Initial VariantAssist Gemma 4 31B GGUF release

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LICENSE

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NOTICE.md

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+# Notice
+
+This repository contains GGUF model files produced from a merged VariantAssist LoRA adapter and Gemma 4 31B IT base model.
+
+Upstream base model:
+
+```text
+google/gemma-4-31B-it
+```
+
+VariantAssist LoRA adapter:
+
+```text
+LocusForge/VariantAssist-Gemma4-31B-LoRA
+```
+
+The GGUF files are derivative quantized artifacts for local inference with llama.cpp-compatible runtimes.
+Use of these files remains subject to the applicable upstream model license and terms.
+
+VariantAssist is intended to support structured expert review and is not a diagnostic device.

README.md

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+---
+license: apache-2.0
+base_model: LocusForge/VariantAssist-Gemma4-31B-LoRA
+base_model_relation: quantized
+library_name: gguf
+pipeline_tag: text-generation
+tags:
+- gguf
+- llama.cpp
+- llama-server
+- unsloth
+- unsloth-quantized
+- llama-cpp-quantized
+- gemma
+- gemma-4
+- clinical-genetics
+- variant-interpretation
+- acmg-amp
+- local-first
+- json
+- variantassist
+language:
+- en
+---
+
+<p align="center">
+  <img src="assets/variantassist-logo.svg" alt="VariantAssist" width="720">
+</p>
+
+<p align="center">
+  <a href="https://variantassist.com/">variantassist.com</a>
+  ·
+  <a href="https://github.com/LocusForge/VariantAssist">GitHub</a>
+  ·
+  <a href="https://huggingface.co/LocusForge/VariantAssist-Gemma4-31B-GGUF/blob/main/LICENSE">License</a>
+</p>
+
+<div style="background-color:#fff6df;border-left:5px solid #d4900a;padding:14px 16px;margin:18px 0;border-radius:6px;">
+  <strong>Compatibility note:</strong> these VariantAssist-tuned GGUF models are currently intended only for <strong>Level-1 Annotation</strong>.
+  For other VariantAssist workflow stages, use the original Q8 model rather than these tuned quantizations.
+</div>
+
+# VariantAssist Gemma 4 31B GGUF
+
+VariantAssist Gemma 4 31B GGUF is the local-inference release of the VariantAssist Gemma 4 31B LoRA model.
+The files in this repository are produced by merging the [VariantAssist LoRA adapter](https://huggingface.co/LocusForge/VariantAssist-Gemma4-31B-LoRA) with Gemma 4 31B IT and converting/quantizing the merged model for llama.cpp-compatible runtimes.
+
+VariantAssist is designed to support structured clinical genetic variant review.
+It is not a diagnostic device and must not replace a clinician, medical geneticist, laboratory director, or ACMG/AMP-trained reviewer.
+
+## Evaluation Protocol
+
+All model scores below are evaluated after the VariantAssist 3-to-5 consensus procedure.
+For each variant, the model is first run three times.
+If all three runs return the same pathogenicity level, that level is accepted.
+If any run differs, two additional runs are performed; a result is accepted only if one pathogenicity level appears at least three times across the five runs.
+If no level reaches that threshold, the result is marked as no consensus and may be rerun.
+
+No dissensus/no-consensus cases occurred in this benchmark.
+In practical use, no-consensus cases have been observed at roughly 1 in 5000 variants.
+
+## Available GGUF Files
+
+| File | Size | Match | Quant | Role |
+|---|---:|---:|---:|---|
+| `VA-Gemma4-31B-UD-Q8_0.gguf` | 31 GB | 86 | UDQ | Best current benchmark result |
+| `VA-Gemma4-31B-Q4_K_M.gguf` | 18 GB | 85 | LQ | Practical default |
+| `VA-Gemma4-31B-Q8_0.gguf` | 31 GB | 83 | LQ | Classic Q8 variant |
+| `VA-Gemma4-31B-UD-Q4_K_M.gguf` | 18 GB | 82 | UDQ | Smaller UDQ variant |
+| `VA-Gemma4-31B-F16.gguf` | 58 GB | 81 | F16 | Reference GGUF |
+| `VA-Gemma4-31B-BF16-00002-of-00002.gguf` | 11 GB | - | BF16 | BF16 export shard |
+| `VA-Gemma4-31B-BF16-mmproj.gguf` | 1.2 GB | - | MMProj | Not needed for text-only runs |
+
+<p style="font-size:0.9em;color:#4f5b66;">
+  <strong>UDQ</strong> = Unsloth dynamic quantization.
+  <strong>LQ</strong> = classic llama.cpp quantization.
+  The Unsloth quantized variants were selected/validated on examples with the correct VariantAssist Level-1 input/output structure.
+</p>
+
+## Benchmark Results
+
+The ATP7B benchmark contains 100 Wilson disease variants with consensus labels from five independent expert annotations.
+The primary ground truth is strict majority consensus.
+
+<p align="center">
+  <img src="assets/accuracy_vs_reasoning_tokens.png" alt="ATP7B benchmark accuracy versus reasoning-token budget">
+</p>
+
+Reasoning budget is usually an important quality driver for classic quantized models.
+In this benchmark, the VariantAssist-tuned quantized runs improve accuracy while also reducing the reasoning-token budget compared with the original quantized baseline.
+
+Current highlighted result:
+
+- `VariantAssist UD-Q8`: 86/100 exact matches on the ATP7B benchmark.
+- No strong errors in the selected released-model comparison.
+- Expert-consensus reference: 15 average expert disagreements, equivalent to 85/100 agreement.
+
+<p align="center">
+  <img src="assets/confusion_matrix_variantassist_ud_q8.png" alt="VariantAssist UD-Q8 ATP7B confusion matrix" width="720">
+</p>
+
+## Prompts, Schema, And Reproducibility
+
+Use the public prompt archive for reproducible evaluation:
+
+- [ATP7B prompt archive](https://github.com/LocusForge/VariantAssist-supplement/tree/main/benchmark/atp7b-prompts)
+- [System instruction](https://github.com/LocusForge/VariantAssist-supplement/blob/main/benchmark/atp7b-prompts/system_instruction.txt)
+- [Response schema](https://github.com/LocusForge/VariantAssist-supplement/blob/main/benchmark/atp7b-prompts/response_schema.json)
+- [Annotation rules](https://github.com/LocusForge/VariantAssist-supplement/blob/main/benchmark/atp7b-prompts/annotation_rules.json)
+- [ATP7B benchmark ground truth](https://github.com/LocusForge/VariantAssist-supplement/tree/main/benchmark)
+
+That archive contains the system prompt, schema, annotation rules, and per-variant prompts used for benchmark-style evaluation.
+
+## Runtime
+
+Recommended runtime is `llama-server` from a recent llama.cpp build with Gemma 4 reasoning support.
+
+Recommended server command:
+
+```bash
+llama-server \
+  -m /path/to/VA-Gemma4-31B-Q4_K_M.gguf \
+  --no-mmproj \
+  --jinja \
+  -ngl auto \
+  -c 32768 \
+  -fa on \
+  --swa-full \
+  -np 1 \
+  --cache-prompt \
+  --cache-reuse 256 \
+  --slot-prompt-similarity 0.10 \
+  --ctx-checkpoints 1 \
+  --checkpoint-every-n-tokens 4096 \
+  --cache-ram 2048 \
+  --kv-unified \
+  --cache-type-k f16 \
+  --cache-type-v f16 \
+  -b 2048 \
+  -ub 512 \
+  --no-cont-batching \
+  --perf \
+  --metrics \
+  --host 127.0.0.1 \
+  --port 8091 \
+  --reasoning on \
+  --reasoning-budget 8192 \
+  -t 24 \
+  -tb 24
+```
+
+Small-machine optimization:
+
+```bash
+-c 8192 --reasoning-budget 4096
+```
+
+What to change:
+
+- `-m`: select the GGUF file.
+- `--host` / `--port`: set your serving endpoint.
+- `-t` / `-tb`: match your CPU thread budget.
+- `-c` and `--reasoning-budget`: reduce on smaller machines if needed.
+
+What to keep for VariantAssist Level-1 runs:
+
+- `--reasoning on`: benchmarked runs use reasoning mode.
+- `--jinja`: uses the Gemma chat template.
+- `--no-mmproj`: this release is text-only.
+- `--cache-type-k f16 --cache-type-v f16`: keeps KV cache quality stable.
+- `--no-cont-batching`: keeps single-review behavior predictable.
+
+Reasoning should remain enabled for VariantAssist-style review.
+In our workflow, no-reasoning runs could generate shorter single responses, but were less reliable in the completed 3-to-5 consensus process and could require reruns.
+
+## Intended Use
+
+Use this release for:
+
+- local-first VariantAssist review workflows;
+- structured evidence synthesis for expert review;
+- JSON-oriented draft outputs;
+- reproducible local benchmarking with the public ATP7B prompt archive.
+
+## Out Of Scope
+
+Do not use this model for:
+
+- autonomous diagnosis;
+- direct patient-facing medical advice;
+- final ACMG/AMP classification without expert review;
+- clinical interpretation outside the supplied evidence context;
+- high-stakes clinical workflows without local validation.
+
+## Training Data
+
+The full fine-tuning corpus is not distributed with this release because it may include clinical-context and literature-derived materials requiring separate privacy and licensing review.
+Public benchmark data, prompt templates, response schema, and de-identified examples are provided separately to support reproducible evaluation.
+
+## Links
+
+- Website: https://variantassist.com/
+- LoRA adapter: https://huggingface.co/LocusForge/VariantAssist-Gemma4-31B-LoRA
+- Main project: https://github.com/LocusForge/VariantAssist
+- Benchmark and prompts: https://github.com/LocusForge/VariantAssist-supplement/tree/main/benchmark
+- Upstream base model: https://huggingface.co/google/gemma-4-31B-it
+- License: [Apache License 2.0](https://huggingface.co/LocusForge/VariantAssist-Gemma4-31B-GGUF/blob/main/LICENSE)
+- Notice: [NOTICE.md](https://huggingface.co/LocusForge/VariantAssist-Gemma4-31B-GGUF/blob/main/NOTICE.md)

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