The Right Fact, the Wrong Decision: SciValidityBench for Scientific Agent Memory
Organizations: Tsinghua University · University of Science and Technology of China
Abstract
Most agent-memory benchmarks frame long-term memory as retrieval: can an agent recover the relevant record from a long and evolving history? Scientific agents face a stricter problem: a correctly remembered fact may still be invalid to use. The same reported test result can support confirmation when the outcome and stopping rule were fixed in advance, yet only exploration when the outcome was selected from twenty inspected results. We call this scientific use validity: whether remembered evidence is eligible to influence a decision under the state governing its interpretation. We introduce SciValidityBench, an executable benchmark factory with 64 TaskSpecs spanning five validity modules and six scientific domains. TaskSpecs couple generated experimental histories with scientific-state definitions, programmatic decision oracles, controlled interventions, and automatic scoring. The SciStateForge compiler-reader framework turns distributed histories into explicit decision-governing state. Counterfactual pairs and targeted corruption-repair controls then test whether models use those dependencies and localize failures. Across four model families, compiled scientific state improves valid decision-making by 9.2-18.8 percentage points over a generic Event Graph. Retrieval alone does not reproduce this cross-family gain, while content-identical flat and typed views show that the improvement comes from exposing governing state rather than a particular graph serialization. SciValidityBench thus shifts memory evaluation from finding the right fact to deciding whether that fact should control the decision.
Figures & tables
| Module | Governing information | Invalid use under test |
|---|---|---|
| Inferential Ledger | Search family, stopping rule, predeclared analysis scope, and evidence consumption | Promoting an adaptively selected or repeatedly consumed result to confirmation |
| Blind Memory | Plan lock, disclosure time, and authorized access roles | Treating an outcome seen too early as an uncontaminated confirmatory analysis |
| Construct Drift | Metric definition, population, replicate meaning, and version relation | Pooling measurements that share a name but are only convertible or incommensurate |
| Absence Algebra | Attempt status, instrument outcome, censoring, and detection mechanism | Collapsing not-run, failure, censoring, and confirmed zero into one kind of blank |
| Sunk Cost | Prospective value and the relevance of historical investment | Allowing irrecoverable past effort to alter a decision with identical future payoffs |
| Domain | Scientific surface | Domain | Scientific surface |
|---|---|---|---|
| Machine learning | Datasets, checkpoints, seeds, metric implementations | A/B testing | Variants, traffic slices, endpoints, scheduled looks |
| Clinical research | Protocols, cohorts, outcomes, censoring records | Bioinformatics | Assays, samples, replicates, pipeline versions |
| Systems | Hardware, workloads, runtime logs, benchmark configurations | Causal inference | Exposures, estimands, adjustment sets, identification choices |
| Model | Raw | BM25 | Event | Flat | SVL | SVL Event (95% CI) |
|---|---|---|---|---|---|---|
| Qwen3-14B | 0.798 | 0.802 | 0.794 | 0.991 | 0.981 | +0.188 [+0.120, +0.255] |
| Gemma-3-12B | 0.733 | 0.719 | 0.719 | 0.903 | 0.902 | +0.183 [+0.116, +0.250] |
| Mistral-7B | 0.556 | 0.586 | 0.566 | 0.692 | 0.678 | +0.113 [+0.059, +0.166] |
| Phi-3.5-mini | 0.480 | 0.475 | 0.478 | 0.609 | 0.570 | +0.092 [+0.055, +0.134] |
| Model | Flat Event Graph | Flat Matched Source | SVL Flat |
|---|---|---|---|
| Qwen3-14B | +0.174 [+0.056, +0.300] | +0.194 [+0.066, +0.335] | +0.003 [+0.000, +0.010] |
| Gemma-3-12B | +0.133 [+0.000, +0.273] | +0.011 [ 0.136, +0.162] | +0.240 [+0.125, +0.356] |
| Mistral-7B | +0.207 [+0.078, +0.347] | +0.193 [+0.064, +0.333] | 0.005 [ 0.023, +0.009] |
| Phi-3.5-mini | +0.189 [+0.045, +0.375] | 0.295 [ 0.460, 0.099] | +0.488 [+0.276, +0.696] |
Appendix figures & tables24 assets
Supplementary material from the paper’s appendix.
Appendix
| Module | ML | A/B | Clinical | Bioinfo. | Systems | Causal | Total |
|---|---|---|---|---|---|---|---|
| Inferential | 4 | 4 | 4 | 4 | 4 | 4 | 24 |
| Blind | 2 | 2 | 2 | 0 | 0 | 2 | 8 |
| Construct | 2 | 2 | 2 | 2 | 2 | 2 | 12 |
| Absence | 2 | 2 | 2 | 2 | 2 | 2 | 12 |
| Sunk Cost | 2 | 2 | 0 | 2 | 2 | 0 | 8 |
| Total | 12 | 12 | 10 | 10 | 10 | 10 | 64 |
| Component | Output | Function |
|---|---|---|
| Domain adapter | Entities, units, and event language | Changes the scientific surface while preserving the validity primitive |
| World generator | Hidden state and public history | Uses a declared seed and version to produce reproducible event sequences |
| State compiler | Public nodes, attributes, and relations | Derives decision-governing state only from model-visible records |
| Action space | Finite legal decisions | Fixes the response contract before evaluation |
| Oracle | Valid action | Computes the answer from the governing state without a free-form model judge |
| Intervention | Counterfactual and corrupted worlds | Changes a decisive value or state component under a declared relation |
| Module | Decisive scientific state | Decision change |
|---|---|---|
| Inferential Ledger | Whether the result followed the declared search family and stopping rule | Confirmation becomes exploratory after adaptive selection |
| Blind Memory | Whether outcome access occurred before the analysis plan was locked | A confirmatory analysis becomes compromised after premature access |
| Construct Drift | Whether two identically named measurements share a comparable definition | Results may be pooled only when their constructs are equivalent or validly converted |
| Absence Algebra | Whether a missing record means not run, failure, censoring, or a true zero | The next action changes among initiating, repeating, censor-aware analysis, and recording zero |
| Sunk Cost | Whether historical investment is relevant to prospective value | The preferred project remains unchanged when only irrecoverable past effort changes |
| Field | Role |
|---|---|
| Stable identifiers | Bind the world, episode, event, actor, and referenced objects |
| Sequence and visibility | Determine event order and when a record becomes public |
| Versioned payload | Store domain values under a declared schema |
| Cost and provenance | Retain resource use and the source that produced the event |
| Event type | Normalize Plan , Run , Observe , Access , Write , Retrieve , and Decide |
| View | Model-visible content | Controlled question |
|---|---|---|
| Raw Events | Complete ordered public event sequence | Can the reader derive the valid action directly from the full history? |
| BM25 Events | Top five request-relevant event chunks | Does conventional retrieval recover the governing evidence? |
| Event Graph | All public events and objects with generic sequence and mention edges | Does organizing events as a graph recover use validity? |
| Flat SSG | Every public compiled node, attribute, and relation as flat records | What changes when decision-governing state is explicit without graph syntax? |
| Typed SVL | The same compiled content as typed nodes and relations | How does a structured scientific ledger affect different readers? |
| Model | Raw | BM25 | Event Graph | Flat SSG | SVL |
|---|---|---|---|---|---|
| Qwen3-14B | 631 | 718 | 1,044 | 460 | 439 |
| Gemma-3-12B | 678 | 775 | 1,112 | 498 | 468 |
| Mistral-7B | 790 | 902 | 1,326 | 598 | 568 |
| Phi-3.5-mini | 798 | 909 | 1,344 | 613 | 580 |
| Purpose | Tasks | Seeds | Readers | Conditions | Decisions |
|---|---|---|---|---|---|
| Primary representations and value pairs | 64 | 10 | 4 | Five original views plus companion worlds for the two compiled views | 17,920 |
| Corruption and repair | 24 | 6 | 4 | Intact, corrupted, exact repair, and matched irrelevant repair | 4,896 |
| Additional memory policies | 24 | 10 | 4 | Seven memory conditions | 6,720 |
| Independent hosted replication | 64 | Two blocks | 2 | Primary representation contrasts | 17,920 |
| Independent Qwen replication | 64 | Matched | 1 | Original views and value pairs | 4,480 |
| Source and serialization controls | 64 | 4 | 4 | Eight views over two source worlds | 16,384 |
| Model | Raw | BM25 | Event Graph | Flat SSG | SVL |
|---|---|---|---|---|---|
| Qwen3-14B | 0.798 | 0.802 | 0.794 | 0.991 | 0.981 |
| Gemma-3-12B | 0.733 | 0.719 | 0.719 | 0.903 | 0.902 |
| Mistral-7B | 0.556 | 0.586 | 0.566 | 0.692 | 0.678 |
| Phi-3.5-mini | 0.480 | 0.475 | 0.478 | 0.609 | 0.570 |
| Model | BM25 Raw | Event Raw |
|---|---|---|
| Qwen3-14B | +0.003 [-0.003, +0.011] | -0.005 [-0.013, +0.000] |
| Gemma-3-12B | -0.014 [-0.031, -0.002] | -0.014 [-0.033, +0.002] |
| Mistral-7B | +0.030 [+0.005, +0.059] | +0.009 [-0.023, +0.044] |
| Phi-3.5-mini | -0.005 [-0.016, +0.003] | -0.002 [-0.011, +0.006] |
| Model | Module | Raw | BM25 | Event | Flat | SVL |
|---|---|---|---|---|---|---|
| Qwen3-14B | Inferential | 0.750 | 0.750 | 0.750 | 1.000 | 1.000 |
| Qwen3-14B | Blind | 0.512 | 0.512 | 0.475 | 1.000 | 1.000 |
| Qwen3-14B | Construct | 0.750 | 0.767 | 0.750 | 1.000 | 1.000 |
| Qwen3-14B | Absence | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
| Qwen3-14B | Sunk Cost | 1.000 | 1.000 | 1.000 | 0.925 | 0.850 |
| Gemma-3-12B | Inferential | 0.633 | 0.625 | 0.617 | 0.875 | 0.875 |
| Model | ML | A/B | Clinical | Bioinfo. | Systems | Causal |
|---|---|---|---|---|---|---|
| Qwen3-14B | +0.183 | +0.183 | +0.250 | +0.120 | +0.120 | +0.270 |
| Gemma-3-12B | +0.192 | +0.167 | +0.260 | +0.110 | +0.120 | +0.250 |
| Mistral-7B | +0.100 | +0.100 | +0.090 | +0.190 | +0.070 | +0.130 |
| Phi-3.5-mini | +0.092 | +0.108 | +0.110 | +0.060 | +0.070 | +0.110 |
| Model | Families | Positive | Effect | 95% interval | Family LOGO |
|---|---|---|---|---|---|
| Qwen3-14B | 12 | 5 | +0.188 | [+0.033, +0.342] | [+0.155, +0.232] |
| Gemma-3-12B | 12 | 6 | +0.181 | [+0.025, +0.336] | [+0.151, +0.227] |
| Mistral-7B | 12 | 6 | +0.112 | [+0.017, +0.217] | [+0.083, +0.134] |
| Phi-3.5-mini | 12 | 4 | +0.099 | [+0.021, +0.194] | [+0.064, +0.108] |
| Model | Tasks | Positive | Effect | 95% interval | LOTO range |
|---|---|---|---|---|---|
| Qwen3-14B | 42 | 12 | +0.143 | [+0.083, +0.214] | [+0.134, +0.146] |
| Gemma-3-12B | 42 | 13 | +0.148 | [+0.081, +0.219] | [+0.137, +0.151] |
| Mistral-7B | 42 | 22 | +0.131 | [+0.057, +0.202] | [+0.122, +0.146] |
| Phi-3.5-mini | 42 | 12 | +0.083 | [+0.043, +0.126] | [+0.076, +0.085] |
| Model | Flat relation acc. | SVL relation acc. | Flat both-valid | SVL both-valid |
|---|---|---|---|---|
| Qwen3-14B | 1.000 | 0.998 | 0.991 | 0.981 |
| Gemma-3-12B | 0.906 | 0.905 | 0.856 | 0.855 |
| Mistral-7B | 0.561 | 0.550 | 0.442 | 0.412 |
| Phi-3.5-mini | 0.436 | 0.361 | 0.327 | 0.270 |
| Model | Infer. | Blind | Construct | Absence | Sunk |
|---|---|---|---|---|---|
| Relation accuracy (Flat/SVL) | |||||
| Qwen3-14B | 1.000/1.000 | 1.000/1.000 | 1.000/1.000 | 1.000/1.000 | 1.000/0.988 |
| Gemma-3-12B | 0.750/0.750 | 1.000/1.000 | 1.000/1.000 | 1.000/1.000 | 1.000/0.988 |
| Mistral-7B | 0.408/0.263 | 0.013/0.388 | 0.500/0.500 | 1.000/1.000 | 1.000/0.975 |
| Phi-3.5-mini | 0.300/0.275 | 0.988/0.613 | 0.300/0.300 | 0.100/0.000 | 1.000/1.000 |
| Both-world validity (Flat/SVL) | |||||
| Operator | State change |
|---|---|
| Omit | Remove one target node and its incident relations |
| Unlink | Remove a governing relation while retaining both endpoints |
| Relabel | Replace a target type or relation label with an incompatible one |
| Merge | Collapse two distinct scientific objects into one identity |
| Duplicate | Add a second copy that creates ambiguous identity or evidence use |
| Inject | Add a plausible but irrelevant node or relation |
| Model | Overall | Infer. | Blind | Construct | Absence | Sunk |
|---|---|---|---|---|---|---|
| Qwen3-14B | +0.269 | +0.000 | +0.500 | +0.681 | +0.833 | -0.333 |
| Gemma-3-12B | +0.328 | +0.000 | +0.500 | +0.667 | +0.875 | +0.083 |
| Mistral-7B | +0.150 | +0.007 | +0.438 | +0.000 | +0.667 | +0.000 |
| Phi-3.5-mini | -0.003 | -0.021 | +0.042 | +0.000 | +0.000 | +0.000 |
| Model | Inject | Merge | Omit | Relabel | Unlink | Duplicate |
|---|---|---|---|---|---|---|
| Qwen3-14B | 1.000 ∗ | 1.000 ∗ | 1.000 ∗ | 0.789 ∗ | 0.866 ∗ | 0.000 |
| Gemma-3-12B | 0.942 ∗ | 1.000 ∗ | 1.000 ∗ | 0.789 ∗ | 1.000 ∗ | 0.000 |
| Mistral-7B | 0.000 | 0.000 | 0.809 ∗ | 0.830 ∗ | 0.000 | 0.000 |
| Phi-3.5-mini | 0.000 | 0.000 | 0.628 ∗ | 0.000 | 0.397 | 0.333 |
| Reader | Flat Event | Flat Matched Source | Opaque Flat Event |
|---|---|---|---|
| Qwen3-14B | +0.174 [+0.056, +0.300] | +0.194 [+0.066, +0.335] | +0.099 [ 0.066, +0.257] |
| Gemma-3-12B | +0.133 [+0.000, +0.273] | +0.011 [ 0.136, +0.162] | +0.280 [+0.153, +0.405] |
| Mistral-7B | +0.207 [+0.078, +0.347] | +0.193 [+0.064, +0.333] | +0.115 [+0.031, +0.215] |
| Phi-3.5-mini | +0.189 [+0.045, +0.375] | 0.295 [ 0.460, 0.099] | +0.550 [+0.439, +0.668] |
| Data block | Reader | Typed SVL Event Graph | Flat Typed SVL | BM25 Raw |
|---|---|---|---|---|
| Block 1 | gpt-5.6-sol | +0.486 [+0.434, +0.534] | 0.011 [ 0.022, 0.002] | 0.053 [ 0.083, 0.027] |
| Block 1 | gpt-5.5 | +0.483 [+0.430, +0.533] | 0.009 [ 0.025, +0.002] | 0.028 [ 0.052, 0.008] |
| Block 2 | gpt-5.6-sol | +0.477 [+0.425, +0.523] | 0.023 [ 0.052, 0.002] | 0.039 [ 0.070, 0.009] |
| Block 2 | gpt-5.5 | +0.470 [+0.419, +0.519] | 0.013 [ 0.028, 0.002] | 0.022 [ 0.039, 0.006] |
| Reader | Typed SVL Event Graph | Flat Typed SVL | BM25 Raw |
|---|---|---|---|
| Qwen3-14B | +0.186 [+0.120, +0.253] | +0.009 [+0.000, +0.023] | +0.008 [+0.000, +0.019] |
| Reader | Effect | 95% interval | Positive tasks | Leave-one-task-out range |
|---|---|---|---|---|
| Qwen3-14B | +0.285 | [+0.228, +0.335] | 20/24 | [+0.279, +0.298] |
| Gemma-3-12B | +0.299 | [+0.238, +0.354] | 20/24 | [+0.291, +0.312] |
| Mistral-7B | +0.144 | [+0.051, +0.238] | 12/24 | [+0.129, +0.160] |
| Phi-3.5-mini | +0.111 | [+0.060, +0.167] | 10/24 | [+0.102, +0.116] |
| Reader | Inferential | Blind | Construct | Absence | Sunk Cost |
|---|---|---|---|---|---|
| Qwen3-14B | +0.292 | +0.306 | +0.375 | +0.406 | +0.000 |
| Gemma-3-12B | +0.304 | +0.306 | +0.392 | +0.444 | +0.000 |
| Mistral-7B | +0.100 | 0.150 | +0.429 | +0.219 | +0.000 |
| Phi-3.5-mini | +0.000 | +0.300 | +0.246 | +0.000 | +0.000 |
| Policy | Nodes | Edges | Node recall | Edge recall | Required-edge recall | Endpoints |
|---|---|---|---|---|---|---|
| None | 0.00 | 0.00 | 0.000 | 0.000 | 0.000 | 0.000 |
| BM25 | 2.65 | 0.68 | 0.601 | 0.246 | 0.186 | 0.000 |
| Summary | 2.25 | 0.67 | 0.510 | 0.271 | 0.111 | 0.000 |
| Selective | 1.58 | 0.42 | 0.379 | 0.167 | 0.111 | 0.000 |
| Provenance | 4.46 | 1.04 | 1.000 | 0.368 | 0.000 | 1.000 |
| ECM | 3.96 | 1.04 | 0.886 | 0.368 | 0.000 | 0.556 |