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CONDITIONAL
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models
A denoising diffusion model conditioned on coarse secondary-structure topology generates physically plausible protein backbones, sequences, and rotamers across diverse CATH domain classes.
arxiv:2205.15019 · q-bio.QM · 2022-05
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CONDITIONAL
Logarithmic-scale variational quantum eigensolver for off-lattice protein structure prediction in continuous torsional angle space
A variational quantum eigensolver maps protein torsions to qubit phases, achieving native-like structure prediction with logarithmic qubit scaling.
arxiv:2609.02113 · quant-ph · 2026-09
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CONDITIONAL
Enhancing Reinforcement learning in 3-Dimensional Hydrophobic-Polar Protein Folding Model with Attention-based layers
A Transformer-enhanced DQN achieves known-best energies on four of seven 3D HP benchmark sequences and near-best on the rest, with reproducibility caveats.
arxiv:2504.15634 · cs.LG · 2025-04
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CONDITIONAL
How to Spend Your Oracle Budget: Practical Guidance for Protein Structure Prediction Models
Under a fixed oracle budget, latent-subspace optimization (O3) beats steering and fine-tuning baselines at low budgets, while FK-steering and DPO catch up as the budget grows.
arxiv:2608.12192 · cs.AI · 2026-08
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CONDITIONAL
Generative diffusion model with inverse renormalization group flows
RGDM generates data by reversing renormalization-group-style coarse-graining, using a colored-noise schedule and projection layers to sample coarse-to-fine, and outperforms a vanilla DDPM on protein and image benchmarks.
arxiv:2501.09064 · cond-mat.stat-mech · 2025-01
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UNVERDICTED
Transformers in Protein: A Survey
A broad but unreliable survey of Transformer applications in protein informatics, with numerous citation errors and unsupported claims.
arxiv:2505.20098 · cs.LG · 2025-05
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CONDITIONAL
Quantum Algorithm for Protein Structure Prediction Using the Face-Centered Cubic Lattice
The authors encode protein structures on an FCC lattice using 4N-10 qubits and demonstrate ground-state sampling for a six-residue peptide on two IBM quantum computers with two slack-variable-free constraint methods.
arxiv:2507.08955 · quant-ph · 2025-07
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CONDITIONAL
Influence of thermal noise on the field-driven dynamics of the non-collinear antiferromagnet Mn3Sn
Field-dependent analytical escape times and octupole relaxation times for strained Mn3Sn, validated by stochastic LLG simulations in the low-barrier regime.
arxiv:2507.09143 · cond-mat.mes-hall · 2025-07
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REJECT
Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances
Across the 68 papers it surveys, domain-specialized generative models usually outperform general-purpose LLMs on biological tasks, and agentic/conversational workflows are the least-covered topics.
arxiv:2511.03354 · cs.CL · 2025-11
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UNVERDICTED
Assessing Cost Hamiltonian Reliability in Quantum Protein Structure Prediction
For small peptides the contact-energy cost Hamiltonian shows insufficient average correlation with RMSD error; correlation improves for larger instances and more interaction shells according to Monte-Carlo estimates.
arxiv:2606.21241 · quant-ph · 2026-06
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UNVERDICTED
Recent Advances in Generative AI for Healthcare Applications
A literature review synthesizing generative AI uses in healthcare with emphasis on diffusion and transformer models.
arxiv:2310.00795 · cs.LG · 2023-10
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UNVERDICTED
Exploring Quantum Annealing for Coarse-Grained Protein Folding
Compares quantum annealing models for coarse-grained protein folding, proposes interleaved-grid tetrahedral encoding, and reports hardware limits from embedding alongside scaling gains over classical simulated annealing on embedded instances.
arxiv:2508.10660 · quant-ph · 2025-08
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UNVERDICTED
Chiral and Clock phases in Twisted Dipolar Clusters
Twist in dipolar rod clusters induces Ising-like chirality and Z_N clock order parameters that switch discontinuously, crossing over to nearly continuous symmetry for large polygons.
arxiv:2601.22325 · cond-mat.mtrl-sci · 2026-01