Publish SLp-1.1 r1 cellular and genomic world model

README.md

@@ -1,21 +1,46 @@
 ---
 license: other
+license_name: mit-weights-with-source-data-terms
+license_link: https://github.com/abiome-org/SLp/blob/main/release/THIRD_PARTY_NOTICES.md
 tags:
 - biology
-- synthetic-lethality
+- genomics
 - world-model
-- single-cell
+- synthetic-lethality
+- pytorch
+datasets:
+- potteryrage/SLp-1.1-data
 ---
 
 # SLp
 
-Public, immutable research artifacts for SL-Predict, a cellular world model developed for cold-start synthetic-lethality research.
+SLp models molecular state and the consequences of genetic interventions.
+Synthetic-lethality prediction is a downstream application of the learned world.
+
+| Release | Artifact path | Description |
+|---|---|---|
+| SLp-1.1 r1 | `checkpoints/v1.1/SLp-1.1-r1/` | 15.12M-parameter molecular and functional world; RNA/protein generation, continuous fitness decoding and ten downstream SL decoders |
+| SLp-1 | `checkpoints/v1/SLp-1/` | Frozen historical proof of concept |
 
-## Layout
+[Source and usage](https://github.com/abiome-org/SLp) ·
+[Model card](https://github.com/abiome-org/SLp/blob/main/MODEL_CARD.md) ·
+[Prepared data](https://huggingface.co/datasets/potteryrage/SLp-1.1-data)
 
-- `checkpoints/v1/SLp-1/`: the 59.7M-parameter SLp-1 checkpoint, loader manifest, and release record.
-- `data/<corpus>/<version>/`: redistributable source or derived data releases with a machine-readable `audit.json`.
+SLp-1.1 r1 includes actual weights, inference source, normalizers, biological
+contexts, a descriptor registry and downstream decoder weights. Use the
+revision-pinned download command in the source repository; inference does not
+require the training corpus. The original SLp code and weights are MIT.
+Bundled biological data retain their source terms; see the release notices.
+Historical artifacts and their terms are preserved.
 
-Each data audit records provenance, license evidence, transformations, population, endpoints, split construction, exclusions, and SHA-256 checksums. Licenses vary by corpus; consult the audit beside each release. No SL decoder is bundled with SLp-1.
+On ten official MuSL CV3 splits, SLp-1.1's downstream decoder has mean AUROC
+0.787830 and AP 0.780602. Its matched untrained functional component reaches
+0.734081/0.729673, while direct descriptors reach 0.798579/0.802964.
+The molecular and functional worlds are trained on quantitative observations;
+human SL labels train only the separate fold-local decoder. These retrospective
+results are research evidence, not a prospective SOTA claim or clinical validation.
 
-The artifacts are research outputs, not clinical software. They do not establish synthetic lethality or treatment efficacy for any individual.
+The pretraining mix combines human CRISPRi/CRISPRa RNA, paired RNA/protein,
+native yeast RNA populations, human single-gene fitness and yeast double-mutant
+fitness. See the model card for exact populations, units, sampling proportions,
+exclusions and species-specific results.

checkpoints/v1.1/SLp-1.1-r1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 SLp contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

checkpoints/v1.1/SLp-1.1-r1/THIRD_PARTY_NOTICES.md

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+# Data and third-party notices
+
+Original SLp source code, documentation and trained SLp weights are distributed
+under the MIT license. This does not relicense third-party observations,
+annotations, benchmark data, software or pretrained feature models. Existing
+third-party LICENSE files continue to apply.
+
+The SLp-1.1 data release contains transformed, filtered research data. Its
+`inventory.json` records exact files, sizes, hashes and roles. Historical input
+manifests are retained byte-for-byte, including historical path strings; loaders
+use the repository-relative paths described in the development guide.
+
+| Source | Released material and attribution | Terms |
+|---|---|---|
+| Replogle et al. (2022), [Figshare 20029387 v1](https://doi.org/10.25452/figshare.plus.20029387.v1) | K562/RPE1 essential and K562 genome-wide CRISPRi counts, filtered populations and fitting indices | CC BY 4.0 |
+| Frangieh et al. (2021), scPerturb [Zenodo 10044268](https://doi.org/10.5281/zenodo.10044268) | Processed public paired RNA/protein data, sparse training shards and population summaries; attribution also to the scPerturb authors | CC BY 4.0; controlled raw sequencing is excluded |
+| Nadal-Ribelles et al. (2025), [Zenodo 14062629](https://doi.org/10.5281/zenodo.14062629) | Yeast Control/NaCl count-derived population means, metadata and reference panels from author-released Seurat objects | CC BY 4.0 |
+| Broad DepMap, [24Q2](https://doi.org/10.25452/figshare.plus.25880521.v1) | Filtered human CRISPR gene effects, observed cell contexts and fitting/development partitions | CC BY 4.0 |
+| Costanzo et al. (2016), [Dryad 4291s](https://doi.org/10.5061/dryad.4291s) | Species-native yeast single/double-mutant fitness, sampled and partitioned from the authors' raw pairwise data | CC0 1.0 |
+| Norman et al. (2019), [GSE133344](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133344) | Processed molecular single/combination population responses | NCBI GEO public-data policy; submitter rights retained |
+| Nadig et al. (2025), [GSE264667](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE264667) | Processed HepG2 molecular responses | NCBI GEO public-data policy; submitter rights retained |
+| Zhao et al. (2021), [GSE164996](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164996) | MCF10A processed molecular population responses in three environments | NCBI GEO public-data policy; submitter rights retained |
+| [Saccharomyces Genome Database](https://www.yeastgenome.org/) and [Gene Ontology](https://geneontology.org/docs/go-citation-policy/) | Stable identities, protein-sequence and shared MF/CC annotation-derived features | CC BY 4.0; source snapshots recorded in `rights/` and feature receipts |
+| [Ensembl](https://www.ensembl.org/info/about/legal/disclaimer.html), [STRING](https://string-db.org/cgi/access.pl), [ESM](https://github.com/facebookresearch/esm) | Human identity/sequence, physical-network features and frozen ESM2-8M protein representations | Ensembl source terms, STRING CC BY 4.0, ESM MIT; original feature-model weights are not redistributed here |
+| [MuSL](https://github.com/JieZheng-ShanghaiTech/MuSL) | Selected official CV folds and the associated gene roster; Jie Zheng (2022) | MIT; upstream LICENSE included with the selected files |
+
+SLp adaptations include gene filtering, population aggregation, log1p(CP10K)
+normalization where recorded, sparse/memory-mapped conversion, descriptor
+projection, species-native partitioning, and frozen-model simulation features.
+Derived files that combine sources retain all applicable component terms.
+Original model predictions and fitted SLp decoder weights are MIT; observed
+contexts and cached input descriptors accompanying them retain source terms.
+
+For the three GEO sources, the redistribution basis is the
+[GEO public-data policy](https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html)
+and the authors' public processed-data deposits. NCBI imposes no distribution
+restriction but does not transfer submitters' rights. These files are therefore
+identified with that policy, not represented as CC BY or MIT. The original
+conditional rights receipts remain intact. No additional source-specific
+restriction was identified in the recorded public-data scopes.
+
+The release excludes controlled Frangieh sequencing, patient-level TCGA data,
+downloaded third-party model weights, credentials, OMF runtime records and the
+separate SLAMR benchmark inputs whose redistribution terms are not established.
+SLAMR aggregate evaluation statistics remain reported in the model card.
+
+Historical input indices cite a yeast summary-only receipt. The accompanying
+`rights/zenodo-14062629-cc-by-4.0.yaml` and
+`rights/slp-1-1-nadal-ribelles-yeast-seus-split-cc-by-4.0.yaml` supply the
+appropriate public Seurat-source scope for the count-derived fitting arrays;
+the original receipt and index are not silently rewritten.

checkpoints/v1.1/SLp-1.1-r1/manifest.json

@@ -0,0 +1,74 @@
+{
+  "decoders": [
+    "decoders/seed42-fold0-world.txt",
+    "decoders/seed42-fold1-world.txt",
+    "decoders/seed42-fold2-world.txt",
+    "decoders/seed42-fold3-world.txt",
+    "decoders/seed42-fold4-world.txt",
+    "decoders/seed432-fold0-world.txt",
+    "decoders/seed432-fold1-world.txt",
+    "decoders/seed432-fold2-world.txt",
+    "decoders/seed432-fold3-world.txt",
+    "decoders/seed432-fold4-world.txt"
+  ],
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+  },
+  "functional_weights_sha256": "a0968b69b4409ac7faa34687b7ae3c3725c34d958e6587e783fa42fb9f1db818",
+  "molecular_weights_sha256": "9ecffff8d83e41878da638847d77a950077d2270e2cf6dc951d3e9e0309c4a15",
+  "schema": "slp.cellular-genomic-world/v1",
+  "scope": "research world with RNA/protein generation, species-native conditional fitness, fixed excess-loss SL scoring, and a separately supervised SL decoder"
+}

checkpoints/v1.1/SLp-1.1-r1/molecular_model/training-index.json

@@ -0,0 +1,188 @@
+{
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+  "exclusionRosterReceipts": {
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+    "weight": 0.15
+  },
+  "populations": [
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+      "name": "k562",
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+      "taxon": 9606,
+      "weight": 0.04
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+      "taxon": 9606,
+      "weight": 0.04
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+      "rows": 1758,
+      "taxon": 9606,
+      "weight": 0.04
+    },
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checkpoints/v1.1/SLp-1.1-r1/molecular_model/training-protocol.json

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+      "mechanism": 2,
+      "name": "yeast",
+      "queries": 6683,
+      "scale_range": [
+        0.5,
+        0.5
+      ],
+      "supported_queries": 6683,
+      "taxon": 4932,
+      "used_shards": {},
+      "weight": 0.2
+    }
+  ],
+  "status": "trained_research_candidate",
+  "steps": 10000
+}

checkpoints/v1.1/SLp-1.1-r1/requirements.lock

@@ -0,0 +1,6 @@
+torch==2.11.0+cu128
+numpy==2.4.4
+scipy==1.17.1
+safetensors==0.7.0
+lightgbm==4.6.0
+scikit-learn==1.9.0