Paper Citation Record · LEDGER

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

As of 18 August 2026, this Paper Citation Record lists 31 of 31 outbound references and 3 inbound Pith citation observations for arXiv:2412.17780.

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

pith.paper-citation-record.v1
2412.17780 v4

Coverage vector

measured 31 of 31 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-11T05:13:37.992758Z

measured 34 of 34 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-18T06:34:40.430872+00:00

measured 3 of 3 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-03T02:57:47.932219Z

measured 0 of 1 external citation measurements

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

Source: arxiv_reference, observed 2026-06-28T23:42:49.829070Z

Reference resolution

31 of 31 outbound references displayed

verified exact4
verified fuzzy13
unresolved14
parse uncertain0
malformed identifier0
metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 361d8eb6-194b-4663-8a63-ed77f4f7e4ff · outbound

This paper cites an unresolved cited work.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Unresolved cited work

Reference 2

Resolution: unresolved; raw_fallback, observed 2026-08-11T05:13:39.035878Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation db2d01f8-6799-4968-bc44-fa9f138fd530 · outbound

This paper cites H., Engler, J.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion H., Engler, J

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:39.276790Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 7267d1b8-eacb-4bd5-9b02-e02ebb3ab764 · outbound

This paper cites Larger scores indicate stronger binding for our classifier.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Larger scores indicate stronger binding for our classifier

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:38.930403Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 23953f62-4d8b-46c2-8ef3-7e00b9e61231 · outbound

This paper cites Two-dimensional chemical structure of (A) PepTune-generated binder 1, (C) established T7 peptide, and (E) PepTune-generated TfR binder 2 and their Vina docking scores to TfR (↓).

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Two-dimensional chemical structure of (A) PepTune-generated binder 1, (C) established T7 peptide, and (E) PepTune-generated TfR binder 2 and their Vina docking scores to TfR (↓)

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:39.008525Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 3a4d6fbe-a337-4752-bcfe-f1ca9335267a · outbound

This paper cites an unresolved cited work.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Unresolved cited work

Reference 8

Resolution: unresolved; raw_fallback, observed 2026-08-11T05:13:38.764754Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 70b182bf-4226-494e-be49-53dc928d408e · outbound

This paper cites RoFormer: Enhanced Transformer with Rotary Position Embedding.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion RoFormer: Enhanced Transformer with Rotary Position Embedding

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-11T05:13:37.794179Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation ddccdccd-5c4f-4df9-bd5d-c335319b2b45 · outbound

This paper cites Protein PDB GFAP 6A9P TfR 3KAS GLP-1R 3C5T AMHR2 7L0J GLAST 5LM4 NCAM1 2HAZ RBX1 1LDJ G.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Protein PDB GFAP 6A9P TfR 3KAS GLP-1R 3C5T AMHR2 7L0J GLAST 5LM4 NCAM1 2HAZ RBX1 1LDJ G

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:38.600082Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation fc683f00-e602-4576-ba75-9505bb63b600 · outbound

This paper cites 13 De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Vinogradov, A.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion 13 De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Vinogradov, A

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:39.197951Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 64bfbbfc-51da-4aba-a6d8-84bd5efd4632 · outbound

This paper cites A., and Riniker, S.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion A., and Riniker, S

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:39.165669Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 056914af-a6ee-4fbf-bf46-dcaad4d8d10b · outbound

This paper cites Pepland: a large-scale pre-trained peptide representation model for a compre- hensive landscape of both canonical and non-canonical amino acids.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Pepland: a large-scale pre-trained peptide representation model for a compre- hensive landscape of both canonical and non-canonical amino acids

Reference 14

Resolution: verified exact; raw_fallback, observed 2026-08-11T05:13:38.207274Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 2af1f7b4-04fc-43e8-b301-3db257b2c68c · outbound

This paper cites an unresolved cited work.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Unresolved cited work

Reference 15

Resolution: unresolved; raw_fallback, observed 2026-08-11T05:13:39.111224Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 53bb4dfc-035e-4d5d-8546-f6db81db98d3 · outbound

This paper cites (Bottom) Plots depicting the average predicted score for NCAM1 binding affinity, solubility, hemolysis, and non-fouling over iterations of MCTS.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion (Bottom) Plots depicting the average predicted score for NCAM1 binding affinity, solubility, hemolysis, and non-fouling over iterations of MCTS

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:38.960929Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation efcb2e05-eff0-44ca-9c6d-859d15f3b6b0 · outbound

This paper cites ( B) Plot of average predicted binding affinity score to TfR over iterations.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion ( B) Plot of average predicted binding affinity score to TfR over iterations

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:38.898687Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 5e63032e-1519-4a55-b2f0-679d43b9a410 · outbound

This paper cites an unresolved cited work.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Unresolved cited work

Reference 22

Resolution: unresolved; raw_fallback, observed 2026-08-11T05:13:38.865582Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation a8d8b9d0-07bc-4e82-b2c7-989277e4366d · outbound

This paper cites an unresolved cited work.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Unresolved cited work

Reference 23

Resolution: unresolved; raw_fallback, observed 2026-08-11T05:13:38.834952Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 4d134236-6c90-4a3e-909a-47e5ed7d6aec · outbound

This paper cites Model Train Loss ( ↓) Train PPL ( ↓) Val Loss ( ↓) Val PPL ( ↓) PepMDLM 0.832 2.460 0.880 2.277 D.3.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Model Train Loss ( ↓) Train PPL ( ↓) Val Loss ( ↓) Val PPL ( ↓) PepMDLM 0.832 2.460 0.880 2.277 D.3

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:38.807151Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation e6f7c609-5a40-475d-a7d3-1ef971281fff · outbound

This paper cites Plot of true permeability (logP) on the x-axis and predicted permeability on the y-axis for the (A) validation set and (B) training set.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Plot of true permeability (logP) on the x-axis and predicted permeability on the y-axis for the (A) validation set and (B) training set

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:38.735454Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 98e8981f-0d36-45c2-b994-01920cfec6bf · outbound

This paper cites an unresolved cited work.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Unresolved cited work

Reference 27

Resolution: unresolved; raw_fallback, observed 2026-08-11T05:13:38.705230Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 5580cd3a-5ac4-4b4a-b415-d3e96bff48ad · outbound

This paper cites an unresolved cited work.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Unresolved cited work

Reference 31

Resolution: unresolved; raw_fallback, observed 2026-08-11T05:13:38.557262Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation ff49f5c7-868a-46e6-b074-bf6fd451ab1e · outbound

This paper cites an unresolved cited work.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Unresolved cited work

Reference 200

Resolution: unresolved; raw_fallback, observed 2026-08-11T05:13:39.075757Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation ee286819-e2a0-4e56-b5c7-c9aceea9ef00 · outbound

This paper cites Z., Bezemek, Z., Patel, S., Rector-Brooks, J., Yao, S., Tong, A., and Chatterjee, P.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Z., Bezemek, Z., Patel, S., Rector-Brooks, J., Yao, S., Tong, A., and Chatterjee, P

Reference 2003

Resolution: unresolved; no resolver link, observed 2026-08-11T05:13:37.770101Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 36423c7f-151c-4d47-b44c-093634baa366 · outbound

This paper cites The final results were visualized in PyMol (Schrödinger, LLC,.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion The final results were visualized in PyMol (Schrödinger, LLC,

Reference 2009

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:38.626807Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation b85ca8fd-01bc-4d1a-8c6d-dc7079349fe7 · outbound

This paper cites The tool is freely available on HuggingFace: https://huggingface.co/spaces/ChatterjeeLab/SMILES2PEPTIDE.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion The tool is freely available on HuggingFace: https://huggingface.co/spaces/ChatterjeeLab/SMILES2PEPTIDE

Reference 2012

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:38.651730Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 2a0c59e4-1694-4524-8558-693770fe70a0 · outbound

This paper cites PepMLM: Target Sequence-Conditioned Generation of Therapeutic Peptide Binders via Span Masked Language Modeling.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion PepMLM: Target Sequence-Conditioned Generation of Therapeutic Peptide Binders via Span Masked Language Modeling

Reference 2016

Resolution: unresolved; no resolver link, observed 2026-08-11T05:13:37.716221Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d4da8b4c-5717-48e0-8b69-183116b425e2 · outbound

This paper cites N., and Bryant, P.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion N., and Bryant, P

Reference 2018

Resolution: verified exact; doi, observed 2026-08-11T05:13:38.055583Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 3d5d7cbe-5c90-4661-97a8-00cbc9d09c14 · outbound

This paper cites Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction

Reference 2020

Resolution: unresolved; no resolver link, observed 2026-08-11T05:13:37.777395Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 914c9004-f6a0-4422-8932-79947dd1f104 · outbound

This paper cites Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation

Reference 2021

Resolution: verified exact; local_arxiv, observed 2026-08-11T05:13:38.265995Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 8d6ace08-2d9b-4621-a00a-7710a11d74dd · outbound

This paper cites Unlocking Guidance for Discrete State-Space Diffusion and Flow Models.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Unlocking Guidance for Discrete State-Space Diffusion and Flow Models

Reference 2022

Resolution: unresolved; no resolver link, observed 2026-08-11T05:13:37.754589Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation f24deb49-25b1-4982-8ae2-dce3ff02997c · outbound

This paper cites mop- pit:de novogeneration of motif-specific binders 10 De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion with protein language models.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion mop- pit:de novogeneration of motif-specific binders 10 De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion with protein language models

Reference 2023

Resolution: verified exact; doi, observed 2026-08-11T05:13:38.084165Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation f1addbb4-23f9-4ab4-8ec7-511ba852ac6c · outbound

This paper cites Your Absorbing Discrete Diffusion Secretly Models the Conditional Distributions of Clean Data.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Your Absorbing Discrete Diffusion Secretly Models the Conditional Distributions of Clean Data

Reference 2024

Resolution: unresolved; no resolver link, observed 2026-08-11T05:13:37.762183Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 56d28f0b-b04e-4100-9b8e-8aa4510a9d14 · outbound

This paper cites Rigon, C., Andrisani, A., Forzan, M., D’Antona, D., Bru- son, A., Cosmi, E., Ambrosini, G., Tiboni, G.

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion Rigon, C., Andrisani, A., Forzan, M., D’Antona, D., Bru- son, A., Cosmi, E., Ambrosini, G., Tiboni, G

Reference 2025

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T05:13:39.246788Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Pith citing papers

Observation 63d6b676-2638-442a-a2c9-8f2658d714ba · inbound

Beyond SMILES: Evaluating Agentic Systems for Drug Discovery cites this paper.

Beyond SMILES: Evaluating Agentic Systems for Drug Discovery PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

Reference 20

Resolution: unresolved; no resolver link, observed 2026-08-03T02:57:47.932219Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 86c6df9e-932f-496e-b9a1-ecc3af5d7fff · inbound

Adaptive Order Policies for Masked Diffusion cites this paper.

Adaptive Order Policies for Masked Diffusion PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

Reference 80

Resolution: verified exact; arxiv_id, observed 2026-06-28T23:42:49.830262Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation b3429398-152b-45ec-80da-1db5e8c1f10b · inbound

On the Design Space of Discrete Diffusion Online Adaptation for Molecular Optimization cites this paper.

On the Design Space of Discrete Diffusion Online Adaptation for Molecular Optimization PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

Reference 63

Resolution: unresolved; no resolver link, observed 2026-07-12T06:44:20.438683Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.