Explore or Confirm? LLM Agents Misallocate Measurements Under Noise
Organizations: Xstendyl
Abstract
As model reasoning gets cheaper, the physical experiment becomes the slow and costly step in discovery. Each experiment returns a noisy reading: a high value can mean a good candidate or a lucky draw. With a fixed budget, an AI agent must keep choosing between exploring a new candidate and confirming a promising one by re-testing it. We measure that choice in Wellocate, a simulated assay campaign with known true values. It is built on a generated landscape and on two real protein datasets, GB1 and PhoQ, scrambled so no model can answer from memory. We test five language models as minimal agents, with no tools and no memory beyond the history in each prompt. They misallocate in both directions. Three over-confirm, spending most of the budget re-testing. On the generated landscape one under-confirms, trusting single readings, and there every model ends with a worse final pick than a basic scripted strategy. Each failure has its own cause. The over-confirmers run short of new candidates worth trying: a list of untried candidates cuts their re-testing and, on real protein data, makes two of them pick much better. A running summary of their readings or a description of the landscape changes it by at most five percentage points. For the under-confirmer, re-testing its top candidates in a final round, replayed on its own campaigns, recovers only about a quarter of what it loses by picking the wrong candidate. This suggests confirmation has to run through the whole campaign. We release Wellocate as a benchmark and reinforcement-learning environment with frozen splits and scripted baselines. With it, anyone can measure how an agent splits its budget before trusting it with real experiments, and train agents to split it better. Code, data and the environment are available at https://github.com/Xstendyl/wellocate.
Figures & tables
| grid | GB1 | PhoQ | ||||
| share (%) | pick | share (%) | pick | share (%) | pick | |
| Opus 4.7 | 74.9 | 7.62 | 63.3 | 4.78 | 62.8 | 1.89 |
| Gemini 2.5 Flash | 94.0 | 7.70 | 91.9 | 1.12 | 63.7 | 2.13 |
| DeepSeek V3.1 | 91.0 | 7.76 | 96.0 | 0.84 | 89.9 | 0.83 |
| GPT-6.1 Sol | 44.1 | 7.67 | 19.4 | 6.36 | 23.9 | 2.37 |
| Gemini 3.1 Pro | 14.0 | 7.69 | 11.1 | 4.90 | 14.7 | 1.72 |
Appendix figures & tables26 assets
Supplementary material from the paper’s appendix.
Appendix
| informed (told which are viable) | guessing (must guess) | |
|---|---|---|
| best re-tests a round, | 1 of 4 slots | 1 of 4 slots |
| mean pick at | 7.8862 | 7.7098 |
| mean pick at | 7.9993 | 7.8659 |
| distinct candidates at | 39.14 | 28.94 |
| rejections per campaign at | 0.00 | 83.02 |
| lost slots per campaign at | 0.00 | 11.70 |
| no re-tests | one re-test a round | |
|---|---|---|
| GB1, 8 times assay noise | 3.60 [3.53, 3.67] | 4.20 [4.11, 4.29] |
| grid, free rejections, assay noise | 7.79 [7.77, 7.82] | 7.95 [7.93, 7.97] |
| track | landscape | train | validation | test | held out | paper |
|---|---|---|---|---|---|---|
| protein | scrambled GB1 | 400 / 100,000 | 10 / 1,500 | 20 / 1,500 | 1 / 1,500 | 1 / 1,500 |
| protein | scrambled PhoQ | 400 / 100,000 | 10 / 1,500 | 20 / 1,500 | 1 / 1,500 | 1 / 1,500 |
| grid | generated NK | 400 / 100,000 | 10 / 1,500 | 20 / 1,500 | : 20 / 1,500 : 20 / 1,500 | 1 / 1,500 |
| model | released | reasoning as run | median reasoning tokens per call |
|---|---|---|---|
| Opus 4.7 | 2026-02 | off | 0 |
| Gemini 2.5 Flash | 2025-06 | off | 0 |
| DeepSeek V3.1 | 2025-08 | off | 0 |
| GPT-6.1 Sol | 2026-09 | minimal | 0 |
| Gemini 3.1 Pro | 2026-02 | minimal | 240 |
| share (%) | share, slots not lost (%) | final pick | exploration loss | selection loss | |
|---|---|---|---|---|---|
| Opus 4.7 | 74.9 [73.5, 76.3] | 77.4 [76.1, 78.7] | 7.621 [7.543, 7.696] | 1.02 [0.96, 1.09] | 0.12 [0.08, 0.16] |
| Gemini 2.5 Flash | 94.0 [93.1, 94.8] | 94.6 [93.8, 95.3] | 7.701 [7.680, 7.720] | 1.04 [1.03, 1.06] | 0.02 [0.00, 0.03] |
| DeepSeek V3.1 | 91.0 [90.3, 91.6] | 91.2 [90.7, 91.8] | 7.760 [7.716, 7.799] | 0.94 [0.90, 0.98] | 0.06 [0.04, 0.08] |
| GPT-6.1 Sol | 44.1 [41.5, 46.7] | 45.7 [43.1, 48.4] | 7.672 [7.582, 7.764] | 0.93 [0.84, 1.01] | 0.16 [0.11, 0.22] |
| Gemini 3.1 Pro | 14.0 [12.6, 15.3] | 17.5 [15.9, 19.1] | 7.688 [7.580, 7.802] | 0.70 [0.60, 0.79] | 0.38 [0.30, 0.46] |
| model | ledger | landscape note | Menu |
|---|---|---|---|
| Opus 4.7 | 4.4 [ 2.6, 6.2] | 4.7 [ 7.8, 1.5] | 18.2 [ 20.8, 15.5] |
| Gemini 2.5 Flash | 0.9 [ 2.1, 0.2] | 0.5 [ 1.8, 0.8] | 26.2 [ 27.9, 24.5] |
| DeepSeek V3.1 | 0.8 [ 0.1, 1.6] | 1.5 [ 0.8, 2.2] | 31.4 [ 33.5, 29.4] |
| GB1 | PhoQ | |
|---|---|---|
| registered: campaigns resampled by seed | 0.28 [ 0.06, 0.53] | 0.32 [ 0.10, 0.54] |
| whole nominees resampled | 0.28 [ 0.01, 0.74] | 0.32 [ 0.09, 0.55] |
| repeated nominee counted once | 0.33 [ 0.01, 0.71] | 0.20 [ 0.14, 0.57] |
| both checks together | – | 0.20 [ 0.16, 0.61] |
| best value measured | selection loss | |
|---|---|---|
| Gemini 2.5 Flash | 0.17 [ 0.11, 0.23] | 0.13 [ 0.10, 0.17] |
| DeepSeek V3.1 | 0.08 [ 0.01, 0.16] | 0.10 [ 0.05, 0.14] |
| Opus 4.7 | – | 0.09 [ 0.03, 0.16] |
| pick minus the guessing rule | |||||
|---|---|---|---|---|---|
| share (%) | final pick | registered | paired, PhoQ | paired, GB1 | |
| Opus 4.7 | 62.8 [61.0, 64.6] | 1.893 [1.753, 2.025] | 0.16 [ 0.30, 0.02] | 0.26 [ 0.60, 0.07] | 1.41 [ 1.92, 0.89] |
| Gemini 2.5 Flash | 63.7 [60.6, 66.6] | 2.130 [2.050, 2.184] | 0.08 [ 0.01, 0.15] | 0.02 [ 0.35, 0.28] | 5.07 [ 5.47, 4.68] |
| DeepSeek V3.1 | 89.9 [87.5, 91.9] | 0.829 [0.757, 0.942] | 1.22 [ 1.31, 1.10] | 1.32 [ 1.68, 0.98] | 5.35 [ 5.75, 4.94] |
| GPT-6.1 Sol | 23.9 [20.8, 27.3] | 2.368 [2.155, 2.582] | 0.32 [ 0.10, 0.54] | 0.22 [ 0.21, 0.62] | 0.06 [ 0.65, 0.52] |
| Gemini 3.1 Pro | 14.7 [13.1, 16.3] | 1.725 [1.601, 1.857] | 0.33 [ 0.46, 0.19] | 0.42 [ 0.78, 0.10] | 1.52 [ 2.44, 0.55] |
| model | replay | change in final pick |
|---|---|---|
| Gemini 3.1 Pro | last round, | 0.088 [ 0.011, 0.171] |
| Gemini 3.1 Pro | last round, | 0.090 [ 0.004, 0.190] |
| Gemini 3.1 Pro | registered rule on unchanged readings | 0.004 [ 0.028, 0.036] |
| Gemini 2.5 Flash | last round, | 0.014 [ 0.002, 0.032] |
| DeepSeek V3.1 | last round, | 0.035 [ 0.016, 0.055] |
| Gemini 3.1 Pro | last two rounds, | 0.100 [ 0.013, 0.191] |
| share (%) | against the guessing rule | |||||||
|---|---|---|---|---|---|---|---|---|
| model | condition | all | excl. start | distinct | pick | tested | picked | net |
| Opus 4.7 | Blind | 75.4 | 62.8 | 11.3 | 7.65 | |||
| Quantitative | 78.4 | 65.5 | 10.4 | 7.73 | ||||
| Mechanism | 81.6 | 68.1 | 9.0 | 7.69 | ||||
| Aggregated | 85.8 | 70.4 | 7.0 | 7.66 | ||||
| Decision-rule | 85.3 | 70.8 | 7.3 | 7.66 | ||||
| model | exact, stated | exact, unstated | noisy, stated | noise effect (paired) |
|---|---|---|---|---|
| Opus 4.7 | 24.2% | 24.2% | 61.7% | pp (SE 5.3) |
| Gemini 2.5 Flash | 45.0% | 50.8% | 95.0% | pp (SE 7.0) |
| DeepSeek V3.1 | 55.8% | 49.2% | 94.2% | pp (SE 8.3) |
| model | contrast | seeds | diff | 95% CI | Holm |
|---|---|---|---|---|---|
| Opus 4.7 | Aggregated | 695 | 0.0873 | ||
| Opus 4.7 | Decision-rule | 695 | 0.0873 | ||
| DeepSeek V3.1 | Aggregated | 181 | 0.3721 | ||
| DeepSeek V3.1 | Decision-rule | 180 | 0.0075 † | ||
| Gemini 2.5 Flash | Aggregated | 139 | 1.0000 | ||
| Gemini 2.5 Flash | Decision-rule | 139 | 1.0000 |
| model | condition | grid | check A | check B | same-day rerun minus grid |
|---|---|---|---|---|---|
| Opus 4.7 | Blind | 76.0 | 76.6 | 74.8 | |
| Mechanism | 82.1 | 81.1 | 80.9 | ||
| Gemini 2.5 Flash | Blind | 94.4 | 89.8 | 83.3 | |
| Mechanism | 95.2 | 95.1 | 89.0 | ||
| DeepSeek V3.1 | Blind | 90.8 | 90.4 | 90.0 | |
| Mechanism | 93.6 | 93.6 | 93.5 |
| Run A, grid | Run A, GB1 | Run A, PhoQ | Run B, PhoQ | |
|---|---|---|---|---|
| trained pick | 7.91 | 4.79 | 2.15 | 1.53 |
| re-testing share (%) | 9.3 | 1.8 | 2.3 | 68.3 |
| minus initialisation | 0.86 [0.83, 0.89] | 3.32 [3.24, 3.40] | 1.49 [1.44, 1.54] | 0.87 [0.84, 0.91] |
| minus random | 0.40 [0.36, 0.44] | 1.43 [1.34, 1.53] | 0.65 [0.58, 0.73] | 0.03 [ 0.03, 0.09] |
| minus guessing rule | 0.03 [ 0.06, 0.01] | 1.32 [ 1.45, 1.20] | 0.07 [ 0.01, 0.15] | 0.55 [ 0.62, 0.48] |
| minus informed rule | 0.05 [ 0.10, 0.00] | 1.16 [ 1.26, 1.07] | 0.52 [ 0.63, 0.41] | 1.14 [ 1.25, 1.03] |
| change | condition | pick | share (%) | minus random | minus best scripted rule |
|---|---|---|---|---|---|
| noise, grid | noise halved (3.65%) | 8.11 | 9.2 | 0.45 [0.40, 0.49] | 0.04 [ 0.08, 0.00] |
| noise doubled (14.6%) | 7.66 | 9.0 | 0.35 [0.31, 0.40] | 0.09 [ 0.14, 0.05] | |
| stress, grid | batch 5% | 7.84 | 9.3 | 0.41 [0.36, 0.46] | 0.13 [ 0.18, 0.07] |
| batch 10% | 7.73 | 9.2 | 0.40 [0.35, 0.45] | 0.13 [ 0.19, 0.08] | |
| floor | 7.89 | 9.3 | 0.40 [0.35, 0.44] | 0.11 [ 0.16, 0.06] | |
| failed wells | 7.90 | 9.5 | 0.39 [0.35, 0.43] | 0.10 [ 0.14, 0.06] |
| run | split | share (%) | retries (%) | same round (%) | top three (%) | parent (%) | nominee (%) | pick cost |
|---|---|---|---|---|---|---|---|---|
| Run A | grid | 9.3 | 62 | 15 | 5 | 61 | 97 | 0.00 [0.00, 0.00] |
| Run A | GB1 | 1.8 | 58 | 29 | 4 | 63 | 51 | 0.71 [ 0.75, 0.67] |
| Run A | PhoQ | 2.3 | 61 | 23 | 2 | 64 | 89 | 0.05 [ 0.06, 0.04] |
| Run B | grid | 72.0 | 3 | 5 | 58 | 43 | 71 | 0.03 [ 0.04, 0.02] |
| Run B | GB1 | 69.5 | 3 | 5 | 42 | 35 | 93 | 0.06 [ 0.07, 0.05] |
| Run B | PhoQ | 68.3 | 3 | 3 | 39 | 31 | 93 | 0.02 [ 0.02, 0.01] |
| Run A, seeds 3 to 7 | Run B, registered | Run B, larger bonus | |
|---|---|---|---|
| grid: minus random | 0.42 [0.37, 0.46] | – | 0.32 [0.28, 0.37] |
| grid: re-testing share (%) | 10.3 | – | 3.2 |
| grid: seeds above random | 5 of 5 | – | 3 of 3 |
| GB1: minus random | 1.63 [1.53, 1.72] | – | 1.66 [1.56, 1.76] |
| GB1: re-testing share (%) | 1.7 | – | 2.7 |
| GB1: seeds above random | 5 of 5 | – | 3 of 3 |
| landscape | model | campaigns | model | Run A | Run A minus model |
|---|---|---|---|---|---|
| grid | Opus 4.7 | 60 | 7.62 (75%) | 7.87 (10%) | 0.25 [0.14, 0.35] |
| grid | Gemini 2.5 Flash | 120 | 7.70 (94%) | 7.86 (9%) | 0.16 [0.11, 0.21] |
| grid | DeepSeek V3.1 | 120 | 7.76 (91%) | 7.86 (9%) | 0.10 [0.04, 0.15] |
| grid | GPT-6.1 Sol | 60 | 7.67 (44%) | 7.87 (10%) | 0.19 [0.07, 0.31] |
| grid | Gemini 3.1 Pro | 60 | 7.69 (14%) | 7.87 (10%) | 0.18 [0.07, 0.29] |
| GB1, scrambled | Opus 4.7 | 60 | 4.78 (63%) | 4.79 (2%) | 0.02 [ 0.37, 0.42] |
| landscape | condition | guessing, best k | guessing, three minus best | informed, best k | informed, three minus best |
|---|---|---|---|---|---|
| grid | batch 5% | 1 (24%) | 0.19 [ 0.22, 0.15] | 1 (23%) | 0.17 [ 0.21, 0.13] |
| grid | batch 10% | 1 (24%) | 0.15 [ 0.19, 0.11] | 1 (23%) | 0.14 [ 0.18, 0.11] |
| grid | floor | 1 (24%) | 0.17 [ 0.21, 0.14] | 1 (23%) | 0.17 [ 0.20, 0.14] |
| grid | failed wells | 1 (24%) | 0.22 [ 0.26, 0.17] | 1 (23%) | 0.21 [ 0.25, 0.17] |
| GB1 | batch 5% | 0 (1%) | 2.21 [ 2.34, 2.08] | 0 (0%) | 1.58 [ 1.70, 1.47] |
| GB1 | batch 10% | 0 (1%) | 2.16 [ 2.30, 2.03] | 0 (0%) | 1.48 [ 1.59, 1.36] |
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