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Merge pull request #93 from twodawg/SeqMedicalExample
Seq medical example
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,152 @@ | ||
| using AdvUtils; | ||
| using Seq2SeqSharp; | ||
| using Seq2SeqSharp.Applications; | ||
| using Seq2SeqSharp.Corpus; | ||
| using Seq2SeqSharp.Enums; | ||
| using Seq2SeqSharp.LearningRate; | ||
| using Seq2SeqSharp.Metrics; | ||
| using Seq2SeqSharp.Optimizer; | ||
| using Seq2SeqSharp.Utils; | ||
| using System.Diagnostics; | ||
|
|
||
| List<string> inputSentences = ["Chest pain with numbness", | ||
| "Pressure or tightness in the chest", | ||
| "Excessive sweating", | ||
| "fever and chills", | ||
| "headache and body pain", | ||
| "cough and nausia", | ||
| "blood in urine", | ||
| "fever and chills", | ||
| "heart murmur", | ||
| "bumps on hands", | ||
| "nausia"]; | ||
| // Cannot contain spaces | ||
| List<string> labels = ["heart_attack", | ||
| "heart_attack", | ||
| "heart_attack", | ||
| "flu", | ||
| "flu", | ||
| "flu", | ||
| "endocarditis", | ||
| "endocarditis", | ||
| "endocarditis", | ||
| "endocarditis", | ||
| "endocarditis"]; | ||
|
|
||
| var training = false; // Toggle depending if a retraining is needed (did the statements change?) | ||
| do | ||
| { | ||
| string prompt = null; | ||
| if (!training) | ||
| { | ||
| Console.WriteLine("What are your symptoms?"); | ||
| prompt = Console.ReadLine(); | ||
| } | ||
| var rootDir = "D:\\Temp\\"; | ||
| // Define model parameters | ||
| var opts = new SeqClassificationOptions | ||
| { | ||
| ModelFilePath = training ? $"{rootDir}model.bin" : $"{rootDir}model.bin.100", | ||
| SrcLang = "Src", | ||
| TgtLang = "Labels", | ||
| ProcessorType = ProcessorTypeEnums.CPU, | ||
| TrainCorpusPath = $"{rootDir}train", | ||
| ValidCorpusPaths = $"{rootDir}valid", | ||
| LogDestination = Logger.Destination.Console, | ||
| TaskParallelism = 4, | ||
|
|
||
| MaxEpochNum = 100, | ||
| //MaxSentLength = 1024, | ||
| //StartLearningRate = 0.01f, | ||
| EncoderLayerDepth = 6, // Increases the model size | ||
|
|
||
| Task = training ? ModeEnums.Train : ModeEnums.Test, | ||
| InputTestFile = $"{rootDir}input.txt", | ||
| OutputFile = $"{rootDir}output.txt", | ||
| LogLevel = training ? Logger.Level.info : Logger.Level.err, | ||
| }; | ||
| Logger.Initialize(opts.LogDestination, opts.LogLevel, $"{opts.Task}_{Utils.GetTimeStamp(DateTime.Now)}.log"); | ||
|
|
||
| DecodingOptions decodingOptions = opts.CreateDecodingOptions(); | ||
| SeqClassification ss = null; | ||
|
|
||
| if (opts.Task == ModeEnums.Train) | ||
| { | ||
| // Save each labels with a tab and then each inputSentences to D:\Temp\train.enu.snt | ||
| Directory.CreateDirectory(opts.TrainCorpusPath); | ||
| File.WriteAllLines($"{opts.TrainCorpusPath}\\train.src.snt", inputSentences.Select((sentence, index) => $"{sentence}")); | ||
| File.WriteAllLines($"{opts.TrainCorpusPath}\\train.labels.snt", inputSentences.Select((sentence, index) => $"{labels[index]}")); | ||
|
|
||
| Directory.CreateDirectory(opts.ValidCorpusPaths); | ||
| File.WriteAllLines($"{opts.ValidCorpusPaths}\\valid.src.snt", inputSentences.Select((sentence, index) => $"{sentence}")); | ||
| File.WriteAllLines($"{opts.ValidCorpusPaths}\\valid.labels.snt", inputSentences.Select((sentence, index) => $"{labels[index]}")); | ||
|
|
||
| // Prepare data for Seq2SeqSharp | ||
| // Load train corpus | ||
| var trainCorpus = new SeqClassificationMultiTasksCorpus(corpusFilePath: opts.TrainCorpusPath, | ||
| srcLangName: opts.SrcLang, tgtLangName: opts.TgtLang, maxTokenSizePerBatch: opts.MaxTokenSizePerBatch, | ||
| maxSentLength: opts.MaxSentLength, paddingEnums: opts.PaddingType, tooLongSequence: opts.TooLongSequence); | ||
|
|
||
| // Valid corpus | ||
| var validCorpusList = new List<SeqClassificationMultiTasksCorpus>(); | ||
| validCorpusList.Add(new SeqClassificationMultiTasksCorpus(opts.ValidCorpusPaths, | ||
| srcLangName: opts.SrcLang, tgtLangName: opts.TgtLang, opts.ValMaxTokenSizePerBatch, | ||
| opts.MaxSentLength, paddingEnums: opts.PaddingType, tooLongSequence: opts.TooLongSequence)); | ||
|
|
||
| // Create optimizer | ||
| IOptimizer optimizer = Misc.CreateOptimizer(opts); | ||
|
|
||
| var (srcVocab, tgtVocab) = trainCorpus.BuildVocabs(opts.SrcVocabSize, opts.TgtVocabSize); | ||
|
|
||
| // Create metrics | ||
| Dictionary<int, List<IMetric>> taskId2metrics = new Dictionary<int, List<IMetric>>(); | ||
| taskId2metrics.Add(0, new List<IMetric>()); | ||
| taskId2metrics[0].Add(new MultiLabelsFscoreMetric("", tgtVocab.GetAllTokens(keepBuildInTokens: false))); | ||
|
|
||
| // Create learning rate | ||
| ILearningRate learningRate = new DecayLearningRate(opts.StartLearningRate, opts.WarmUpSteps, opts.WeightsUpdateCount, | ||
| opts.LearningRateStepDownFactor, opts.UpdateNumToStepDownLearningRate); | ||
|
|
||
| // Train the model | ||
| ss = new SeqClassification(opts, srcVocab, tgtVocab); | ||
|
|
||
| // Add event handler for monitoring | ||
| ss.StatusUpdateWatcher += Misc.Ss_StatusUpdateWatcher; | ||
| ss.EvaluationWatcher += Ss_EvaluationWatcher; | ||
|
|
||
| ss.Train(opts.MaxEpochNum, trainCorpus, validCorpusList.ToArray(), | ||
| learningRate, taskId2metrics: taskId2metrics, optimizer, decodingOptions); | ||
|
|
||
| Console.WriteLine("Training complete!"); | ||
| } | ||
| else if (opts.Task == ModeEnums.Test) | ||
| { | ||
| File.WriteAllText(opts.InputTestFile, prompt); | ||
|
|
||
| if (File.Exists(opts.OutputFile)) | ||
| { | ||
| Logger.WriteLine(Logger.Level.info, ConsoleColor.Yellow, $"Output file '{opts.OutputFile}' exist. Delete it."); | ||
| File.Delete(opts.OutputFile); | ||
| } | ||
|
|
||
| //Test trained model | ||
| ss = new SeqClassification(opts); | ||
| Stopwatch stopwatch = Stopwatch.StartNew(); | ||
|
|
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| ss.Test<SeqClassificationMultiTasksCorpusBatch>(opts.InputTestFile, opts.OutputFile, opts.BatchSize, decodingOptions, opts.SrcSentencePieceModelPath, opts.TgtSentencePieceModelPath); | ||
|
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| stopwatch.Stop(); | ||
|
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| Logger.WriteLine($"Test mode execution time elapsed: '{stopwatch.Elapsed}'"); | ||
|
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| Console.WriteLine(File.ReadAllText(opts.OutputFile)); | ||
| } | ||
| void Ss_EvaluationWatcher(object sender, EventArgs e) | ||
| { | ||
| EvaluationEventArg ep = e as EvaluationEventArg; | ||
|
|
||
| Logger.WriteLine(Logger.Level.info, ep.Color, ep.Message); | ||
| } | ||
| } | ||
| while (!training); | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| <Project Sdk="Microsoft.NET.Sdk"> | ||
|
|
||
| <PropertyGroup> | ||
| <OutputType>Exe</OutputType> | ||
| <TargetFramework>net8.0</TargetFramework> | ||
| <ImplicitUsings>enable</ImplicitUsings> | ||
| <Nullable>enable</Nullable> | ||
| </PropertyGroup> | ||
|
|
||
| <ItemGroup> | ||
| <ProjectReference Include="..\..\Seq2SeqSharp\Seq2SeqSharp.csproj" /> | ||
| </ItemGroup> | ||
|
|
||
| </Project> |