scDEFT: A deep learning framework for drug-effect prediction and counterfactual reasoning
Updated 1 h ago · first seen 11 Sept 2026
paper_01M294FQ74RNJFA9R7MDRQDQXC
- Published
- 11 Sept 2026
- T1 · 1 h ago
- arXiv
- 2609.10831
- T1 · 1 h ago
- Category
- q-bio.QM
- T1 · 1 h ago
Abstract
Longitudinal single cell atlases now capture matched pre treatment and post treatment states from responders and non responders, presenting an opportunity to mechanistically explain why two patients on the same drug diverge. We introduce scDEFT (single cell Drug EFfect Transducer), which treats a drug as a conditioning operator on cell representations, enabling prediction and explanation. In scDEFT, feature wise linear modulation produces drug conditioned cell latents, learned under abundant per cell supervision and then frozen. Two independent heads aggregate those latents over shared transcriptional neighborhoods to predict drug induced state change and responder status. A backward stage ranks the latent dimensions by how strongly they separate responders from non responders and maps them to genes under a cell composition control. On a harmonized inflammatory bowel disease atlas of 1.16 million cells, three cohorts and two drug classes, scDEFT predicts state change at 45% of the baseline to reproducibility ceiling headroom and stratifies responders before treatment at AUROC 0.70, where standard predictors remain at chance. These predictions and the drivers behind them support target and co target nomination, patient stratification, and counterfactual prediction of unseen drug cohort effects.
Authors 1
Murthy Devarakonda
Specification
- Official page
Source:arXiv (Atom API + RSS)T1observed 1 h agohigh
- Arxiv announce type
- cross
Source:arXiv (Atom API + RSS)T1observed 1 h agohigh
- arXiv id
- 2609.10831
Source:arXiv (Atom API + RSS)T1observed 1 h agohigh
- Categories
- q-bio.QM, cs.LG
Source:arXiv (Atom API + RSS)T1observed 1 h agohigh
Source:arXiv (Atom API + RSS)T1observed 1 h agohigh
- Primary category
- q-bio.QM
Source:arXiv (Atom API + RSS)T1observed 1 h agohigh
- Published
- 11 Sept 2026
Source:arXiv (Atom API + RSS)T1observed 1 h agohigh
Each value shows its source, tier and observation time. Conflicting claims are kept side by side and flagged — never averaged. How AI Atlas records facts →
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9
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T19
Freshest observation
1 h ago
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- Authors
- Murthy Devarakonda
As of
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Claim history
Official pageofficial_url1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| https://arxiv.org/abs/2609.10831 | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Abstractabstract1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| Longitudinal single cell atlases now capture matched pre treatment and post treatment states from responders and non responders, presenting an opportunity to mechanistically explain why two patients on the same drug diverge. We introduce scDEFT (single cell Drug EFfect Transducer), which treats a drug as a conditioning operator on cell representations, enabling prediction and explanation. In scDEFT, feature wise linear modulation produces drug conditioned cell latents, learned under abundant per cell supervision and then frozen. Two independent heads aggregate those latents over shared transcriptional neighborhoods to predict drug induced state change and responder status. A backward stage ranks the latent dimensions by how strongly they separate responders from non responders and maps them to genes under a cell composition control. On a harmonized inflammatory bowel disease atlas of 1.16 million cells, three cohorts and two drug classes, scDEFT predicts state change at 45% of the baseline to reproducibility ceiling headroom and stratifies responders before treatment at AUROC 0.70, where standard predictors remain at chance. These predictions and the drivers behind them support target and co target nomination, patient stratification, and counterfactual prediction of unseen drug cohort effects. | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Arxiv announce typearxiv_announce_type1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| cross | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
arXiv idarxiv_id1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| 2609.10831 | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Categoriescategories1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| q-bio.QM, cs.LG | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
PDFpdf_url1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| https://arxiv.org/pdf/2609.10831 | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Primary categoryprimary_category1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| q-bio.QM | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Publishedpublished_at1
| Value | Valid from → to | Status | Source | Confidence | Extractor |
|---|---|---|---|---|---|
| 11 Sept 2026 | → current | current | arXiv (Atom API + RSS)T1 | high | deterministic |
Claims are temporal and append-only: a new observation closes the previous claim (valid_to) instead of overwriting it. Conflicting claims from different sources are kept side by side and flagged — never averaged. Methodology →
- New paperPaperscDEFT: A deep learning framework for drug-effect prediction and counterfactual reasoning
New paper: scDEFT: A deep learning framework for drug-effect prediction and counterfactual reasoning
arxiv
| Source | Document | Type | Tier | Last observed | Snapshots |
|---|---|---|---|---|---|
| arXiv (Atom API + RSS) | rss.arxiv.org/rss/cs.LG | feed | T1· Official | 1 h ago | 1 |
Tier 1 = official/primary, 2 = quality secondary, 3 = community, 4 = unverified. Every snapshot is archived; see all sources and the methodology.