Do Language Models Know What Compelling Scientific Evidence Looks Like?
Organizations: Edison Scientific Inc., San Francisco, CA, USA · MIT CSAIL, Cambridge, MA, USA
Abstract
Expert scientists excel at weighing empirical findings from multiple sources that vary in both statistical reliability and epistemic relevance. To what extent are language models, which are increasingly driving autonomous discovery systems, capable of such evidence deliberation? We introduce EDB-Bio, a scientific reasoning benchmark curated from real-world data in three biological domains: drug-perturbation transcriptomics, CRISPR screens, and human genome-wide association studies (GWAS). Each of EDB-Bio's 96k episodes presents a sequence of experimental results from published studies and asks the model to predict the probability that a target hypothesis is true. Out-of-the-box, open-weight and frontier models alike demonstrate systematic underconfidence and attain Brier scores comparable to a trivial base-rate forecaster. Post-training against strictly proper scoring rules significantly improves both calibration and discrimination. This calibration pays off downstream: in a sequential experiment selection task, our Ibis0 model is 2.5 times more efficient than the best frontier model. Throughout, quantifying evidence weights as Bayes factors reveals how models update their beliefs over time, whether they agree with expert biologists on relevance, and where they exhibit inconsistencies and biases. Our work extends calibration training and uncertainty analysis to a realistic scientific forecasting setting with applications to human cancer biology. We release all code, data, and trained models.
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Appendix
| Tahoe | DepMap | GWAS | |
|---|---|---|---|
| P1 Targets | Mitochondrial, ribosomal, pseudogene and housekeeping-lncRNA genes excluded, as are near-zero base-mean measurements | Pan-essential and non-expressed genes excluded; targets drawn from the selective -dependency genes (essential in – of lines) | MHC/HLA variants excluded (long-range linkage disequilibrium makes single-variant labels unreliable), as are heavily replicated “textbook” pairs |
| P2 Diversity | cell lines, drugs across mechanisms, genes; balanced within every cell line | lineages, thousands of genes, at most episodes per gene | Thousands of genes and traits across EFO parent categories, with per-gene and per-trait caps; one episode per unique (SNP, trait) pair |
| P3 Hierarchy | Within-assay: same drug, other line same mechanism other drug, same line aggregate summary unrelated control | Cross-modal: same gene, same lineage same gene, other lineage co-essential partner drug targeting molecular state of in unrelated control | Locus and trait proximity: other SNP in gene, same trait same gene, related trait target SNP, related trait target SNP, unrelated trait pathway neighbor unrelated control |
| P4 Sufficiency | Significance-rich ( significant stubs), -moderate ( – ), or -poor (none) | Rich, moderate or poor in dependency-supporting evidence: dependent related lines, over-expression, amplification, damaging mutation, drug sensitivity | Rich, moderate or poor by capping significant related stubs. Non-significant related evidence is scarce in a catalog of significant hits, so poor pools fill largely with controls |
| P5 Leakage | No pool stub shares the target’s exact (drug, cell line) pair | Same-gene stubs come only from other lines; the molecular state of in is a different assay from the held-out fitness readout, so it is evidence rather than leakage | The exact (SNP, trait) pair is excluded. A different SNP in high linkage disequilibrium carries nearly the same signal; filtering it needs an LD reference panel and is deferred |
| Primary | Sensitivity | |
|---|---|---|
| Episodes per domain | ||
| Episodes, all three domains | ||
| Context lengths per episode | , from | , all of |
| Rows per domain | ||
| Rows, all three domains | ||
| Models evaluated |
| Domain | Measurement key | Measurement space | Exposed as stubs | Coverage | Test overlap |
|---|---|---|---|---|---|
| Tahoe | (drug, cell line, gene) | ( ) | |||
| DepMap | (gene, cell line) | ( ) | |||
| GWAS | (SNP, trait) | ( ) |
| Run | Training domains | Selection metric | Best value | Step |
| Ibis0 (classifier) | Tahoe, DepMap, GWAS | in-domain BCE | ||
| Ibis0 (non-thinking) | Tahoe, DepMap, GWAS | eval reward | ||
| Ibis0 (thinking) | Tahoe, DepMap, GWAS | eval reward | ||
| Ibis0 (classifier), Tahoe held out | DepMap, GWAS | in-domain BCE | ||
| Ibis0 (classifier), DepMap held out | Tahoe, GWAS | in-domain BCE | ||
| Ibis0 (classifier), GWAS held out | Tahoe, DepMap | in-domain BCE |
| Model | Brier Score ( ) | sMECE ( ) | AUROC ( ) | Reliability ( ) | Resolution ( ) | |
|---|---|---|---|---|---|---|
| Qwen3 (non-thinking) | 6,000 | 0.3336 [0.3237, 0.3436] | 0.3101 [0.2990, 0.3229] | 0.6608 [0.6471, 0.6752] | 0.1096 [0.1024, 0.1189] | 0.0250 [0.0226, 0.0295] |
| Tahoe | 2,000 | 0.3634 [0.3459, 0.3827] | 0.3367 [0.3201, 0.3589] | 0.6039 [0.5805, 0.6279] | 0.1277 [0.1140, 0.1452] | 0.0147 [0.0111, 0.0204] |
| DepMap | 2,000 | 0.2860 [0.2715, 0.2995] | 0.2773 [0.2575, 0.2978] | 0.7454 [0.7239, 0.7671] | 0.0854 [0.0754, 0.0977] | 0.0485 [0.0414, 0.0577] |
| GWAS | 2,000 | 0.3513 [0.3333, 0.3694] | 0.3162 [0.2966, 0.3391] | 0.6333 [0.6080, 0.6571] | 0.1156 [0.1022, 0.1314] | 0.0120 [0.0089, 0.0176] |
| Qwen3 (thinking) | 6,000 | 0.2973 [0.2896, 0.3047] | 0.2696 [0.2607, 0.2818] | 0.7040 [0.6914, 0.7170] | 0.0829 [0.0772, 0.0907] | 0.0339 [0.0307, 0.0387] |
| Tahoe | 2,000 | 0.3235 [0.3103, 0.3373] | 0.3014 [0.2770, 0.3244] | 0.6822 [0.6586, 0.7049] | 0.0988 [0.0877, 0.1131] | 0.0224 [0.0172, 0.0288] |
| A. Absolute Brier performance | ||||
|---|---|---|---|---|
| Training mix | Tahoe | DepMap | GWAS | Macro |
| DepMap + GWAS (Tahoe held out) | 0.2535 [0.2426, 0.2641] | 0.1641 [0.1539, 0.1739] | 0.1483 [0.1367, 0.1599] | 0.1886 [0.1825, 0.1945] |
| Tahoe + GWAS (DepMap held out) | 0.2072 [0.1994, 0.2151] | 0.2337 [0.2253, 0.2417] | 0.1509 [0.1400, 0.1613] | 0.1972 [0.1919, 0.2025] |
| Tahoe + DepMap (GWAS held out) | 0.2047 [0.1955, 0.2139] | 0.1639 [0.1534, 0.1743] | 0.2993 [0.2870, 0.3114] | 0.2226 [0.2165, 0.2287] |
| All domains | 0.2063 [0.1971, 0.2157] | 0.1713 [0.1602, 0.1821] | 0.1537 [0.1416, 0.1654] | 0.1771 [0.1707, 0.1831] |
| Model | Brier Score ( ) | sMECE ( ) | AUROC ( ) | Reliability ( ) | Resolution ( ) | |
|---|---|---|---|---|---|---|
| As reported | ||||||
| Qwen3 (non-thinking) | 6,000 | 0.3336 [0.3237, 0.3436] | 0.3101 [0.2990, 0.3229] | 0.6608 [0.6471, 0.6752] | 0.1096 [0.1024, 0.1189] | 0.0250 [0.0226, 0.0295] |
| Qwen3 (thinking) | 6,000 | 0.2973 [0.2896, 0.3047] | 0.2696 [0.2607, 0.2818] | 0.7040 [0.6914, 0.7170] | 0.0829 [0.0772, 0.0907] | 0.0339 [0.0307, 0.0387] |
| Ibis0 (non-thinking) | 6,000 | 0.1933 [0.1888, 0.1977] | 0.0316 [0.0258, 0.0450] | 0.7729 [0.7616, 0.7846] | 0.0020 [0.0017, 0.0038] | 0.0579 [0.0540, 0.0631] |
| Ibis0 (thinking) | 6,000 | 0.2069 [0.2025, 0.2111] | 0.0327 [0.0296, 0.0431] | 0.7329 [0.7209, 0.7450] | 0.0023 [0.0021, 0.0044] | 0.0448 [0.0413, 0.0500] |
| Ibis0 (classifier) | 6,000 | 0.1771 [0.1707, 0.1831] | 0.0658 [0.0588, 0.0762] | 0.8195 [0.8099, 0.8295] | 0.0075 [0.0065, 0.0104] | 0.0790 [0.0753, 0.0849] |
| Model | Brier Score ( ) | sMECE ( ) | AUROC ( ) | Reliability ( ) | Resolution ( ) | |
|---|---|---|---|---|---|---|
| Qwen3 (non-thinking) | 6,000 | 0.2315 [0.2274, 0.2353] | 0.0603 [0.0417, 0.0657] | 0.6580 [0.6363, 0.6698] | 0.0043 [0.0027, 0.0075] | 0.0214 [0.0180, 0.0266] |
| Tahoe | 2,000 | 0.2451 [0.2419, 0.2487] | 0.0656 [0.0383, 0.0743] | 0.6034 [0.5508, 0.6223] | 0.0029 [0.0006, 0.0078] | 0.0048 [0.0007, 0.0138] |
| DepMap | 2,000 | 0.2092 [0.1987, 0.2186] | 0.0703 [0.0469, 0.0968] | 0.7431 [0.7218, 0.7654] | 0.0082 [0.0041, 0.0154] | 0.0486 [0.0410, 0.0588] |
| GWAS | 2,000 | 0.2401 [0.2348, 0.2443] | 0.0450 [0.0165, 0.0634] | 0.6274 [0.5936, 0.6502] | 0.0018 [0.0003, 0.0051] | 0.0109 [0.0051, 0.0177] |
| Qwen3 (thinking) | 6,000 | 0.2148 [0.2109, 0.2192] | 0.0281 [0.0239, 0.0380] | 0.7033 [0.6880, 0.7152] | 0.0018 [0.0013, 0.0034] | 0.0363 [0.0324, 0.0407] |
| Tahoe | 2,000 | 0.2245 [0.2182, 0.2312] | 0.0302 [0.0204, 0.0455] | 0.6814 [0.6540, 0.7027] | 0.0023 [0.0010, 0.0050] | 0.0278 [0.0204, 0.0338] |
| Model | Position-1 bias (dB) | 95% CI |
|---|---|---|
| Ibis0 (classifier) | +1.01 | |
| Qwen3 (non-thinking) | +0.69 | |
| Qwen3 (thinking) | +0.20 | |
| Ibis0 (non-thinking) | +0.18 | |
| GPT-5.6-sol | -0.03 | |
| Claude Opus 5 | -0.27 |
| Baseline | Fit data | Coverage | Brier ( ) | Hard Brier ( ) |
|---|---|---|---|---|
| Rhaister prompt-local | Prompt evidence only | 85.1% | 0.2310 | 0.4130 |
| Rhaister all-context | Train targets + context | 88.5% | 0.2295 | 0.3968 |
| Numeric-only GBM | DESeq2 numeric features | 100.0% | 0.2206 | n/a |
| All-domain classifier | Three-domain training | 100.0% | 0.2063 | n/a |
Scientific Reasoning in Language Models
Scientific reasoning in language models studies how AI systems use evidence, domain knowledge, and tools to solve problems and support discovery.
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