mlx-swift

.gitignore

@@ -28,3 +28,14 @@ xcuserdata/
 report.junit
 report.html
 *.xcresult
+
+# Local ML artifacts
+checkpoints/
+data/
+HealthyLLM/Supporting Files/LocalLLM/model.safetensors
+HealthyLLM/Supporting Files/OpenTSLM/sleep_cot.csv
+HealthyLLM/Supporting Files/OpenTSLM/ecg_qa_cot_test.csv
+HealthyLLM/Supporting Files/OpenTSLM/ecg_qa_waveforms/
+HealthyLLM/Supporting Files/OpenTSLM/ecg_qa_template_answers.json
+HealthyLLM/Supporting Files/OpenTSLM/ecg_qa_waveforms.json
+jsons/model.safetensors

HealthyLLM.xcodeproj/project.pbxproj

@@ -544,7 +544,7 @@
 				CODE_SIGN_STYLE = Automatic;
 				CURRENT_PROJECT_VERSION = 1;
 				DEVELOPMENT_ASSET_PATHS = "\"HealthyLLM/Supporting Files/Preview Content\"";
-				DEVELOPMENT_TEAM = CQRZ4E7K9U;
+				DEVELOPMENT_TEAM = V5G338H5V6;
 				ENABLE_PREVIEWS = YES;
 				GENERATE_INFOPLIST_FILE = YES;
 				INFOPLIST_KEY_ITSAppUsesNonExemptEncryption = NO;
@@ -586,7 +586,7 @@
 				CODE_SIGN_STYLE = Automatic;
 				CURRENT_PROJECT_VERSION = 1;
 				DEVELOPMENT_ASSET_PATHS = "\"HealthyLLM/Supporting Files/Preview Content\"";
-				DEVELOPMENT_TEAM = CQRZ4E7K9U;
+				DEVELOPMENT_TEAM = V5G338H5V6;
 				ENABLE_PREVIEWS = YES;
 				GENERATE_INFOPLIST_FILE = YES;
 				INFOPLIST_KEY_ITSAppUsesNonExemptEncryption = NO;
@@ -628,7 +628,7 @@
 				CODE_SIGN_STYLE = Automatic;
 				CURRENT_PROJECT_VERSION = 1;
 				DEVELOPMENT_ASSET_PATHS = "\"HealthyLLMStudy/Supporting Files/Preview Content\"";
-				DEVELOPMENT_TEAM = CQRZ4E7K9U;
+				DEVELOPMENT_TEAM = C496LC49DH;
 				ENABLE_PREVIEWS = YES;
 				GENERATE_INFOPLIST_FILE = YES;
 				INFOPLIST_FILE = "HealthyLLMStudy/Supporting Files/Info.plist";
@@ -653,7 +653,7 @@
 					"@executable_path/Frameworks",
 				);
 				MARKETING_VERSION = 1.0;
-				PRODUCT_BUNDLE_IDENTIFIER = edu.maxrosenblattl.bdhg.healthyllm;
+				PRODUCT_BUNDLE_IDENTIFIER = edu.maxrosenblattl.bdhg.healthyllm.co;
 				PRODUCT_NAME = "$(TARGET_NAME)";
 				SUPPORTED_PLATFORMS = "iphoneos iphonesimulator";
 				SUPPORTS_MACCATALYST = NO;
@@ -675,7 +675,7 @@
 				CODE_SIGN_STYLE = Automatic;
 				CURRENT_PROJECT_VERSION = 1;
 				DEVELOPMENT_ASSET_PATHS = "\"HealthyLLMStudy/Supporting Files/Preview Content\"";
-				DEVELOPMENT_TEAM = CQRZ4E7K9U;
+				DEVELOPMENT_TEAM = C496LC49DH;
 				ENABLE_PREVIEWS = YES;
 				GENERATE_INFOPLIST_FILE = YES;
 				INFOPLIST_FILE = "HealthyLLMStudy/Supporting Files/Info.plist";
@@ -700,7 +700,7 @@
 					"@executable_path/Frameworks",
 				);
 				MARKETING_VERSION = 1.0;
-				PRODUCT_BUNDLE_IDENTIFIER = edu.maxrosenblattl.bdhg.healthyllm;
+				PRODUCT_BUNDLE_IDENTIFIER = edu.maxrosenblattl.bdhg.healthyllm.co;
 				PRODUCT_NAME = "$(TARGET_NAME)";
 				PROVISIONING_PROFILE_SPECIFIER = "";
 				SUPPORTED_PLATFORMS = "iphoneos iphonesimulator";

HealthyLLM.xcodeproj/xcshareddata/xcschemes/HealthyLLM.xcscheme

@@ -79,6 +79,38 @@
             ReferencedContainer = "container:HealthyLLM.xcodeproj">
          </BuildableReference>
       </BuildableProductRunnable>
+      <EnvironmentVariables>
+         <EnvironmentVariable
+            key = "HEALTHYLLM_USE_CUSTOM_CHAT_TEMPLATE"
+            value = "0"
+            isEnabled = "YES">
+         </EnvironmentVariable>
+         <EnvironmentVariable
+            key = "HEALTHYLLM_INCLUDE_HARDCODED_ECG"
+            value = "0"
+            isEnabled = "YES">
+         </EnvironmentVariable>
+         <EnvironmentVariable
+            key = "HEALTHYLLM_OPEN_TSLM_MAX_SERIES_LENGTH"
+            value = "250"
+            isEnabled = "YES">
+         </EnvironmentVariable>
+         <EnvironmentVariable
+            key = "HEALTHYLLM_OPEN_TSLM_RUN_LLM"
+            value = "0"
+            isEnabled = "YES">
+         </EnvironmentVariable>
+         <EnvironmentVariable
+            key = "HEALTHYLLM_SKIP_LLM_LOAD"
+            value = "1"
+            isEnabled = "YES">
+         </EnvironmentVariable>
+         <EnvironmentVariable
+            key = "HEALTHYLLM_AUTO_ECG_SAMPLE"
+            value = "1"
+            isEnabled = "YES">
+         </EnvironmentVariable>
+      </EnvironmentVariables>
    </LaunchAction>
    <ProfileAction
       buildConfiguration = "Release"

HealthyLLM/HealthyLLM/Fetcher/HealthDataFetcher+Electrocardiogram.swift

@@ -0,0 +1,94 @@
+//
+// This source file is part of the HealthyLLM based on the Stanford Spezi Template Application project
+//
+// SPDX-FileCopyrightText: 2026 Stanford University
+//
+// SPDX-License-Identifier: MIT
+//
+
+import Foundation
+import HealthKit
+import SpeziHealthKit
+
+extension HealthDataFetcher {
+    func fetchElectrocardiograms(
+        _ healthKit: HealthKit,
+        limit: Int = 1
+    ) async throws -> [ElectrocardiogramData] {
+        let samples = try await fetchElectrocardiogramSamples(healthKit, limit: limit)
+
+        var records: [ElectrocardiogramData] = []
+        for sample in samples {
+            let voltages = try await fetchVoltageMeasurements(for: sample, healthKit: healthKit)
+            records.append(
+                .init(
+                    startDate: sample.startDate,
+                    endDate: sample.endDate,
+                    classification: String(describing: sample.classification),
+                    symptomsStatus: String(describing: sample.symptomsStatus),
+                    averageHeartRate: sample.averageHeartRate?.doubleValue(
+                        for: .count().unitDivided(by: .minute())
+                    ),
+                    samplingFrequency: sample.samplingFrequency?.doubleValue(for: .hertz()),
+                    numberOfVoltageMeasurements: voltages.count,
+                    voltages: voltages
+                )
+            )
+        }
+
+        return records
+    }
+
+    private func fetchElectrocardiogramSamples(
+        _ healthKit: HealthKit,
+        limit: Int
+    ) async throws -> [HKElectrocardiogram] {
+        try await withCheckedThrowingContinuation { continuation in
+            let query = HKSampleQuery(
+                sampleType: HKObjectType.electrocardiogramType(),
+                predicate: nil,
+                limit: limit,
+                sortDescriptors: [NSSortDescriptor(key: HKSampleSortIdentifierStartDate, ascending: false)]
+            ) { _, samples, error in
+                if let error {
+                    continuation.resume(throwing: error)
+                    return
+                }
+
+                continuation.resume(returning: samples as? [HKElectrocardiogram] ?? [])
+            }
+
+            healthKit.healthStore.execute(query)
+        }
+    }
+
+    private func fetchVoltageMeasurements(
+        for sample: HKElectrocardiogram,
+        healthKit: HealthKit
+    ) async throws -> [Double] {
+        try await withCheckedThrowingContinuation { continuation in
+            var voltages: [Double] = []
+            var didResume = false
+
+            let query = HKElectrocardiogramQuery(electrocardiogram: sample) { _, measurement, done, error in
+                if let error, !didResume {
+                    didResume = true
+                    continuation.resume(throwing: error)
+                    return
+                }
+
+                if let measurement,
+                   let voltageQuantity = measurement.quantity(for: .appleWatchSimilarToLeadI) {
+                    voltages.append(voltageQuantity.doubleValue(for: .volt()))
+                }
+
+                if done, !didResume {
+                    didResume = true
+                    continuation.resume(returning: voltages)
+                }
+            }
+
+            healthKit.healthStore.execute(query)
+        }
+    }
+}

HealthyLLM/HealthyLLM/Fetcher/HealthDataFetcher.swift

@@ -17,7 +17,8 @@ class HealthDataFetcher: DefaultInitializable, Module, EnvironmentAccessible {
         let readTypes = Set([
             HKSeriesType.activitySummaryType(),
             HKSeriesType.workoutRoute(),
-            HKSeriesType.workoutType()
+            HKSeriesType.workoutType(),
+            HKObjectType.electrocardiogramType()
         ]).union(
             Set(allHKQuantityTypeIdentifiers().map { HKQuantityType($0) })
         )

HealthyLLM/HealthyLLM/HealthContextGenerator.swift

@@ -11,4 +11,92 @@ import Spezi
 
 class HealthContextGenerator: DefaultInitializable, Module, EnvironmentAccessible {
     required init() { }
+
+    func buildSystemPrompt(userInfo: UserInfo?, electrocardiograms: [ElectrocardiogramData]) -> HealthyLLMContextEntity {
+        var prompt = """
+        You are a health assistant. Provide a careful, non-diagnostic interpretation of the user's health data.
+        If ECG data is present, focus on signal quality, rhythm regularity, heart rate, and any notable abnormalities.
+        Do not claim to diagnose a condition.
+        """
+
+        if let userInfo {
+            prompt += "\n\nUser profile:\n"
+            prompt += userInfo.asJSONRepresentation(.prettyPrinted) ?? "No Data"
+        }
+
+        if !electrocardiograms.isEmpty {
+            prompt += "\n\nLatest ECG samples:\n"
+            prompt += electrocardiograms.enumerated().map { index, sample in
+                formatECGSample(sample, index: index + 1)
+            }.joined(separator: "\n\n")
+        } else {
+            prompt += "\n\nLatest ECG samples: No Data"
+        }
+
+        prompt += "\n\nRespond with a concise clinical-style summary and a safety note if the tracing looks concerning."
+
+        return .init(.system, content: prompt)
+    }
+
+    private func formatECGSample(_ sample: ElectrocardiogramData, index: Int) -> String {
+        let voltages = sample.voltages
+        let average = voltages.isEmpty ? nil : voltages.reduce(0, +) / Double(voltages.count)
+        let minimum = voltages.min()
+        let maximum = voltages.max()
+        let preview = voltages.prefix(24).map { String(format: "%.4f", $0) }.joined(separator: ", ")
+
+                let normalizedVoltages = zNormalize(voltages)
+                let normalizedPreview = normalizedVoltages.prefix(48).map { String(format: "%.6f", $0) }.joined(separator: ", ")
+
+        let averageHeartRateText = sample.averageHeartRate.map(String.init(describing:)) ?? "No Data"
+        let samplingFrequencyText = sample.samplingFrequency.map(String.init(describing:)) ?? "No Data"
+        let voltageMeanText = average.map(String.init(describing:)) ?? "No Data"
+        let voltageMinText = minimum.map(String.init(describing:)) ?? "No Data"
+        let voltageMaxText = maximum.map(String.init(describing:)) ?? "No Data"
+
+                let sleepCotStylePrompt = """
+                sleep_cot_style_sample:
+                    pre_prompt: You are given a short single-lead ECG time series segment. Analyze rhythm, signal quality, and notable concerns conservatively.
+                    time_series_text:
+                        - The following is the ECG time series with mean \(String(format: "%.6f", average ?? 0)) and min/max \(String(format: "%.6f", minimum ?? 0))/\(String(format: "%.6f", maximum ?? 0)).
+                    time_series_normalized_preview: [\(normalizedPreview)]
+                    post_prompt: First summarize waveform quality and rhythm regularity, then provide brief safety guidance and when to seek care.
+                """
+
+        var lines: [String] = [
+            "ECG sample #\(index)",
+            "start_date: \(sample.startDate.formatted(date: .abbreviated, time: .shortened))",
+            "end_date: \(sample.endDate.formatted(date: .abbreviated, time: .shortened))",
+            "classification: \(sample.classification)",
+            "symptoms_status: \(sample.symptomsStatus)",
+            "average_heart_rate: \(averageHeartRateText)",
+            "sampling_frequency_hz: \(samplingFrequencyText)",
+            "voltage_count: \(sample.numberOfVoltageMeasurements)",
+            "voltage_mean: \(voltageMeanText)",
+            "voltage_min: \(voltageMinText)",
+            "voltage_max: \(voltageMaxText)"
+        ]
+
+        if !preview.isEmpty {
+            lines.append("voltage_preview: [\(preview)]")
+        }
+
+        lines.append(sleepCotStylePrompt)
+
+        return lines.joined(separator: "\n")
+    }
+
+    private func zNormalize(_ values: [Double]) -> [Double] {
+        guard !values.isEmpty else {
+            return []
+        }
+
+        let mean = values.reduce(0, +) / Double(values.count)
+        let variance = values.reduce(0) { partial, value in
+            let delta = value - mean
+            return partial + delta * delta
+        } / Double(values.count)
+        let std = max(sqrt(variance), 1e-6)
+        return values.map { ($0 - mean) / std }
+    }
 }