diff --git a/.gitignore b/.gitignore index 592d77a..d6e217a 100644 --- a/.gitignore +++ b/.gitignore @@ -143,6 +143,10 @@ !/src/Informedica.Utils.Lib/BCL/ !/src/Informedica.Utils.Lib/Scripts/ !/src/Informedica.Utils.Lib/Notebooks/ +# Informedica.Ollama.Lib +!/src/Informedica.Ollama.Lib/ +!/src/Informedica.Ollama.Lib/Scripts/ +!/src/Informedica.Ollama.Lib/Notebooks/ # Informedica.GenCore.Lib !/src/Informedica.GenCore.Lib/ !/src/Informedica.GenCore.Lib/Scripts/ diff --git a/GenPres.sln b/GenPres.sln index c7f28ed..a2074bf 100644 --- a/GenPres.sln +++ b/GenPres.sln @@ -55,6 +55,8 @@ Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "Informedica.KinderFormulari EndProject Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "Informedica.GenForm.Tests", "tests\Informedica.GenForm.Tests\Informedica.GenForm.Tests.fsproj", "{73C084AF-54F4-4B39-A7F9-F0A2A3AB9DD5}" EndProject +Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "Informedica.Ollama.Lib", "src\Informedica.Ollama.Lib\Informedica.Ollama.Lib.fsproj", "{5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}" +EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution Debug|Any CPU = Debug|Any CPU @@ -281,6 +283,18 @@ Global {73C084AF-54F4-4B39-A7F9-F0A2A3AB9DD5}.Release|x64.Build.0 = Release|Any CPU {73C084AF-54F4-4B39-A7F9-F0A2A3AB9DD5}.Release|x86.ActiveCfg = Release|Any CPU {73C084AF-54F4-4B39-A7F9-F0A2A3AB9DD5}.Release|x86.Build.0 = Release|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Debug|Any CPU.ActiveCfg = Debug|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Debug|Any CPU.Build.0 = Debug|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Debug|x64.ActiveCfg = Debug|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Debug|x64.Build.0 = Debug|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Debug|x86.ActiveCfg = Debug|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Debug|x86.Build.0 = Debug|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Release|Any CPU.ActiveCfg = Release|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Release|Any CPU.Build.0 = Release|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Release|x64.ActiveCfg = Release|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Release|x64.Build.0 = Release|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Release|x86.ActiveCfg = Release|Any CPU + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2}.Release|x86.Build.0 = Release|Any CPU EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE @@ -304,6 +318,7 @@ Global {CEB3D1F1-0D5B-4438-B0EC-F448430E1635} = {E75733BC-FF1B-477D-AEAE-43CD0DE5490B} {8CFFC9FE-B559-48F6-80E6-D2D4B9CCE219} = {F84DCF8A-FC1A-4677-AF4D-616AD7DB3470} {73C084AF-54F4-4B39-A7F9-F0A2A3AB9DD5} = {E75733BC-FF1B-477D-AEAE-43CD0DE5490B} + {5B13678B-1260-4B21-B5FF-7F8C8A9B1BD2} = {F84DCF8A-FC1A-4677-AF4D-616AD7DB3470} EndGlobalSection GlobalSection(ExtensibilityGlobals) = postSolution SolutionGuid = {E6B79611-4632-4CCC-BE40-0FF3202E49DF} diff --git a/paket.lock b/paket.lock index 8aff4c7..7fd6c33 100644 --- a/paket.lock +++ b/paket.lock @@ -188,7 +188,7 @@ NUGET FSharp.Control.Websockets (0.2.3) FSharp.Core (>= 6.0) Microsoft.IO.RecyclableMemoryStream (>= 2.2.1) - FSharp.Core (8.0.101) + FSharp.Core (8.0.200) FSharp.Data (6.3) FSharp.Core (>= 5.0.1) FSharp.Data.Csv.Core (>= 6.3) diff --git a/src/Informedica.Ollama.Lib/Informedica.Ollama.Lib.fsproj b/src/Informedica.Ollama.Lib/Informedica.Ollama.Lib.fsproj new file mode 100644 index 0000000..579fbf0 --- /dev/null +++ b/src/Informedica.Ollama.Lib/Informedica.Ollama.Lib.fsproj @@ -0,0 +1,16 @@ + + + + net8.0 + true + + + + + + + + + + + diff --git a/src/Informedica.Ollama.Lib/Notebooks/Examples.dib b/src/Informedica.Ollama.Lib/Notebooks/Examples.dib new file mode 100644 index 0000000..47c2f38 --- /dev/null +++ b/src/Informedica.Ollama.Lib/Notebooks/Examples.dib @@ -0,0 +1,7 @@ +#!meta + +{"kernelInfo":{"defaultKernelName":"csharp","items":[{"aliases":[],"name":"csharp"}]}} + +#!fsharp + +#load "load.fsx" diff --git a/src/Informedica.Ollama.Lib/Notebooks/load.fsx b/src/Informedica.Ollama.Lib/Notebooks/load.fsx new file mode 100644 index 0000000..129f3d2 --- /dev/null +++ b/src/Informedica.Ollama.Lib/Notebooks/load.fsx @@ -0,0 +1,5 @@ +# r "nuget: Newtonsoft.Json" + +#r "../bin/Debug/net8.0/Informedica.Utils.Lib.dll" +#r "../bin/Debug/net8.0/Informedica.Ollama.Lib.dll" + diff --git a/src/Informedica.Ollama.Lib/Ollama.fs b/src/Informedica.Ollama.Lib/Ollama.fs new file mode 100644 index 0000000..4e46d09 --- /dev/null +++ b/src/Informedica.Ollama.Lib/Ollama.fs @@ -0,0 +1,476 @@ +namespace Informedica.Ollama.Lib + + +/// Utility methods to use ollama +/// https://github.com/ollama/ollama/blob/main/docs/api.md#generate-a-chat-completion +module Ollama = + + open System + open System.Net.Http + open System.Text + open Newtonsoft.Json + + + type Configuration() = + member val num_keep: Nullable = Nullable() with get, set + member val seed: Nullable = Nullable() with get, set + member val num_predict: Nullable = Nullable() with get, set + member val top_k: Nullable = Nullable() with get, set + member val top_p: Nullable = Nullable() with get, set + member val tfs_z: Nullable = Nullable() with get, set + member val typical_p: Nullable = Nullable() with get, set + member val repeat_last_n: Nullable = Nullable() with get, set + member val temperature: Nullable = Nullable() with get, set + member val repeat_penalty: Nullable = Nullable() with get, set + member val presence_penalty: Nullable = Nullable() with get, set + member val frequency_penalty: Nullable = Nullable() with get, set + member val mirostat: Nullable = Nullable() with get, set + member val mirostat_tau: Nullable = Nullable() with get, set + member val mirostat_eta: Nullable = Nullable() with get, set + member val penalize_newline: Nullable = Nullable() with get, set + member val stop: string[] = [||] with get, set + member val numa: Nullable = Nullable() with get, set + member val num_ctx: Nullable = Nullable() with get, set + member val num_batch: Nullable = Nullable() with get, set + member val num_gqa: Nullable = Nullable() with get, set + member val num_gpu: Nullable = Nullable() with get, set + member val main_gpu: Nullable = Nullable() with get, set + member val low_vram: Nullable = Nullable() with get, set + member val f16_kv: Nullable = Nullable() with get, set + member val vocab_only: Nullable = Nullable() with get, set + member val use_mmap: Nullable = Nullable() with get, set + member val use_mlock: Nullable = Nullable() with get, set + member val rope_frequency_base: Nullable = Nullable() with get, set + member val rope_frequency_scale: Nullable = Nullable() with get, set + member val num_thread: Nullable = Nullable() with get, set + + + let options = + let opts = Configuration() + opts.seed <- 101 + opts.temperature <- 0. + opts.repeat_last_n <- 64 + opts.num_ctx <- 2048 + opts.mirostat <- 0 + + opts + + + module Roles = + + let user = "user" + let system = "system" + let assistent = "assistent" + + + type Message = + { + Role : string + Content : string + Validator : string -> Result + } + + + type Conversation = + { + Model : string + Messages : QuestionAnswer list + } + and QuestionAnswer = + { + Question : Message + Answer : Message + } + + + module Conversation = + + let print (conversation : Conversation) = + for qAndA in conversation.Messages do + printfn $""" +## Question: +{qAndA.Question.Content.Trim()} + +## Answer: +{qAndA.Answer.Content.Trim()} + +""" + + + module Message = + + let create validator role content = + { + Role = role + Content = content + Validator = validator + } + + let user = create Result.Ok Roles.user + + let system = create Result.Ok Roles.system + + + type Response = + | Success of ModelResponse + | Error of string + and ModelResponse = { + model: string + created_at: string + response: string + message: Message + ``done``: bool + context: int list + total_duration: int64 + load_duration: int64 + prompt_eval_duration: int64 + eval_count: int + eval_duration: int64 + } + + + type ModelDetails = { + format: string + family: string + families : string [] + parameter_size: string + quantization_level: string + } + + type Model = { + name: string + modified_at: string + size: int64 + digest: string + details: ModelDetails + } + + type Models = { + models: Model list + } + + + type Embedding = { + embedding : float [] + } + + + type Details = { + format: string + family: string + families: string list + parameter_size: string + quantization_level: string + } + + type ModelConfig = { + modelfile: string + parameters: string + template: string + details: Details + } + + module EndPoints = + + [] + let generate = "http://localhost:11434/api/generate" + + [] + let pull = "http://localhost:11434/api/pull" + + [] + let chat = "http://localhost:11434/api/chat" + + [] + let tags = "http://localhost:11434/api/tags" + + [] + let embeddings = "http://localhost:11434/api/embeddings" + + [] + let show = "http://localhost:11434/api/show" + + + + // Create an HTTP client + let client = new HttpClient() + + let pullModel name = + + let pars = + {| + name = name + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(pars, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.pull, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + return responseBody + } + + + let generate model prompt = + + let pars = + {| + model = model + prompt = prompt + options = options + (* + {| + seed = 101 + temperature = 0. + |} + *) + stream = false + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(pars, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.generate, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + + let modelResponse = + try + responseBody + |> JsonConvert.DeserializeObject + |> Success + with + | e -> e.ToString() |> Error + return modelResponse + } + + + let chat model messages (message : Message) = + let map msg = + {| + role = msg.Role + content = msg.Content + |} + + let messages = + {| + model = model + messages = + [ message |> map ] + |> List.append (messages |> List.map map) + options = options + stream = false + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(messages, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.chat, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + + let modelResponse = + try + responseBody + |> JsonConvert.DeserializeObject + |> Success + with + | e -> + e.ToString() |> Error + + return modelResponse + } + + + let listModels () = + + // Asynchronous API call + async { + let! response = client.GetAsync(EndPoints.tags) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + let models = + try + responseBody + |> JsonConvert.DeserializeObject + with + | e -> e.ToString() |> failwith + + return models + } + |> Async.RunSynchronously + + + let showModel model = + let prompt = + {| + name = model + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(prompt, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.show, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + + let modelConfig = + try + responseBody + |> JsonConvert.DeserializeObject + with + | e -> e.ToString() |> failwith + return modelConfig + } + + + let embeddings model prompt = + let prompt = + {| + model = model + prompt = prompt + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(prompt, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.embeddings, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + let models = + try + responseBody + |> JsonConvert.DeserializeObject + with + | e -> e.ToString() |> failwith + + return models + } + + + + let run (model : string) messages message = + message + |> chat model messages + |> Async.RunSynchronously + |> function + | Success response -> + [message; response.message] + |> List.append messages + | Error s -> + printfn $"oops: {s}" + messages + + + module Models = + + let llama2 = "llama2" + + let ``llama2:13b-chat`` = "llama2:13b-chat" + + let gemma = "gemma" + + let ``gemma:7b-instruct`` = "gemma:7b-instruct" + + let mistral = "mistral" + + let ``mistral:7b-instruct`` = "mistral:7b-instruct" + + let ``openchat:7b`` = "openchat:7b" + + + + let runLlama2 = run Models.llama2 + + + let runLlama2_13b_chat = run Models.``llama2:13b-chat`` + + + let runGemma = run Models.gemma + + + let runGemma_7b_instruct = run Models.``gemma:7b-instruct`` + + + let runMistral = run Models.mistral + + + let runMistral_7b_instruct = run Models.``mistral:7b-instruct`` + + + module Operators = + + open Newtonsoft.Json + + + let init model msg = + printfn $"""Starting conversation with {model} + +Options: +{options |> JsonConvert.SerializeObject} +""" + + let msg = msg |> Message.system + + msg + |> run model [] + |> fun msgs -> + printfn $"Got an answer" + + { + + Model = model + Messages = + [{ + Question = msg + Answer = msgs |> List.last + }] + } + + + let (>>?) (conversation : Conversation) msg = + + let rec loop tryAgain conversation msg = + let msg = msg |> Message.user + + msg + |> run conversation.Model (conversation.Messages |> List.map (_.Question)) + |> fun msgs -> + let answer = msgs |> List.last + + match answer.Content |> msg.Validator with + | Ok _ -> + { conversation with + Messages = + [{ + Question = msg + Answer = answer + }] + |> List.append conversation.Messages + } + | Result.Error err -> + if not tryAgain then + { conversation with + Messages = + [{ + Question = msg + Answer = answer + }] + |> List.append conversation.Messages + } + + else + $""" +It seems the answer was not correct because: {err} +Can you try again answering? +{msg.Content} +""" + |> loop false conversation + + loop true conversation msg + diff --git a/src/Informedica.Ollama.Lib/Scripts/AI.fsx b/src/Informedica.Ollama.Lib/Scripts/AI.fsx new file mode 100644 index 0000000..44d0bd3 --- /dev/null +++ b/src/Informedica.Ollama.Lib/Scripts/AI.fsx @@ -0,0 +1,876 @@ + + +#r "nuget: Newtonsoft.Json" + + +module Texts = + + let testTexts = [ + """ +alprazolam +6 jaar tot 18 jaar Startdosering: 0,125 mg/dag, éénmalig. Onderhoudsdosering: Op geleide van klinisch beeld verhogen met stappen van 0,125-0,25 mg/dosis tot max 0,05 mg/kg/dag in 3 doses. Max: 3 mg/dag. Advies inname/toediening: De dagdosis indien mogelijk verdelen over 3 doses.Bij plotselinge extreme slapeloosheid: alleen voor de nacht innemen; dosering op geleide van effect ophogen tot max 0,05 mg/kg, maar niet hoger dan 3 mg/dag.De effectiviteit bij de behandeling van acute angst is discutabel. +""" + """ +acetylsalicylzuur +1 maand tot 18 jaar Startdosering:Acetylsalicylzuur: 30 - 50 mg/kg/dag in 3 - 4 doses. Max: 3.000 mg/dag. +""" + """ +paracetamol +Oraal: Bij milde tot matige pijn en/of koorts: volgens het Kinderformularium van het NKFK bij een leeftijd van 1 maand–18 jaar: 10–15 mg/kg lichaamsgewicht per keer, zo nodig 4×/dag, max. 60 mg/kg/dag en max. 4 g/dag. +""" + """ +amitriptyline +6 jaar tot 18 jaar Startdosering: voor de nacht: 10 mg/dag in 1 dosisOnderhoudsdosering: langzaam ophogen met 10 mg/dag per 4-6 weken naar 10 - 30 mg/dag in 1 dosis. Max: 30 mg/dag. Behandeling met amitriptyline mag niet plotseling worden gestaakt vanwege het optreden van ontwenningsverschijnselen; de dosering moet geleidelijk worden verminderd.Uit de studie van Powers (2017) blijkt dat de werkzaamheid van amitriptyline bij migraine profylaxe niet effectiever is t.o.v. placebo. Desondanks menen experts dat in individuele gevallen behandeling met amitriptyline overwogen kan worden. +""" + ] + + + + let systemDoseIndicationExpert = """ +You are an expert on medication prescribing, preparation and administration. +You have to answer questions about texts that describing a drug dose. +You are asked to extract structured information from that text. + +Are the indications for a specific drug. An indication for the drug is the reason to +prescribe the drug with a dose advice. + +You answer all questions with ONLY the shortest possible answer to the question. + """ + + + let systemDosePatientExpert = """ +You are an expert on medication prescribing, preparation and administration. +You have to answer questions about texts that describing a drug dose. +You are asked to extract structured information from that text. + +The information you are looking for pertains to the patient category the dose text applies to: +- the gender of the patient +- the minimum age of the patient +- the maximum age of the patient +- the minimum weight of the patient +- the maximum weight of the patient +- the minimum body surface area of the patient +- the maximum body surface area of the patient +- the minimum gestational age of the patient +- the maximum gestational age of the patient +- the minimum post menstrual age of the patient +- the maximum post menstrual age of the patient + +If the required answer is not available you return an empty string + +You answer all questions with ONLY the shortest possible answer to the question. + """ + + + let systemDoseQuantityExpert = """ +You are an expert on medication prescribing, preparation and administration. +You have to answer questions about texts that describing a drug dose. +You are asked to extract structured information from that text. + +The information will one of the following: +- a quantity with a number and a unit, example: 40 mg/day +- or a single unit, example: day +- or a list of numbers, example: 1;2;3 + +An adjust unit (AdjustUnit) can only be 'kg' body weight or 'mˆ2' body surface area. +A substance unit is a unit that belongs to either a mass unit group, molar unit group +or is an IU/IE (international unit of measurement). + +You answer all questions with ONLY the shortest possible answer to the question. + """ + + let doseRuleStructure = """ + { + "doseRule": { + "generic": "acetaminophen/ibuprofen", // "The generic name in all small caps, for multiple substances drugs concatenated with '/'" + "shape": "tablet", // "The shape name of the generic drug from the Z-index" + "brand": "BrandX", // "The specific Brand a dose rule applies to" + "GPKs": ["GPK123", "GPK456"], // "Specific medication identifiers (Generic Product Codes)" + "route": "oral", // "The route name using the mapping in the Routes sheet" + "indication": "pain relief", // "The indication of the dose rule from the Kinderformularium or Farmacotherapeutisch Kompas" + "dep": "pediatrics", // "The department the dose rule applies to" + "gender": "any", // "The gender the dose rule applies to" + "ageRange": { + "minAge": "0 days", // "The minimum age in days the dose rule applies to" + "maxAge": "6570 days" // "The maximum age in days the dose rule applies to" + }, + "weightRange": { + "minWeight": "1000 gram", // "The minimum weight in grams the dose rule applies to" + "maxWeight": "50000 gram" // "The maximum weight in grams the dose rule applies to" + }, + "BSARange": { + "minBSA": "0.5 mˆ2", // "The minimum BSA in m2 the dose rule applies to" + "maxBSA": "1.5 mˆ2" // "The maximum BSA in m2 the dose rule applies to" + }, + "gestationalAgeRange": { + "minGestAge": "0 days", // "The minimum gestational age in days the dose rule applies to" + "maxGestAge": "280 days" // "The maximum gestational age in days the dose rule applies to" + }, + "postmenstrualAgeRange": { + "minPMAge": "0 days", // "The minimum postmenstrual age in days the dose rule applies to" + "maxPMAge": "294 days" // "The maximum postmenstrual age in days the dose rule applies to" + }, + "doseType": "continuous", // "The dose type ('once', 'onceTimed', 'discontinuous', 'timed', 'continuous')" + "doseText": "Continuous intravenous infusion", // "Description of the DoseType" + "substance": "acetaminophen", // "The substance used, part of the generic name" + "timeRange": { + "minTime": 30, // "The minimum time for infusion of a dose" + "maxTime": 120, // "The maximum time for infusion of a dose" + "timeUnit": "minutes" // "The time unit to measure the infusion" + }, + "intervalRange": { + "minInt": 4, // "The minimum interval between two doses" + "maxInt": 8, // "The maximum interval between two doses" + "intUnit": "hours" // "The interval unit" + }, + "durationRange": { + "minDur": 1, // "The minimum duration of the dose rule" + "maxDur": 7, // "The maximum duration of the dose rule" + "durUnit": "days" // "The duration time unit" + }, + "quantityRange": { + "minQty": "10 mg", // "The minimum dose quantity per dose" + "maxQty": "15 mg", // "The maximum dose quantity per dose" + "normQtyAdj": "10 mg/kg", // "The normal adjusted quantity per dose" + "minQtyAdj": "9 mg/kg", // "The minimum adjusted quantity per dose" + "maxQtyAdj": "11 mg/kg", // "The maximum adjusted quantity per dose" + "doseUnit": "mg", // "The dose unit of the substance" + "adjustUnit": "kg", // "The unit to adjust the dose with" + }, + "frequencyRange": { + "minPerTime": "40 mg/day", // "The minimum dose quantity per freq time unit" + "maxPerTime": "60 mg/day", // "The maximum dose quantity per freq time unit" + "normPerTimeAdj": "40/kg/day", // "The normal adjusted dose quantity per frequency unit" + "minPerTimeAdj": "36/kg/day", // "The minimum adjusted dose quantity per freq time unit" + "maxPerTimeAdj": "44/kg/day" // "The maximum dose adjusted quantity per freq time unit" + "doseUnit": "mg", // "The dose unit of the substance" + "adjustUnit": "kg", // "The unit to adjust the dose with" + "freqs": "4;6;8", // "The possible frequencies, i.e. doses per freq unit, number list separated with ';'" + "freqUnit": "day", // "The time unit of the frequencies" + }, + "rateRange": { + "minRate": "2 mg/hour", // "The minimum dose rate" + "maxRate": "4 mg/hour", // "The maximum dose rate" + "minRateAdj": "2 mg/kg/hour", // "The minimum adjusted dose rate" + "maxRateAdj": "4 mg/kg/hour" // "The maximum adjusted dose rate" + "adjustUnit": "kg", // "The unit to adjust the dose with" + "rateUnit": "hour", // "The time unit for a dose rate" + } + } + } + """ + + + let doseQuantity = """ + { + "doseQuantity": { + "timeRange": { + "minTime": "", // "A Quantity. The minimum time for infusion of a dose" + "maxTime": "", // "A Quantity. The maximum time for infusion of a dose" + "timeUnit": "" // "A Unit. The time unit to measure the infusion" + }, + "intervalRange": { + "minInt": "", // "A Quantity. The minimum interval between two doses" + "maxInt": "", // "A Quantity. The maximum interval between two doses" + "intUnit": "" // "A Unit. The interval unit" + }, + "durationRange": { + "minDur": "", // "A Quantity. The minimum duration of the dose rule" + "maxDur": "", // "A Quantity. The maximum duration of the dose rule" + "durUnit": "" // "A Unit. The duration time unit" + }, + "quantityRange": { + "minQty": "", // "A Quantity. The minimum dose quantity per dose" + "maxQty": "", // "A Quantity. The maximum dose quantity per dose" + "normQtyAdj": "", // "A Quantity. The normal adjusted quantity per dose" + "minQtyAdj": "", // "A Quantity. The minimum adjusted quantity per dose" + "maxQtyAdj": "", // "A Quantity. The maximum adjusted quantity per dose" + "doseUnit": "", // "A Unit. The dose unit of the substance" + "adjustUnit": "" // "A Unit. The unit to adjust the dose with" + }, + "frequencyRange": { + "minPerTime": "", // "A Quantity. The minimum dose quantity per freq time unit" + "maxPerTime": "", // "A Quantity. The maximum dose quantity per freq time unit" + "normPerTimeAdj": "", // "A Quantity. The normal adjusted dose quantity per frequency unit" + "minPerTimeAdj": "", // "A Quantity. The minimum adjusted dose quantity per freq time unit" + "maxPerTimeAdj": "", // "A Quantity. The maximum dose adjusted quantity per freq time unit" + "doseUnit": "", // "A Unit. The dose unit of the substance" + "adjustUnit": "", // "A Unit. The unit to adjust the dose with" + "freqs": "", // "A list of numbers. The possible frequencies, i.e. doses per freq unit, number list separated with ';'" + "freqUnit": "" // "A Unit. The time unit of the frequencies" + }, + "rateRange": { + "minRate": "", // "A Quantity. The minimum dose rate" + "maxRate": "", // "A Quantity. The maximum dose rate" + "minRateAdj": "", // "A Quantity. The minimum adjusted dose rate" + "maxRateAdj": "", // "A Quantity. The maximum adjusted dose rate" + "doseUnit": "", // "A Unit. The dose unit of the substance" + "adjustUnit": "", // "A Unit. The unit to adjust the dose with" + "rateUnit": "" // "A Unit. The time unit for a dose rate" + } + } + } + """ + + + let context = $""" + A dose quantity can be characterized by the following structure: + + {doseQuantity} + + Each field is either + - a quantity with a number and a unit, example: 40 mg/day + - or a single unit: example: day + - or a list of numbers: example: 1;2;3 + """ + + let freqRange = """ + "frequencyRange": { + "minPerTime": , + "maxPerTime": , + "normPerTimeAdj": , + "minPerTimeAdj": , + "maxPerTimeAdj": , + "doseUnit": , + "adjustUnit": , + "freqs": , + "freqUnit": + } + """ + + +/// Utility methods to use ollama +/// https://github.com/ollama/ollama/blob/main/docs/api.md#generate-a-chat-completion +module Ollama = + + open System + open System.Net.Http + open System.Text + open Newtonsoft.Json + + + type Configuration() = + member val num_keep: Nullable = Nullable() with get, set + member val seed: Nullable = Nullable() with get, set + member val num_predict: Nullable = Nullable() with get, set + member val top_k: Nullable = Nullable() with get, set + member val top_p: Nullable = Nullable() with get, set + member val tfs_z: Nullable = Nullable() with get, set + member val typical_p: Nullable = Nullable() with get, set + member val repeat_last_n: Nullable = Nullable() with get, set + member val temperature: Nullable = Nullable() with get, set + member val repeat_penalty: Nullable = Nullable() with get, set + member val presence_penalty: Nullable = Nullable() with get, set + member val frequency_penalty: Nullable = Nullable() with get, set + member val mirostat: Nullable = Nullable() with get, set + member val mirostat_tau: Nullable = Nullable() with get, set + member val mirostat_eta: Nullable = Nullable() with get, set + member val penalize_newline: Nullable = Nullable() with get, set + member val stop: string[] = [||] with get, set + member val numa: Nullable = Nullable() with get, set + member val num_ctx: Nullable = Nullable() with get, set + member val num_batch: Nullable = Nullable() with get, set + member val num_gqa: Nullable = Nullable() with get, set + member val num_gpu: Nullable = Nullable() with get, set + member val main_gpu: Nullable = Nullable() with get, set + member val low_vram: Nullable = Nullable() with get, set + member val f16_kv: Nullable = Nullable() with get, set + member val vocab_only: Nullable = Nullable() with get, set + member val use_mmap: Nullable = Nullable() with get, set + member val use_mlock: Nullable = Nullable() with get, set + member val rope_frequency_base: Nullable = Nullable() with get, set + member val rope_frequency_scale: Nullable = Nullable() with get, set + member val num_thread: Nullable = Nullable() with get, set + + + let options = + let opts = Configuration() + opts.seed <- 101 + opts.temperature <- 0. + opts.repeat_last_n <- 64 + opts.num_ctx <- 2048 + opts.mirostat <- 0 + + opts + + + module Roles = + + let user = "user" + let system = "system" + let assistent = "assistent" + + + type Message = + { + Role : string + Content : string + Validator : string -> Result + } + + + type Conversation = + { + Model : string + Messages : QuestionAnswer list + } + and QuestionAnswer = + { + Question : Message + Answer : Message + } + + + module Conversation = + + let print (conversation : Conversation) = + for qAndA in conversation.Messages do + printfn $""" +## Question: +{qAndA.Question.Content.Trim()} + +## Answer: +{qAndA.Answer.Content.Trim()} + +""" + + + module Message = + + let create validator role content = + { + Role = role + Content = content + Validator = validator + } + + let user = create Result.Ok Roles.user + + let system = create Result.Ok Roles.system + + + type Response = + | Success of ModelResponse + | Error of string + and ModelResponse = { + model: string + created_at: string + response: string + message: Message + ``done``: bool + context: int list + total_duration: int64 + load_duration: int64 + prompt_eval_duration: int64 + eval_count: int + eval_duration: int64 + } + + + type ModelDetails = { + format: string + family: string + families : string [] + parameter_size: string + quantization_level: string + } + + type Model = { + name: string + modified_at: string + size: int64 + digest: string + details: ModelDetails + } + + type Models = { + models: Model list + } + + + type Embedding = { + embedding : float [] + } + + + type Details = { + format: string + family: string + families: string list + parameter_size: string + quantization_level: string + } + + type ModelConfig = { + modelfile: string + parameters: string + template: string + details: Details + } + + module EndPoints = + + [] + let generate = "http://localhost:11434/api/generate" + + [] + let pull = "http://localhost:11434/api/pull" + + [] + let chat = "http://localhost:11434/api/chat" + + [] + let tags = "http://localhost:11434/api/tags" + + [] + let embeddings = "http://localhost:11434/api/embeddings" + + [] + let show = "http://localhost:11434/api/show" + + + + // Create an HTTP client + let client = new HttpClient() + + let pullModel name = + + let pars = + {| + name = name + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(pars, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.pull, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + return responseBody + } + + + let generate model prompt = + + let pars = + {| + model = model + prompt = prompt + options = options + (* + {| + seed = 101 + temperature = 0. + |} + *) + stream = false + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(pars, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.generate, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + + let modelResponse = + try + responseBody + |> JsonConvert.DeserializeObject + |> Success + with + | e -> e.ToString() |> Error + return modelResponse + } + + + let chat model messages (message : Message) = + let map msg = + {| + role = msg.Role + content = msg.Content + |} + + let messages = + {| + model = model + messages = + [ message |> map ] + |> List.append (messages |> List.map map) + options = options + stream = false + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(messages, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.chat, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + + let modelResponse = + try + responseBody + |> JsonConvert.DeserializeObject + |> Success + with + | e -> + e.ToString() |> Error + + return modelResponse + } + + + let listModels () = + + // Asynchronous API call + async { + let! response = client.GetAsync(EndPoints.tags) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + let models = + try + responseBody + |> JsonConvert.DeserializeObject + with + | e -> e.ToString() |> failwith + + return models + } + |> Async.RunSynchronously + + + let showModel model = + let prompt = + {| + name = model + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(prompt, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.show, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + + let modelConfig = + try + responseBody + |> JsonConvert.DeserializeObject + with + | e -> e.ToString() |> failwith + return modelConfig + } + + + let embeddings model prompt = + let prompt = + {| + model = model + prompt = prompt + |} + |> JsonConvert.SerializeObject + + let content = new StringContent(prompt, Encoding.UTF8, "application/json") + + // Asynchronous API call + async { + let! response = client.PostAsync(EndPoints.embeddings, content) |> Async.AwaitTask + let! responseBody = response.Content.ReadAsStringAsync() |> Async.AwaitTask + let models = + try + responseBody + |> JsonConvert.DeserializeObject + with + | e -> e.ToString() |> failwith + + return models + } + + + + let run (model : string) messages message = + message + |> chat model messages + |> Async.RunSynchronously + |> function + | Success response -> + [message; response.message] + |> List.append messages + | Error s -> + printfn $"oops: {s}" + messages + + + module Models = + + let llama2 = "llama2" + + let ``llama2:13b-chat`` = "llama2:13b-chat" + + let gemma = "gemma" + + let ``gemma:7b-instruct`` = "gemma:7b-instruct" + + let mistral = "mistral" + + let ``mistral:7b-instruct`` = "mistral:7b-instruct" + + let ``openchat:7b`` = "openchat:7b" + + + + let runLlama2 = run Models.llama2 + + + let runLlama2_13b_chat = run Models.``llama2:13b-chat`` + + + let runGemma = run Models.gemma + + + let runGemma_7b_instruct = run Models.``gemma:7b-instruct`` + + + let runMistral = run Models.mistral + + + let runMistral_7b_instruct = run Models.``mistral:7b-instruct`` + + + module Operators = + + open Newtonsoft.Json + + + let init model msg = + printfn $"""Starting conversation with {model} + +Options: +{options |> JsonConvert.SerializeObject} +""" + + let msg = msg |> Message.system + + msg + |> run model [] + |> fun msgs -> + printfn $"Got an answer" + + { + + Model = model + Messages = + [{ + Question = msg + Answer = msgs |> List.last + }] + } + + + let (>>?) (conversation : Conversation) msg = + + let rec loop tryAgain conversation msg = + let msg = msg |> Message.user + + msg + |> run conversation.Model (conversation.Messages |> List.map (_.Question)) + |> fun msgs -> + let answer = msgs |> List.last + + match answer.Content |> msg.Validator with + | Ok _ -> + { conversation with + Messages = + [{ + Question = msg + Answer = answer + }] + |> List.append conversation.Messages + } + | Result.Error err -> + if not tryAgain then + { conversation with + Messages = + [{ + Question = msg + Answer = answer + }] + |> List.append conversation.Messages + } + + else + $""" +It seems the answer was not correct because: {err} +Can you try again answering? +{msg.Content} +""" + |> loop false conversation + + loop true conversation msg + + +open Ollama.Operators + + +let extractDoseQuantities model text = + Texts.systemDoseQuantityExpert + |> init model + >>? $""" +The text between the ''' describes dose quantities for a +substance: + +'''{text}''' + +For which substance? +Give the answer as Substance : ? +""" + >>? """ +What is the unit used for the substance, the substance unit? +Give the answer as SubstanceUnit : ? +""" + >>? """ +What is the unit to adjust the dose for? +Give the answer as AdjustUnit : ? +""" + >>? """ +What is the time unit for the dose frequency? +Give the answer as TimeUnit : ? +""" + >>? """ +What is the maximum dose per time in SubstanceUnit/TimeUnit? +Give the answer as MaximumDosePerTime: ? +""" + >>? """ +What is the dose, adjusted for weight in SubstanceUnit/AdjustUnit/TimeUnit? +Give the answer as AdjustedDosePerTime: ? +""" + >>? """ +What is the number of doses per TimeUnit? +Give the answer as Frequency: ? +""" + >>? """ +Summarize the previous answers as: + +- Substance: ? +- SubstanceUnit: ? +- AdjustUnit: ? +- TimeUnit: ? +- MaximumDosePerTime: ? +- AdjustedDosePerTime: ? +- Frequency: ? + +""" + + +let testModel model = + + printfn $"\n\n# Running: {model}\n\n" + for text in Texts.testTexts do + extractDoseQuantities model text + |> Ollama.Conversation.print + + +let testAll () = + + [ + Ollama.Models.gemma + Ollama.Models.``gemma:7b-instruct`` + Ollama.Models.llama2 + Ollama.Models.``llama2:13b-chat`` + Ollama.Models.mistral + Ollama.Models.``mistral:7b-instruct`` + ] + |> List.iter testModel + + + +Ollama.options.penalize_newline <- true +Ollama.options.top_k <- 10 +Ollama.options.top_p <- 0.95 + + +Ollama.Models.``openchat:7b`` +|> testModel + + +module BNFC = + + let paracetamolPO = + [ + """ +paracetamol +Neonate 28 weeks to 32 weeks corrected gestational age +20 mg/ kg for 1 dose, then 10–15 mg/kg every 8–12 hours as required, maximum daily dose to be given in divided doses; maximum 30 mg/kg per day. +""" + """ +Child 1–2 months +30–60 mg every 8 hours as required, maximum daily dose to be given in divided doses; maximum 60 mg/kg per day. +""" + """ +paracetamol +Child 3–5 months +60 mg every 4–6 hours; maximum 4 doses per day. +""" + """ +paracetamol +Child 6–23 months +120 mg every 4–6 hours; maximum 4 doses per day. +""" + ] + + + +"You are a helpful assistant" +|> init Ollama.Models.``openchat:7b`` +>>? "Why is the sky blue?" +|> Ollama.Conversation.print + + +Ollama.options.temperature <- 0 +Ollama.options.seed <- 101 +Ollama.options.penalize_newline <- true +Ollama.options.top_k <- 10 +Ollama.options.top_p <- 0.95 + + +BNFC.paracetamolPO[0] +|> extractDoseQuantities Ollama.Models.``openchat:7b`` +|> Ollama.Conversation.print + + +Ollama.options.temperature <- 0.5 +Ollama.options.seed <- 101 +Ollama.options.penalize_newline <- false +Ollama.options.top_k <- 50 +Ollama.options.top_p <- 0.5 + + +""" +You are an empathic medical professional and translate medical topics to parents +that have a child admitted to a pediatric critical care unit. +""" +|> init Ollama.Models.``openchat:7b`` +>>? """ +Explain to the parents that there child as to be put on a ventilator and has to +be intubated. +""" +//>>? "translate the previous message to Dutch" +|> Ollama.Conversation.print + + +""" +Je bent een empathische zorgverlener die ouders uitleg moet geven over hun kind +dat op de kinder IC ligt. + +Je geeft alle uitleg en antwoorden in het Nederlands. +""" +|> init Ollama.Models.``openchat:7b`` +>>? """ +Leg aan ouders uit dat hun kind aan de beademing moet worden gelegd en daarvoor +geintubeerd moet worden. +""" +|> Ollama.Conversation.print diff --git a/src/Informedica.Ollama.Lib/paket.references b/src/Informedica.Ollama.Lib/paket.references new file mode 100644 index 0000000..a65178e --- /dev/null +++ b/src/Informedica.Ollama.Lib/paket.references @@ -0,0 +1,2 @@ +Newtonsoft.Json +FSharp.Core \ No newline at end of file diff --git a/src/Server/ScenarioResult.fs b/src/Server/ScenarioResult.fs index 4d8fb07..c23148a 100644 --- a/src/Server/ScenarioResult.fs +++ b/src/Server/ScenarioResult.fs @@ -405,7 +405,7 @@ let print (sc: ScenarioResult) = let msg stage (sc: ScenarioResult)= let s = sc.Scenarios - |> Array.collect (fun sc -> sc.Prescription) + |> Array.collect _.Prescription $""" {stage}: {s} """