track · audited · verified 2026-07-21

Biology-Instructions Non-coding RNA Function Classification

Thirteen-class functional classification of a non-coding RNA sequence, evaluated with exact extracted-label accuracy.

Benchmark definition

What is counted

Version
emnlp-2025
Total
11160 (distinct examples across the published train, validation, and test splits)
Task formats
RNA-sequence 13-class classification
Capabilities
PredictionClassification
Modalities
TextDNA or RNA sequence

Version history

VersionStatusRelease / as-ofTotalFormal tracks
emnlp-2025
bioinstruction-ncrna-emnlp-2025
current2025-11-0411160 (distinct examples across the published train, validation, and test splits)None registered

Tracks and subsets

IDCountBasisPartition?Notes
Training split
bioinstruction-ncrna-train
5670examplesExclusive & exhaustivePublished training split.
Validation split
bioinstruction-ncrna-validation
650examplesExclusive & exhaustivePublished validation split.
Test split
bioinstruction-ncrna-test
4840examplesExclusive & exhaustiveHeld-out split used for creator-paper Tables 4-7.

Scientific Task Atlas

Scientific task classification

complete for emnlp-2025. Single-purpose formal Biology-Instructions evaluation track.

Scientific taskCoverageCountMappingEvidence
RNA function classificationexplicitly-in-scope11160 examples
distinct examples across the published train, validation, and test splits
official-track
high confidence
bioinstruction-ncrna-evidence-paper
Non-coding RNA function classification.

Evaluation registry

Works and run settings

A setting change—scope, prompt, tools, budget, grader, or repeats—creates a separate run. Charts never cross a comparability group.

bioinstruction-ncrna-closed-baselines-emnlp-2025vemnlp-2025

Evaluated models / systems: GPT-4o (Biology-Instructions snapshot not reported), GPT-4o-mini (Biology-Instructions snapshot not reported)

Scopesubset · n=4840
Shots0
Turnssingle-turn
System prompt publicYes
Reasoning / effortThe prompt requests a direct JSON answer and no chain-of-thought.
BrowserNo
InternetNo
DatabasesNo
Code executionNo
ContainerNot reported
External toolsNo
Token budgetNot reported
Time / cost budgetNot reported
TemperatureNot reported
SeedNot reported
RepeatsNot reported
Graderordered RNA-family name extraction followed by exact accuracy · human review: no
StatisticsPoint metric over the complete published test split, scaled by 100 and rounded to two decimals; no confidence interval is reported.
ContaminationNot reported
Metrics, results, and full protocol

Metrics

MetricKind / baselineUnitAggregationThreshold / tolerance
AccuracyabsolutepercentExact extracted-class accuracy across held-out test examples, scaled by 100Not reported

Results

ModelMetricValuen
GPT-4o-mini (Biology-Instructions snapshot not reported)Accuracy3 percent
ncRNA creator-paper result; metric scaled by 100.
4840
GPT-4o (Biology-Instructions snapshot not reported)Accuracy5.6 percent
ncRNA creator-paper result; metric scaled by 100.
4840

Evidence

  • table: Table 2 (ncRNA test split); Appendix A.3; Table 8; Table 9 closed-source prompt (Scope, prompt, output parser, grader, scaling, and aggregation.) — supports /scope, /benchmark_version, /model_ids, /protocol, /metrics
  • table: Table 5 (ncRNA column) (All registered model values; literature-SOTA row omitted.) — supports /results
bioinstruction-ncrna-creator-systems-emnlp-2025vemnlp-2025

Evaluated models / systems: ChatMultiOmics stage 1 + balanced stage 2, ChatMultiOmics stage 1 + stage 2, ChatMultiOmics, ChatMultiOmics stage 2 only

Scopesubset · n=4840
Shots0
Turnssingle-turn
System prompt publicYes
Reasoning / effortPsc requests clear, concise task answers and numeric output for regression tasks.
BrowserNo
InternetNo
DatabasesNo
Code executionNo
ContainerNot reported
External toolsNo
Token budgetNot reported
Time / cost budgetNot reported
TemperatureNot reported
SeedNot reported
RepeatsNot reported
Graderordered RNA-family name extraction followed by exact accuracy · human review: no
StatisticsPoint metric over the complete published test split, scaled by 100 and rounded to two decimals; no confidence interval is reported.
ContaminationNot reported
Metrics, results, and full protocol

Metrics

MetricKind / baselineUnitAggregationThreshold / tolerance
AccuracyabsolutepercentExact extracted-class accuracy across held-out test examples, scaled by 100Not reported

Results

ModelMetricValuen
ChatMultiOmics stage 1 + balanced stage 2Accuracy35.68 percent
ncRNA creator-paper result; metric scaled by 100.
4840
ChatMultiOmics stage 2 onlyAccuracy0 percent
ncRNA creator-paper result; metric scaled by 100.
4840
ChatMultiOmics stage 1 + stage 2Accuracy62.77 percent
ncRNA creator-paper result; metric scaled by 100.
4840
ChatMultiOmicsAccuracy63.09 percent
ncRNA creator-paper result; metric scaled by 100.
4840

Evidence

  • table: Table 2 (ncRNA test split); Appendix A.3; Table 8; Section 4.2 Psc prompt (Scope, prompt, output parser, grader, scaling, and aggregation.) — supports /scope, /benchmark_version, /model_ids, /protocol, /metrics
  • table: Table 5 (ncRNA column) (All registered model values; literature-SOTA row omitted.) — supports /results
bioinstruction-ncrna-open-baselines-emnlp-2025vemnlp-2025

Evaluated models / systems: Alpaca-7B (Biology-Instructions label), BioMedGPT-LM-7B (Biology-Instructions label), Galactica-1.3B (Biology-Instructions label), GLM-4-9B-Chat (Biology-Instructions label), InstructProtein-1.3B (Biology-Instructions label), Llama-molinst-protein-7B (Mol-Ins), Llama2-7B-Chat (Biology-Instructions label), LLaMA3.1-8B-Instruct (Biology-Instructions label), Qwen2-7B (Biology-Instructions label), Vicuna-v1.5-7B (Biology-Instructions label)

Scopesubset · n=4840
Shots0
Turnssingle-turn
System prompt publicNo
Reasoning / effortThe prompt requests the task-formatted answer and says not to explain or repeat.
BrowserNo
InternetNo
DatabasesNo
Code executionNo
ContainerNot reported
External toolsNo
Token budgetNot reported
Time / cost budgetNot reported
TemperatureNot reported
SeedNot reported
RepeatsNot reported
Graderordered RNA-family name extraction followed by exact accuracy · human review: no
StatisticsPoint metric over the complete published test split, scaled by 100 and rounded to two decimals; no confidence interval is reported.
ContaminationNot reported
Metrics, results, and full protocol

Metrics

MetricKind / baselineUnitAggregationThreshold / tolerance
AccuracyabsolutepercentExact extracted-class accuracy across held-out test examples, scaled by 100Not reported

Results

ModelMetricValuen
LLaMA3.1-8B-Instruct (Biology-Instructions label)Accuracy6.32 percent
ncRNA creator-paper result; metric scaled by 100.
4840
Qwen2-7B (Biology-Instructions label)Accuracy7.08 percent
ncRNA creator-paper result; metric scaled by 100.
4840
Llama2-7B-Chat (Biology-Instructions label)Accuracy4.88 percent
ncRNA creator-paper result; metric scaled by 100.
4840
Alpaca-7B (Biology-Instructions label)Accuracy7.42 percent
ncRNA creator-paper result; metric scaled by 100.
4840
GLM-4-9B-Chat (Biology-Instructions label)Accuracy8.23 percent
ncRNA creator-paper result; metric scaled by 100.
4840
Vicuna-v1.5-7B (Biology-Instructions label)Accuracy3.81 percent
ncRNA creator-paper result; metric scaled by 100.
4840
Galactica-1.3B (Biology-Instructions label)Accuracy6.73 percent
ncRNA creator-paper result; metric scaled by 100.
4840
InstructProtein-1.3B (Biology-Instructions label)Accuracy0 percent
ncRNA creator-paper result; metric scaled by 100.
4840
Llama-molinst-protein-7B (Mol-Ins)Accuracy0 percent
ncRNA creator-paper result; metric scaled by 100.
4840
BioMedGPT-LM-7B (Biology-Instructions label)Accuracy1.62 percent
ncRNA creator-paper result; metric scaled by 100.
4840

Evidence

  • table: Table 2 (ncRNA test split); Appendix A.3; Table 8; Table 9 open-source prompt (Scope, prompt, output parser, grader, scaling, and aggregation.) — supports /scope, /benchmark_version, /model_ids, /protocol, /metrics
  • table: Table 5 (ncRNA column) (All registered model values; literature-SOTA row omitted.) — supports /results

Comparable result views

Accuracy

bioinstruction-ncrna-closed-baselines · bioinstruction-ncrna-closed-baselines-emnlp-2025

CSV ↓
Accessible data table
ModelValueComparability group
GPT-4o-mini (Biology-Instructions snapshot not reported)3bioinstruction-ncrna-closed-baselines-emnlp-2025
GPT-4o (Biology-Instructions snapshot not reported)5.6bioinstruction-ncrna-closed-baselines-emnlp-2025

Accuracy

bioinstruction-ncrna-creator-systems · bioinstruction-ncrna-creator-systems-emnlp-2025

CSV ↓
Accessible data table
ModelValueComparability group
ChatMultiOmics stage 1 + balanced stage 235.68bioinstruction-ncrna-creator-systems-emnlp-2025
ChatMultiOmics stage 2 only0bioinstruction-ncrna-creator-systems-emnlp-2025
ChatMultiOmics stage 1 + stage 262.77bioinstruction-ncrna-creator-systems-emnlp-2025
ChatMultiOmics63.09bioinstruction-ncrna-creator-systems-emnlp-2025

Accuracy

bioinstruction-ncrna-open-baselines · bioinstruction-ncrna-open-baselines-emnlp-2025

CSV ↓
Accessible data table
ModelValueComparability group
LLaMA3.1-8B-Instruct (Biology-Instructions label)6.32bioinstruction-ncrna-open-baselines-emnlp-2025
Qwen2-7B (Biology-Instructions label)7.08bioinstruction-ncrna-open-baselines-emnlp-2025
Llama2-7B-Chat (Biology-Instructions label)4.88bioinstruction-ncrna-open-baselines-emnlp-2025
Alpaca-7B (Biology-Instructions label)7.42bioinstruction-ncrna-open-baselines-emnlp-2025
GLM-4-9B-Chat (Biology-Instructions label)8.23bioinstruction-ncrna-open-baselines-emnlp-2025
Vicuna-v1.5-7B (Biology-Instructions label)3.81bioinstruction-ncrna-open-baselines-emnlp-2025
Galactica-1.3B (Biology-Instructions label)6.73bioinstruction-ncrna-open-baselines-emnlp-2025
InstructProtein-1.3B (Biology-Instructions label)0bioinstruction-ncrna-open-baselines-emnlp-2025
Llama-molinst-protein-7B (Mol-Ins)0bioinstruction-ncrna-open-baselines-emnlp-2025
BioMedGPT-LM-7B (Biology-Instructions label)1.62bioinstruction-ncrna-open-baselines-emnlp-2025

Evidence and change history

Source locators remain visible; expand an item to inspect the exact Registry fields it supports.

Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models · table: Table 2 (ncRNA row); Appendix A.2-A.3; Table 8; Tables 4-7 (Task definition, split counts, input/output format, metric, and creator evaluation.) · Supports 29 fields

Open source →

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  • /task_formats
  • /task_counts/total
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bioinstruction-ncrna-repository-resource · repository-path: evaluation/evaluate.py and evaluation/register_tasks.json at 600acaa08c0302e8f5ce86de0fe041f21c13b53e (Public grader implementation, partial artifact release, and absent repository license.) · Supports 7 fields

Open source →

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View source-level modification history on GitHub →