Add prompt optimizers to LiSSA #44

DanielDango · 2025-11-28T11:14:37Z

This PR aims to introduce prompt optimizers developed during my bachelors thesis into the LiSSA framework.
They can be used as a standalone interaction with the framework, as well as chained with regular evaluation pipeline runs.

The ProTeGi optimizer is suggested in #57

This commit introduces a prompt optimization system that enables automatic tuning of classification prompts to improve trace link recovery performance. Core Components: - PromptOptimizer interface and IterativeOptimizer implementation for iterative naive prompt refinement - Optimization class as the main orchestrator for running optimization workflows - OptimizeCommand CLI integration for executing optimizations from command line Evaluation Framework: - Evaluator base class with strategy pattern for different evaluation approaches - BruteForceEvaluator for exhaustive prompt candidate evaluation - UpperConfidenceBoundBanditEvaluator for efficient exploration-exploitation tradeoff using UCB1 algorithm to reduce computational costs - MockEvaluator for testing purposes Metrics System: - Metric interface with PointwiseMetric and GlobalMetric implementations - FBetaMetric for computing precision, recall, and F-beta scores - Scorer interface with BinaryScorer for trace link classification scoring - Reductor interface with MeanReductor for aggregating pointwise metrics - Factory classes (MetricFactory, ScorerFactory, ReductorFactory) for instantiation Infrastructure Updates: - Extended ModuleConfiguration with prompt management capabilities - Added OptimizerConfiguration for optimizer-specific settings - Enhanced CacheManager with scorer-specific caching via ScorerCacheKey - Added ChatLanguageModelUtils for LLM interaction helpers - Updated Statistics class with methods for computing evaluation metrics Classifier Modifications: - Used setClassificationPrompt() and getClassificationPromptKey() to Classifier abstract class to support dynamic prompt updates - Replaced cache parameters with map Testing: - Added PromptOptimizationUtilsTest with Markdown escaping tests - Extended Requirement2RequirementE2ETest with optimizer test cases - Added test resources with expected outputs and cache files for iterative and simple optimizer configurations - Updated ArchitectureTest to ensure correct usage of dangerous overwrite methods Configuration: - Added example-configs/optimizer-config.json demonstrating optimizer setup

DanielDango · 2025-11-28T11:17:33Z

@dfuchss, your review is not yet required. I intended to request an initial review from @copilot. I will request your review when the ProTeGi (Gradient) and naive optimizer with feedback of misclassified TLs (Feedback) are added.

Copilot · 2025-11-28T11:17:43Z

@DanielDango I've opened a new pull request, #45, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot

Pull request overview

This PR introduces a comprehensive prompt optimization framework to the LiSSA trace link analysis system. The framework enables iterative improvement of classification prompts through automated optimization strategies, integrating metrics, evaluators, and optimizer implementations.

Key Changes:

Adds prompt optimizer framework with iterative optimization support
Introduces metric system (pointwise and global metrics) for evaluating prompt performance
Implements evaluator strategies (brute-force and Upper Confidence Bound bandit algorithms)
Extends configuration system to support optimization workflows

Reviewed changes

Copilot reviewed 52 out of 54 changed files in this pull request and generated 28 comments.

Show a summary per file

File	Description
src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptoptimizer/*	Core optimizer interfaces and implementations (IterativeOptimizer, MockOptimizer, OptimizerFactory, utilities)
src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptmetric/*	Metric system with scorers (BinaryScorer), reductors (MeanReductor), and metric implementations (PointwiseMetric, GlobalMetric, FBetaMetric)
src/main/java/edu/kit/kastel/sdq/lissa/ratlr/evaluator/*	Evaluator base class with BruteForceEvaluator and UpperConfidenceBoundBanditEvaluator implementations
src/main/java/edu/kit/kastel/sdq/lissa/ratlr/Optimization.java	New optimization pipeline that extends evaluation with prompt optimization step
src/main/java/edu/kit/kastel/sdq/lissa/ratlr/Evaluation.java	Extended to support prompt overwriting for optimization workflow
src/main/java/edu/kit/kastel/sdq/lissa/ratlr/configuration/*	OptimizerConfiguration record and ModuleConfiguration setArgument methods
src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/*	Added getCacheParameters() method and changed copyOf() visibility to public
src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/*	New ScorerCacheKey and CacheManager enhancements for optimizer caching
src/main/java/edu/kit/kastel/sdq/lissa/cli/command/OptimizeCommand.java	CLI command for running optimization and optional evaluation pipelines
src/test/java/edu/kit/kastel/sdq/lissa/ratlr/*	Test files including PromptOptimizationUtilsTest and E2E optimizer tests
src/test/resources/warc/*	Test configurations and expected outputs for optimizer validation
example-configs/optimizer-config.json	Example optimizer configuration file

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src/main/java/edu/kit/kastel/sdq/lissa/ratlr/evaluator/UpperConfidenceBoundBanditEvaluator.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptoptimizer/IterativeOptimizer.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptoptimizer/EvaluationResult.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/evaluator/UpperConfidenceBoundBanditEvaluator.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptmetric/PointwiseMetric.java

Copilot

Pull request overview

Copilot reviewed 52 out of 54 changed files in this pull request and generated 10 comments.

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src/main/java/edu/kit/kastel/sdq/lissa/ratlr/evaluator/UpperConfidenceBoundBanditEvaluator.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/ChatLanguageModelProvider.java

src/test/java/edu/kit/kastel/sdq/lissa/ratlr/ArchitectureTest.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptmetric/GlobalMetric.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/Evaluation.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/evaluator/UpperConfidenceBoundBanditEvaluator.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptmetric/GlobalMetric.java

src/test/java/edu/kit/kastel/sdq/lissa/ratlr/e2e/Requirement2RequirementE2ETest.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptmetric/PointwiseMetric.java

…ented by @copilot on #44

- refines iterative optimizer with feedback on misclassified trace links (false positive or false negative) - add sample strategy to configure which TLs will be used as feedback

- add SLF4J Simple Logger configuration for improved logging in tests

…g and Simple Classifiers

… correctly.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

… optimization

… feature/add-prompt-optimization-module # Conflicts: # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/ChatLanguageModelProvider.java

Copilot · 2025-12-23T14:12:50Z

@DanielDango I've opened a new pull request, #49, to work on those changes. Once the pull request is ready, I'll request review from you.

…tive optimization prompt - update e2e test cases - add missing spaces in optimization prompt - revert "revert reduced target store deduplication" This reverts commit 63df5fb.

…er exceptions

…optimization-module

Copilot

Pull request overview

Copilot reviewed 86 out of 89 changed files in this pull request and generated 9 comments.

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src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptoptimizer/IterativeFeedbackOptimizer.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/MockClassifier.java

Copilot · 2026-01-22T11:50:12Z

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/Evaluation.java

+     * @param config The configuration object
+     * @throws IOException If there are issues setting up the cache
+     */
+    public Evaluation(Configuration config) throws IOException {
+        this.configuration = config;
+        // TODO maybe dont?


The comment states "TODO maybe dont?" regarding setting configFile to null. This suggests uncertainty about the design. Null config files could cause NullPointerExceptions downstream. Either handle this case properly or document why null is acceptable here.

Suggested change

* @param config The configuration object

* @throws IOException If there are issues setting up the cache

*/

public Evaluation(Configuration config) throws IOException {

this.configuration = config;

// TODO maybe dont?

* <p>

* Note: When using this constructor there is no associated configuration file on disk.

* Consequently, {@link #configFile} is set to {@code null} by design and any code accessing

* it must first check for {@code null}.

* </p>

*

* @param config The configuration object

* @throws IOException If there are issues setting up the cache

*/

public Evaluation(Configuration config) throws IOException {

this.configuration = config;

// No configuration file is associated with this instance; configFile remains null by design.

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/Evaluation.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/evaluator/UpperConfidenceBoundBanditEvaluator.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptmetric/PointwiseMetric.java

dfuchss · 2026-01-22T12:21:24Z

@DanielDango I think now, the challenge is to merge after changes from #48. Afterward, I can review this part of the PR :)

…optimization-module # Conflicts: # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/CacheKey.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/CacheManager.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/CacheParameter.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/classifier/ClassifierCacheKey.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/classifier/ClassifierCacheParameter.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/embedding/EmbeddingCacheKey.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/embedding/EmbeddingCacheParameter.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/ReasoningClassifier.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/SimpleClassifier.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/embeddingcreator/CachedEmbeddingCreator.java # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/preprocessor/SummarizePreprocessor.java # src/test/java/edu/kit/kastel/sdq/lissa/ratlr/ArchitectureTest.java

DanielDango · 2026-01-22T14:27:26Z

@dfuchss the cache update has been merged

Copilot

Pull request overview

Copilot reviewed 74 out of 77 changed files in this pull request and generated 6 comments.

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Copilot · 2026-01-22T14:32:35Z

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/SimpleClassifier.java

-    @Override
-    public String getClassificationPromptKey() {
+    public static String getClassificationPromptKey() {
        return PROMPT_TEMPLATE_KEY;


The method getClassificationPromptKey() has been changed from an instance method to a static method in SimpleClassifier and ReasoningClassifier. However, the method is still being removed from the abstract Classifier class rather than being changed to static there. This creates an inconsistency where individual classifier implementations have static methods but there's no common static interface. Consider whether a static factory method in the base Classifier class would be more appropriate, as shown in the new createClassificationPromptKey() method.

Suggested change

return PROMPT_TEMPLATE_KEY;

return Classifier.createClassificationPromptKey(PROMPT_TEMPLATE_KEY);

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/ClassificationResult.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/classifier/ClassifierCacheKey.java

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/embedding/EmbeddingCacheKey.java

Copilot · 2026-01-22T14:32:36Z

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/Evaluation.java

+        // TODO: careful, this is a hack to allow the optimization to overwrite the prompt and store it to the config
+        //  for serialization. Maybe you can utilize ModuleConfiguration.with() instead?
+        if (!prompt.isEmpty()) {
+            configuration
+                    .classifier()
+                    .setArgument(Classifier.createClassificationPromptKey(configuration.classifier()), prompt);


The TODO comment indicates this is a known workaround that should be addressed. The hack modifies the configuration's classifier argument directly to inject the optimized prompt. Consider using ModuleConfiguration.with() or a cleaner approach to avoid mutating configuration state after initialization, which could lead to inconsistencies and make the code harder to maintain.

Suggested change

// TODO: careful, this is a hack to allow the optimization to overwrite the prompt and store it to the config

// for serialization. Maybe you can utilize ModuleConfiguration.with() instead?

if (!prompt.isEmpty()) {

configuration

.classifier()

.setArgument(Classifier.createClassificationPromptKey(configuration.classifier()), prompt);

// Update the classifier configuration immutably so the optimized prompt is stored for serialization

if (!prompt.isEmpty()) {

var promptKey = Classifier.createClassificationPromptKey(configuration.classifier());

var updatedClassifierConfig = configuration.classifier().withArgument(promptKey, prompt);

configuration = configuration.withClassifier(updatedClassifierConfig);

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/Classifier.java

…ation prompt without modifying the base configuration

dfuchss

I left some comments. Nice work :)

example-configs/optimizer-config.json

src/main/java/edu/kit/kastel/sdq/lissa/cli/command/EvaluateCommand.java

dfuchss · 2026-01-22T14:32:10Z

src/main/java/edu/kit/kastel/sdq/lissa/cli/command/OptimizeCommand.java

+        for (Path optimizationConfig : configsToOptimize) {
+            LOGGER.info("Invoking the optimization pipeline with '{}'", optimizationConfig);
+            String optimizedPrompt = "";
+            try {
+                var optimization = new Optimization(optimizationConfig);
+                optimizedPrompt = optimization.run();
+            } catch (IOException e) {
+                LOGGER.warn(
+                        "Optimization configuration '{}' threw an exception: {} \n Maybe the file does not exist?",
+                        optimizationConfig,
+                        e.getMessage());
+            }
+            for (Path evaluationConfig : configsToEvaluate) {
+                runEvaluation(evaluationConfig, optimizedPrompt);
+            }
+        }


Move to own method to match the description in the JavaDoc :)

dfuchss · 2026-01-22T14:32:55Z

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/classifier/ClassifierCacheKey.java

-public final class ClassifierCacheKey implements CacheKey {
-    private final String model;
-    private final int seed;
-    private final double temperature;
-    private final LargeLanguageModelCacheMode mode;
-    private final String content;
-
-    @JsonIgnore
-    private final String localKey;
+public record ClassifierCacheKey(
+        String model,
+        int seed,
+        double temperature,
+        LargeLanguageModelCacheMode mode,
+        String content,
+        @JsonIgnore String localKey)
+        implements CacheKey {



Please do not revert the change of the classifiercacheKey

dfuchss · 2026-01-22T14:33:14Z

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/cache/classifier/ClassifierCacheKey.java

-     * @return A new classifier cache key
-     */
-    static ClassifierCacheKey of(ClassifierCacheParameter cacheParameter, String content) {
+    public static ClassifierCacheKey of(ClassifierCacheParameter cacheParameter, String content) {


They shall not be public

dfuchss · 2026-01-22T14:48:28Z

pom.xml

    <dependency>
      <groupId>org.junit.jupiter</groupId>
      <artifactId>junit-jupiter-params</artifactId>
+      <version>${junit.version}</version>


Why? That should be managed by the parent.

dfuchss · 2026-01-22T14:48:47Z

pom.xml

        <groupId>com.diffplug.spotless</groupId>
        <artifactId>spotless-maven-plugin</artifactId>
        <configuration combine.self="append">
+          <lineEndings>UNIX</lineEndings>


Nice catch. I will move that to the parent.

dfuchss · 2026-01-22T14:51:10Z

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/Evaluation.java

+        // TODO: careful, this is a hack to allow the optimization to overwrite the prompt and store it to the config
+        //  for serialization. Maybe you can utilize ModuleConfiguration.with() instead?


If possible, resove todo

dfuchss · 2026-01-22T14:52:59Z

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptoptimizer/OptimizerFactory.java

+    /**
+     * Separator used in configuration names.
+     */
+    public static final String CONFIG_NAME_SEPARATOR = "_";


Isnt that defined publicly in configuration ?

dfuchss · 2026-01-22T14:54:01Z

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptoptimizer/samplestrategy/SamplerFactory.java

+    public static final String FIRST_SAMPLER = "first";
+    public static final String ORDERED_SAMPLER = "ordered";
+    public static final String SHUFFLED_SAMPLER = "shuffled";


Strings used elswhere?

Copilot

Pull request overview

Copilot reviewed 72 out of 75 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/promptmetric/GlobalMetric.java:1

The logger variable name 'logger' is inconsistent with the naming convention used in other classes in the codebase, which use 'LOGGER' in uppercase. For consistency, this should be renamed to 'LOGGER'.

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Copilot · 2026-01-22T14:58:58Z

src/main/java/edu/kit/kastel/sdq/lissa/ratlr/Evaluation.java

+    public Evaluation(Configuration config) throws IOException {
+        this.configuration = config;
+        // TODO maybe dont?
+        this.configFile = null;


The TODO comment on line 152 suggests uncertainty about setting configFile to null. This should either be resolved with a proper implementation or the TODO should be removed if null is the intended behavior. Consider clarifying whether configFile is optional for evaluation instances created from Configuration objects.

sonarqubecloud · 2026-01-22T15:04:43Z

Quality Gate passed

Issues
14 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

DanielDango marked this pull request as ready for review November 28, 2025 11:15

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[WIP] Add prompt optimizers to LiSSA #45

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DanielDango and others added 14 commits November 28, 2025 13:16

fix: correct typos and improve documentation in various files as comm…

7887f8d

…ented by @copilot on #44

add feedback optimizer implementation

4a7744a

- refines iterative optimizer with feedback on misclassified trace links (false positive or false negative) - add sample strategy to configure which TLs will be used as feedback

wip: add more logging

75dddd1

- add SLF4J Simple Logger configuration for improved logging in tests

feat: enhance cache parameters to include classifier type in Reasonin…

565a80e

…g and Simple Classifiers

feat: Enhance logging for cache operations and misclassification checks

883ede1

Rework caching. Now it shall be ensured that Cacheparameters are used…

cb89983

… correctly.

Update ArchitectureTest.java

fb1de00

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

feat: Remove caching from GlobalMetric and PointwiseMetric for prompt…

3e7facf

… optimization

Merge remote-tracking branch 'upstream/feature/simplify-caching' into…

e31c6c1

… feature/add-prompt-optimization-module # Conflicts: # src/main/java/edu/kit/kastel/sdq/lissa/ratlr/classifier/ChatLanguageModelProvider.java

chore: update formatting

c5fff3f

chore: update cache parameter usage

abd5a4f

feat: add additional logging

317d3cc

fix: revert reduced target store deduplication

63df5fb

fix: re-enable other e2e optimizer tests

a8d1d47

Copilot AI mentioned this pull request Dec 23, 2025

Remove TODO comment from MockClassifier.setClassificationPrompt #49

Closed

DanielDango added 4 commits January 22, 2026 11:16

fix: enable correct element store deduplication and fix typo in itera…

b09dea2

…tive optimization prompt - update e2e test cases - add missing spaces in optimization prompt - revert "revert reduced target store deduplication" This reverts commit 63df5fb.

chore: bump license to 2026

93f87e5

fix: make prompt key field statically available to resolve null point…

4929a71

…er exceptions

Merge remote-tracking branch 'upstream/main' into feature/add-prompt-…

a14496b

…optimization-module

DanielDango force-pushed the feature/add-prompt-optimization-module branch from 6bef3cb to a14496b Compare January 22, 2026 11:44

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DanielDango added 6 commits January 22, 2026 13:24

revert: Evaluator module only required for future gradient optimizer

83b5b7b

refactor: address review of copilot

6cbd159

docs: add docstrings missed in #48

bc44e6b

fix: revert evaluator param from javadoc

03d1d0d

docs: add missing javadoc

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DanielDango added 2 commits January 22, 2026 15:42

feat: introduce ModuleConfiguration.with() to overwrite the classific…

d0240e9

…ation prompt without modifying the base configuration

revert: apparently I accidentally reverted changes to CacheKey changes?

1dc90b1

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revert: Classifier copyOf visibility returned to protected

e7bf61b

	return PROMPT_TEMPLATE_KEY;
	return Classifier.createClassificationPromptKey(PROMPT_TEMPLATE_KEY);

		// TODO: careful, this is a hack to allow the optimization to overwrite the prompt and store it to the config
		// for serialization. Maybe you can utilize ModuleConfiguration.with() instead?

Add prompt optimizers to LiSSA #44

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