# From Retrieval to Typed Decisions: Calibrated System One Models from Biomedical Sentence Encoders

arXiv: https://arxiv.org/abs/2610.02486 · HTML: https://mlsanity.com/paper/2610.02486/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 26 of its 58 references that are in the map.
- First posted on arXiv 1 Oct 2026.

## Builds on (most cited first, 26 of 26)

- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [On Calibration of Modern Neural Networks](https://mlsanity.com/paper/1706.04599/) (2017)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [MS MARCO: A Human Generated MAchine Reading COmprehension Dataset](https://mlsanity.com/paper/1611.09268/) (2016)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [BEIR: A Heterogenous Benchmark for Zero-shot Evaluation of Information Retrieval Models](https://mlsanity.com/paper/2104.08663/) (2021)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [MPNet: Masked and Permuted Pre-training for Language Understanding](https://mlsanity.com/paper/2004.09297/) (2020)
- [FrugalGPT: How to Use Large Language Models While Reducing Cost and Improving Performance](https://mlsanity.com/paper/2305.05176/) (2023)
- [Towards General Text Embeddings with Multi-stage Contrastive Learning](https://mlsanity.com/paper/2308.03281/) (2023)
- [Passage Re-ranking with BERT](https://mlsanity.com/paper/1901.04085/) (2019)
- [C-Pack: Packed Resources For General Chinese Embeddings](https://mlsanity.com/paper/2309.07597/) (2023)
- [Fact or Fiction: Verifying Scientific Claims](https://mlsanity.com/paper/2004.14974/) (2020)
- [Smarter, Better, Faster, Longer: A Modern Bidirectional Encoder for Fast, Memory Efficient, and Long Context Finetuning and Inference](https://mlsanity.com/paper/2412.13663/) (2024)
- [Calibration of Pre-trained Transformers](https://mlsanity.com/paper/2003.07892/) (2020)
- [Benchmarking Zero-shot Text Classification: Datasets, Evaluation and Entailment Approach](https://mlsanity.com/paper/1909.00161/) (2019)
- [Explainable Automated Fact-Checking for Public Health Claims](https://mlsanity.com/paper/2010.09926/) (2020)
- [MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval](https://mlsanity.com/paper/2307.00589/) (2023)
- [Lessons from Natural Language Inference in the Clinical Domain](https://mlsanity.com/paper/1808.06752/) (2018)
- [BioClinical ModernBERT: A State-of-the-Art Long-Context Encoder for Biomedical and Clinical NLP](https://mlsanity.com/paper/2506.10896/) (2025)
- [Calibrated Decisions at Scale: Converting Police Crash Narratives into Probabilistic Crash Variables with a System One Model (Jev)](https://mlsanity.com/paper/2609.24052/) (2026)
- [Calibrated Decision Models for Autonomous Penetration-Testing Harnesses: JEV and Laya as System One Decision Layers for LLM-Driven Pentest Agents](https://mlsanity.com/paper/2609.28940/) (2026)
- [LAVOIR: Teaching a Single-Pass Decision Encoder When and What to Ask with Amortized Value of Information](https://mlsanity.com/paper/2609.30706/) (2026)

## Abstract (arXiv)

Typed decision models answer schema-constrained questions about a text in one forward pass and return probabilities meant to be thresholded. We ask whether biomedical sentence encoders trained for retrieval are good starting points for such models. We present SBERT2S1, which converts Sentence-Transformers encoders into bi-encoder, cross-head (C) and prior-fused residual (PFR) decision models, together with BIODECIDE, a biomedical typed-decision suite, and MEDLINE-S1, 243k training decisions derived from NLM indexing. Across six parent-retriever pairs, retrieval training improves zero-shot matching of content-bearing options. After fine-tuning, its effect depends on the head: across five pairs and three training-set sizes, retrieval training significantly helps PFR, which keeps the retrieval prior, in 10 of 15 comparisons, but helps C in one and hurts it in five. A matched grid of two heads and five training objectives shows that C outperforms PFR under every objective, and that the released RLCD recipe of open System One models trails cross-entropy by 2.5-3.0 points. The deficit stems mainly from its reward normalisation, which inflates the noisy score-function term 3.6-15-fold; an unbiased leave-one-out estimator recovers most of the gap. After temperature scaling, no objective is clearly better calibrated than cross-entropy. We release the code, the MEDLINE-S1 labels and a model.