Tommaso Biancalani

1. Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding
   2024/08/15 by Xiner Li, Yulai Zhao, Li, Xiner +20 · 1 voice · 55 citations
   Biochemistry, Genetics and Molecular Biology · Computer Science · Engineering · Mathematics · #Artificial Intelligence (cs.AI) #Computational Fluid Dynamics and Aerodynamics #FOS: Biological sciences #FOS: Computer and information sciences #Gas Dynamics and Kinetic Theory #Genomics (q-bio.GN) #Guidance and Control Systems #Machine Learning (cs.LG) #Machine Learning (stat.ML) #cs.AI #cs.LG #q-bio.GN #stat.ML
2. Fine-Tuning of Continuous-Time Diffusion Models as Entropy-Regularized Control
   2024/02/23 by Masatoshi Uehara, Yulai Zhao, Uehara, Masatoshi +15 · 35 citations
   Computer Science · Mathematics · Physics and Astronomy · #Advanced Mathematical Modeling in Engineering #Artificial Intelligence (cs.AI) #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning (stat.ML) #Model Reduction and Neural Networks #Numerical methods in inverse problems
3. Understanding Reinforcement Learning-Based Fine-Tuning of Diffusion Models: A Tutorial and Review
   2024/07/18 by Masatoshi Uehara, Uehara, Masatoshi, Yulai Zhao +5 · 1 voice · 28 citations
   Biochemistry, Genetics and Molecular Biology · Computer Science · Engineering · Mathematics · #Artificial Intelligence (cs.AI) #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning (stat.ML) #Quantitative Methods (q-bio.QM) #Traffic control and management #cs.AI #cs.LG #q-bio.QM #stat.ML
4. Inference-Time Alignment in Diffusion Models with Reward-Guided Generation: Tutorial and Review
   2025/01/16 by Masatoshi Uehara, Uehara, Masatoshi, Yulai Zhao +11 · 1 voice · 34 citations
   Biochemistry, Genetics and Molecular Biology · Computer Science · Mathematics · Physics and Astronomy · #Model Reduction and Neural Networks #cs.AI #cs.LG #q-bio.QM #stat.ML
5. Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design
   2024/10/17 by Chenyu Wang, Wang, Chenyu, Masatoshi Uehara +17 · 33 citations
   Biochemistry, Genetics and Molecular Biology · #DNA and Nucleic Acid Chemistry
6. Towards Understanding and Improving GFlowNet Training
   2023/05/11 by Max W. Shen, Emmanuel Bengio, Shen, Max W. +9 · 13 citations
   Computer Science · #FOS: Computer and information sciences #Generative Adversarial Networks and Image Synthesis #Machine Learning (cs.LG) #Machine Learning and Algorithms #Machine Learning and Data Classification
7. Feedback Efficient Online Fine-Tuning of Diffusion Models
   2024/02/26 by Masatoshi Uehara, Yulai Zhao, Uehara, Masatoshi +15 · 15 citations
   Mathematics · Computer Science · Physics and Astronomy · #Numerical methods for differential equations #Matrix Theory and Algorithms #Model Reduction and Neural Networks
8. Dynamic Search for Inference-Time Alignment in Diffusion Models
   2025/03/03 by Xiner Li, Masatoshi Uehara, Li, Xiner +13 · 21 citations
   Physics and Astronomy · #Model Reduction and Neural Networks
9. Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models
   2024/05/30 by Masatoshi Uehara, Uehara, Masatoshi, Yulai Zhao +13 · 10 citations
   Computer Science · Engineering · Physics and Astronomy · #Advanced Mathematical Modeling in Engineering #Artificial Intelligence (cs.AI) #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning (stat.ML) #Model Reduction and Neural Networks #Topology Optimization in Engineering
10. Stochastic Turing patterns in the Brusselator model
    2009/10/31 by Tommaso Biancalani, Duccio Fanelli, Francesca Di Patti · 4 citations
    Computer Science · Environmental Science · Mathematics · Physics and Astronomy · #Advanced Thermodynamics and Statistical Mechanics #Applied mathematics #Brusselator #Computer science #Ecosystem dynamics and resilience #Field (mathematics) #Heuristic #Instability #Mathematical optimization #Mathematics #Mean field theory #Mechanics #Nonlinear Dynamics and Pattern Formation #Nonlinear system #Physics #Pure mathematics #Stability (learning theory) #Statistical physics #Turing #cond-mat.stat-mech #nlin.AO
11. Reward-Guided Iterative Refinement in Diffusion Models at Test-Time with Applications to Protein and DNA Design
    2025/02/20 by Masatoshi Uehara, Uehara, Masatoshi, Xingyu Su +13 · 1 voice · 11 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · Physics and Astronomy · #Gene Regulatory Network Analysis #Generative Adversarial Networks and Image Synthesis #Model Reduction and Neural Networks
12. Noise-Induced Bistable States and Their Mean Switching Time in Foraging Colonies
    2013/06/30 by Tommaso Biancalani, Louise Dyson, Alan J. McKane · 3 citations
    Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Neuroscience · Physics and Astronomy · #Acoustics #Biology #Bistability #Computer science #Ecology #Foraging #Gene Regulatory Network Analysis #Materials science #Neural dynamics and brain function #Noise (video) #Optoelectronics #Physics #Plant and Biological Electrophysiology Studies #Statistical physics #cond-mat.stat-mech #q-bio.PE
13. Improving Graph Generation by Restricting Graph Bandwidth
    2023/01/25 by Nathaniel Diamant, Alex M. Tseng, Diamant, Nathaniel +7 · 4 citations
    Computer Science · Decision Sciences · #Advanced Graph Neural Networks #FOS: Computer and information sciences #Graph Theory and Algorithms #Machine Learning (cs.LG) #Scientific Computing and Data Management #Social and Information Networks (cs.SI)
14. Adding Conditional Control to Diffusion Models with Reinforcement Learning
    2024/06/17 by Yulai Zhao, Zhao, Yulai, Masatoshi Uehara +10 · 6 citations
    Engineering · #Advanced Control Systems Optimization #Artificial Intelligence (cs.AI) #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning (stat.ML)
15. RAG-Enhanced Collaborative LLM Agents for Drug Discovery
    2025/02/22 by Namkyeong Lee, Lee, Namkyeong, Edward De Brouwer +9 · 10 citations
    Biochemistry, Genetics and Molecular Biology · Chemistry · Medicine · #Analytical Chemistry and Chromatography #Artificial Intelligence (cs.AI) #FOS: Computer and information sciences #Machine Learning (cs.LG) #Monoclonal and Polyclonal Antibodies Research #Protein purification and stability
16. Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism
    2016/08/24 by Tim A. Hoek, Kevin Axelrod, Tommaso Biancalani +3 · 2 citations
    Social Sciences · Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Evolutionary Game Theory and Cooperation #Plant and animal studies #Evolution and Genetic Dynamics
17. NODAGS-Flow: Nonlinear Cyclic Causal Structure Learning
    2023/01/04 by Muralikrishnna G. Sethuraman, Romain Lopez, Sethuraman, Muralikrishnna G. +9 · 4 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Bayesian Modeling and Causal Inference #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning (stat.ML) #Machine Learning in Healthcare #Methodology (stat.ME) #Single-cell and spatial transcriptomics
18. Joint Embedding vs Reconstruction: Provable Benefits of Latent Space Prediction for Self Supervised Learning
    2025/05/18 by Hugues Van Assel, Van Assel, Hugues, Mark Ibrahim +7 · 6 citations
    Computer Science · #Artificial Intelligence (cs.AI) #Computer Vision and Pattern Recognition (cs.CV) #Domain Adaptation and Few-Shot Learning #FOS: Computer and information sciences #Face recognition and analysis #Generative Adversarial Networks and Image Synthesis #Machine Learning (cs.LG)
19. Stochastic pattern formation and spontaneous polarisation: the linear noise approximation and beyond
    2012/11/02 by Alan J. McKane, Tommaso Biancalani, McKane, Alan J. +3 · 1 citation
    Biochemistry, Genetics and Molecular Biology · Computer Science · Physics and Astronomy · #Evolution and Genetic Dynamics #FOS: Biological sciences #FOS: Physical sciences #Gene Regulatory Network Analysis #Nonlinear Dynamics and Pattern Formation #Pattern Formation and Solitons (nlin.PS) #Populations and Evolution (q-bio.PE) #Statistical Mechanics (cond-mat.stat-mech) #cond-mat.stat-mech #nlin.PS #q-bio.PE
20. Conformalized Deep Splines for Optimal and Efficient Prediction Sets
    2023/11/01 by Nathaniel Diamant, Diamant, Nathaniel, Ehsan Hajiramezanali +5 · 2 citations
    Computer Science · Mathematics · #Machine Learning and Data Classification #Statistical Methods and Inference #Adversarial Robustness in Machine Learning
21. Cell Morphology-Guided Small Molecule Generation with GFlowNets
    2024/08/09 by Stephen Zhewen Lu, Lu, Stephen Zhewen, Ziqing Lu +11 · 2 citations
    Biochemistry, Genetics and Molecular Biology · #Cell Image Analysis Techniques #Genetics, Bioinformatics, and Biomedical Research
22. Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction
    2024/12/18 by S. Maleki, Jan-Christian Huetter, Maleki, Sepideh +8 · 2 citations
    Biochemistry, Genetics and Molecular Biology · Medicine · #Advanced Electron Microscopy Techniques and Applications #Advanced Fluorescence Microscopy Techniques #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Medical Imaging Techniques and Applications #Quantitative Methods (q-bio.QM)
23. GraphGUIDE: interpretable and controllable conditional graph generation with discrete Bernoulli diffusion
    2023/02/07 by Alex M. Tseng, Nathaniel Diamant, Tseng, Alex M. +5 · 1 citation
    Computer Science · #Explainable Artificial Intelligence (XAI) #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning and Data Classification #Machine Learning in Healthcare
24. MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction
    2024/11/01 by Carl N. Edwards, Ziqing Lu, Edwards, Carl +9 · 2 citations
    Chemistry · Computer Science · Materials Science · #Artificial intelligence #Benchmark (surveying) #Cartography #Closed captioning #Computational Drug Discovery Methods #Computer science #Epistemology #Geography #History and advancements in chemistry #Machine Learning in Materials Science #Natural language processing #Philosophy #Property (philosophy)
25. LLM-Guided Retrieval for Prediction of Molecular Perturbation Responses
    2026/08/03 by Betty Xiong, Jan-Christian Huetter, Gabriele Scalia +2
    Computer Science · #cs.LG