Paper Citation Record · LEDGER

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation

As of 12 August 2026, this Paper Citation Record lists 32 of 32 outbound references and 0 inbound Pith citation observations for arXiv:2501.15631.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2501.15631 v1

Coverage vector

measured 32 of 32 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-10T14:09:57.715369Z

measured 32 of 32 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-12T06:34:41.77262+00:00

measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: cited_works

Reference resolution

32 of 32 outbound references displayed

verified exact1
verified fuzzy16
unresolved15
parse uncertain0
malformed identifier0
metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 832e22d5-10f3-4f71-a274-381efba4e45e · outbound

This paper cites The process of structure-based drug design.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation The process of structure-based drug design

Reference 1

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.147091Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation 2bc47c8f-9b8a-43cf-acfa-99c78c08d0d7 · outbound

This paper cites Quantifying the chemical beauty of drugs.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Quantifying the chemical beauty of drugs

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.134754Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation 2d365b00-c70e-40f0-9e40-a7805de205d4 · outbound

This paper cites Training Diffusion Models with Reinforcement Learning.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Training Diffusion Models with Reinforcement Learning

Reference 3

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.597778Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a5727722-75a3-4584-abee-402b01148b9c · outbound

This paper cites Deep reinforcement learning from human preferences.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Deep reinforcement learning from human preferences

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.602465Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e87c12f4-0128-41eb-8552-89ed2d788065 · outbound

This paper cites RAFT: Reward rAnked FineTuning for Generative Foundation Model Alignment.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation RAFT: Reward rAnked FineTuning for Generative Foundation Model Alignment

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.606883Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 5b1ca58a-a6d7-4f01-b8ef-b5669ad27548 · outbound

This paper cites Autodock vina 1.2.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Autodock vina 1.2

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.112652Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation b774cbf9-566a-4985-bb2a-306544bda18a · outbound

This paper cites Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.098305Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation dab9cf22-df2d-4bfa-9203-a868addb5d21 · outbound

This paper cites Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.085838Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation 9747d446-a356-403e-baec-5f5c9871fba0 · outbound

This paper cites Reinforced genetic algorithm for structure-based drug design.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Reinforced genetic algorithm for structure-based drug design

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.072776Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation 4a7166d4-b622-4630-8c2b-cf9903486bd8 · outbound

This paper cites 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.627357Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 910e07ef-83f8-4799-9e3a-bcdf71fe7faa · outbound

This paper cites DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design

Reference 11

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.631730Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 6c82f396-8222-435c-935f-81f828343a2b · outbound

This paper cites BoNBoN Alignment for Large Language Models and the Sweetness of Best-of-n Sampling.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation BoNBoN Alignment for Large Language Models and the Sweetness of Best-of-n Sampling

Reference 12

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.636495Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 623e2507-331c-4c27-9877-2df774121d38 · outbound

This paper cites Multi-objective molecule generation using interpretable substructures.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Multi-objective molecule generation using interpretable substructures

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.059992Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation 50593311-01c0-42e2-a441-b4fc7f42f2da · outbound

This paper cites DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding

Reference 14

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.644237Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 6bbe93b6-0643-4b28-82df-7f45985bc0ea · outbound

This paper cites Generating 3D Molecules for Target Protein Binding.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Generating 3D Molecules for Target Protein Binding

Reference 15

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.648852Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d75035c3-d850-4a22-9e19-fe1a0784bc77 · outbound

This paper cites A 3d generative model for structure-based drug design.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation A 3d generative model for structure-based drug design

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.047051Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation 9a97e3d6-bdbd-465e-b02e-1f25f3bec0ae · outbound

This paper cites Training language models to follow instructions with human feedback.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Training language models to follow instructions with human feedback

Reference 17

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.657171Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 2fa6bd2a-1904-40d9-97bd-b729c874dcdc · outbound

This paper cites Pocket2mol: Efficient molecular sampling based on 3d protein pockets.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Pocket2mol: Efficient molecular sampling based on 3d protein pockets

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.025519Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation 07865d78-bce4-46a3-806f-9ee760c8f03b · outbound

This paper cites Geometric deep learning for structure-based ligand design.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Geometric deep learning for structure-based ligand design

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:58.012371Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation e00ad9f1-9298-4df7-85ab-9e03ad223717 · outbound

This paper cites Direct preference optimization: Your language model is secretly a reward model.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Direct preference optimization: Your language model is secretly a reward model

Reference 20

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.668603Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation cf7027bc-b7d0-4484-963a-1928ccb975cb · outbound

This paper cites Generating 3d molecules conditional on receptor binding sites with deep generative models.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Generating 3d molecules conditional on receptor binding sites with deep generative models

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:57.991189Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation cf95e5c9-74c6-4dad-93f0-608b78fe7847 · outbound

This paper cites Structure-based Drug Design with Equivariant Diffusion Models.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Structure-based Drug Design with Equivariant Diffusion Models

Reference 22

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.675908Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a48c4e82-21da-4881-adfb-1feb0372b3cb · outbound

This paper cites Proximal Policy Optimization Algorithms.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Proximal Policy Optimization Algorithms

Reference 23

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.680165Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 082bf1f7-3c0c-4223-bde0-848e7864f462 · outbound

This paper cites Autogrow4: an open- source genetic algorithm for de novo drug design and lead optimization.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Autogrow4: an open- source genetic algorithm for de novo drug design and lead optimization

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:57.977372Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation a47a0f12-87ec-4a4a-ba9b-17fae1e88d75 · outbound

This paper cites Applications of machine learning in drug discovery and development.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Applications of machine learning in drug discovery and development

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:57.963419Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation d2601c78-c844-4928-9a07-b5590f7aaa33 · outbound

This paper cites Diffusion model alignment using direct preference optimization.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Diffusion model alignment using direct preference optimization

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:57.949379Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation 350640ad-7c2a-4d4e-aead-85b3e9a81a52 · outbound

This paper cites Large-scale Reinforcement Learning for Diffusion Models.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Large-scale Reinforcement Learning for Diffusion Models

Reference 27

Resolution: verified exact; local_arxiv, observed 2026-08-10T14:09:57.795567Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation f36a3d71-168f-4f5c-82b3-37edb60370ee · outbound

This paper cites Learning subpocket prototypes for generalizable structure-based drug design.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Learning subpocket prototypes for generalizable structure-based drug design

Reference 28

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:57.936309Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation 2dc4ce4a-fadb-4a8e-a855-4cb471c83937 · outbound

This paper cites Molecule generation for target protein binding with structural motifs.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Molecule generation for target protein binding with structural motifs

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T14:09:57.922771Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-12T06:34:41.77262+00:00.

Observation fb0f87ab-afc0-4788-a58e-ebb0b2214c6b · outbound

This paper cites DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization

Reference 30

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.706871Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e8bcfed2-7dc0-4ece-a4e8-1ecf34f54075 · outbound

This paper cites Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization

Reference 31

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.711200Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation f751566a-5e19-42f2-84a2-ebae2a3a017f · outbound

This paper cites Fine-Tuning Language Models from Human Preferences.

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Fine-Tuning Language Models from Human Preferences

Reference 32

Resolution: unresolved; no resolver link, observed 2026-08-10T14:09:57.715369Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Pith citing papers

No inbound Pith citation observations are available.