS 2025)orbit-count
Publicrnaglib-experiments
Publicesm3_on_raven
PublicPCR-bias
PublicNeuralWalker
PublicOfficial Pytorch implementation of NeuralWalker (ICLR 2025)MLDEEP
Publicproteinshake
PublicConformalAMR
Public- Code and Data for the paper: "Graph Neural Networks Can (Often) Count Substructures" (ICLR 2025 Spotlight)
- Official implementation of the ANFM graph generative model (TMLR, 2026)
NodeIndividualizedGNNs
PublicCode and Data for the paper: On the Expressivity and Sample Complexity of Node-Individualized Graph Neural Networks (NeurIPS 2024)PST
PublicProtein Structure Transformer (PST): Endowing pretrained protein language models with structural knowledgeWWL
Public- Code and Data for the paper: Structure- and Function-Aware Substitution Matrices via Learnable Graph Matching (RECOMB 2024 & ICML 2024 Differentiable Almost Eve…
WTK
PublicA Wasserstein Subsequence Kernel for Time Series.CARPE
PublicMultimodalAMR
Public
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