PxCorpus : A Spoken Drug Prescription Dataset in French for Spoken Language Understanding and Dialogue

PxCorpus : A Spoken Drug Prescription Dataset in French

PxCorpus is to the best of our knowledge, the first spoken medical drug prescriptions corpus to be distributed.

It contains 4 hours of transcribed and annotated dialogues of drug prescriptions in French acquired through an experiment with 55 participants experts and non-experts  in drug prescriptions.

The automatic transcriptions were verified by human effort and aligned with semantic labels to allow training of NLP models. The data acquisition protocol was reviewed by medical experts and permit free distribution without breach of privacy and regulation.

Overview of the Corpus

The experiment has been performed in wild conditions with naive participants and medical experts.

In total, the dataset includes 2067 recordings of 55 participants (38% non-experts, 25% doctors, 36% medical practitioners), manually transcribed and semantically annotated.

| Category             | Sessions | Recordings | Time(m)|

|-----------------------| ------------- | --------------- | ----------- |

| Medical experts  |     258      |       434       |    94.83  |

| Doctors               |     230      |       570       |  105.21  |

| Non experts        |     415      |       977       |    62.13  |

| Total                   |     903      |      1981      |  262.27  |

License

We hope that that the community will be able to benefit from the dataset which is distributed with an attribution 4.0 International (CC BY 4.0) Creative Commons licence.

How to cite this corpus

If you use the corpus or need more details please refer to the following paper: A spoken drug prescription datset in French for spoken Language Understanding

@InProceedings{Kocabiyikoglu2022,

 author =  "Alican Kocabiyikoglu and Fran{\c c}ois Portet and Prudence Gibert and Hervé Blanchon and Jean-Marc Babouchkine and Gaëtan Gavazzi",

 title =  "A spoken drug prescription datset in French for spoken Language Understanding",

 booktitle =  "13th Language Ressources and Evaluation Conference (LREC 2022)",

 year =  "2022",

 location =  "Marseille, France"

}

a more complete description of the corpus acquisition is available on arxiv 

@misc{kocabiyikoglu2023spoken,

     title={Spoken Dialogue System for Medical Prescription Acquisition on Smartphone: Development, Corpus and Evaluation},

     author={Ali Can Kocabiyikoglu and François Portet and Jean-Marc Babouchkine and Prudence Gibert and Hervé Blanchon and Gaëtan Gavazzi},

     year={2023},

     eprint={2311.03510},

     archivePrefix={arXiv},

     primaryClass={cs.CL}

}

Project Structure

The project contains the following elements

.

├── LICENSE

├── PxDialogue/

├── PxSLU/

├── readme.md

PxSLU : Prescription Corpus for Spoken Language Understanding

Directory Structure

.

├── LICENSE

├── metadata.txt

├── paths.txt

├── PxSLU_conll.txt

├── readme.md

├── recordings

├── seq.in

├── seq.label

├── seq.out

├── Demo.ipynb

└── verifications.py

Recordings

The recordings directory contains the 903 recording sessions. Each session can contain several recordings. For instance,

the directory

   recordings/J7aVvWb67L

contains the records    

   recording_0.wav  recording_2.wav

which represent two attempts to record a drug prescription

All records are stored as mono channel wav files of 16kHz 16bits signed PCM

Paths

contains the list of all the .wav files in the recordings directory

00MYcyVK0t/recording_0.wav

00MYcyVK0t/recording_2.wav

02Qp6ICj9Q/recording_0.wav

02Qp6ICj9Q/recording_1.wav

...

All other files (metadata.txt, seq.*) refer to this list to describe the recording.

Metadata

contains the information about the participants:

48,60+,F,non-expert

48,60+,F,non-expert

24,18–28,F,doctor

24,18–28,F,doctor

...

The first column is the participant unique id, the second is the age range, the third is the gender and the final is the category of the participant in {doctor,expert, non-expert}. doctor correspond to a physician, (other)expert to a pharmacist or a biologist specialized in drugs while non-expert are other people not entering in these categories. The lines are synchronised with the paths.txt lines.

Labels

the three files seq.label, seq.in, seq.out represent respectivly the intent, the transcript and the entities in BIO format.

     seq.label               |                 seq.in                                 |                            seq.out

medical_prescription | flagyl 500 milligrammes euh qu/ en... | B-drug B-d_dos_val B-d_dos_up O O ...

medical_prescription |   3 comprimés par jour matin midi ...   | B-dos_val B-dos_uf O O B-rhythm_tdte B-rhythm_tdte O B-rhythm_tdte ...

              ...                 |                             ...                             |                             ...

These lines are synchronised with the paths.txt lines.

Another file "PxSLU_conll.txt" is provided in a format inspired by the conll format (https://universaldependencies.org/format.html). However, this one is *not* aligned with the acoustic records file paths.txt.

Scripts

verifications.py performs the checking of the alignement of all the seq.* paths.txt and metadata files. A user of the dataset does not need to use this script unless she plan to extend the datasets with her own data.

Demo.ipynb is a jupyter notebook that a user can run to search through the dataset. It is intended to let the user have a quicker and smoother view on the dataset.

Data splits

In the data_splits folder, you can find a data split of this dataset organized as following:

- train.txt: medical experts + non experts (80%) = 1128 samples

- dev.txt: medical experts + non experts (20%) = 283 samples

- test.txt: doctors (100%) = 570 samples

Each file contains references to line numbers of the corpus. For example, first line of the test.txt is 904, seq.in file contains the utterance "nicopatch". Users can access the labels, slots, metadata using the same line number 904 in the parallel files (paths.txt,seq.out,seq.label,...).

PxDialogue : Prescription recording corpus for dialogue systems

PxDialogue corpus comes as an extension of the PxSLU corpus and provides additional information about the dialogues that was collected through spoken dialogue. This corpus includes two additional files:

├── events.txt

├── dialogue_annotations.txt

Events.txt:

For each dialogue session, all dialogue events are given in this text file

which can be used to train/evaluate dialogue systems.

Usage example:

PxSLU (paths.txt)

- 00MYcyVK0t/recording_0.wav

- 00MYcyVK0t/recording_2.wav

PxDialogue (events.txt)

- (-1, 'START', 'APP', None, 0) (1, 'user', 'ASR', 'flagyl 500 mg en cachet pendant 8 jours', 30) (1, 'system', 'TTS', 'Choisissez le médicament correspondant à votre recherche', 34) (2, 'user', 'UI', 'listview_item_clicked', 40) (2, 'system', 'TTS', 'Pourriez vous préciser la posologie pour le patient?', 40) (3, 'user', 'ASR', '3 comprimés par jour matin midi et soir pendant 10 jours', 64) (3, 'system', 'TTS', "Est-ce que vous confirmez l'ajout de cette prescription sur la liste?", 66) (4, 'user', 'UI', '/inform{"validate":"validate"}', 73) (4, 'system', 'TTS', 'Prescription validée avec succès. Traitement ajouté sur le dossier du patient', 73) (-1, 'END', 'APP', '', 73)

- N/A

For example, in this dialogue session (00MYcyVK0t), there are two recordings.

The events are given in a single row for each dialogue session once in the

first recording (recording_0). Dialogues are described in form of events

where each action taken by the user or the system is considered as a dialogue

turn in a tuple form.

(-1, 'START', 'APP', None, 0)

- First element of the event is the dialogue turn number. -1 means that the application

is initialized.

- Second element describes who initiated the event: user, system, START, END

- Third element describes the type of the event: APP (start and end events)

, ASR (automatic speech recognition), TTS (text-to-speech), UI (user interface)

User clicks on buttons triggers sometimes explicit intent recognition. For

example (4, 'user', 'UI', '/inform{"validate":"validate"}') describes the

explicit intent of validation of the prescription.

- Fourth element is the timestamp (in seconds)

Dialogue annotations

We also include a manual annotation for dialogues (dialogue_annotations.txt) which indicates for each recording, if the system gave the correct answer given the utterance.

Each line contains a keyword, either [Fail] or [OK]. The following example shows a dialogue sample with annotations:

| dialogue_annotations.txt |  paths.txt                                | seq.in                                                                                            |

|----------------------------------|----------------------------------------|--------------------------------------------------------------------------------------|

| OK                                  | 14yHtAe555/recording_0.wav | oxytetracycline solution euh                                                          |

| OK                                  | 14yHtAe555/recording_1.wav | oxytetracycline solution 5 gouttes matin et soir pendant 14 jours |

| Fail                                  | 14yHtAe555/recording_2.wav | oxytetracycline solution 5 gouttes matin et soir pendant 14 jours |

For these 3 dialogues, the dialogue annotations are accordingly OK, OK and Fail.

[Ok] means that the dialogue system reacted correctly to the input.

[Fail] means that the action of the system after this utterance should not be used

for evaluation or training.  

We can notice that in the first utterance, the information are missing, however

after the second example the system normally have all of the required slots

for the prescription validation.

It is to note that free comments added using the ASR system were noted as

Fail as these dialogues did not enter the dialogue state tracking. In this

example, the last utterance is recorded as a free comment by the prescriber

and was annotated as Fail.

Linking audio records to ASR events

In order to link audio records to ASR events, the user has to use both paths.txt and events.txt

For example for the following dialogue session (lines 1:2 of paths.txt):

00MYcyVK0t/recording_0.wav

00MYcyVK0t/recording_2.wav

Events.txt include two ASR events:

(1, 'user', 'ASR', 'flagyl 500 mg en cachet pendant 8 jours', 30)

(3, 'user', 'ASR', '3 comprimés par jour matin midi et soir pendant 10 jours', 64)

These ASR events corresponds to the recording files that can be found in the recordings folder.

Available user action annotations

Events.txt include annotations such as below with the following explanation:

- /inform{"validate":"validate"} : User clicks on the validate button after seeing the prescription

- /inform{"validate":"refuse"} : User clicks on the refuse button after seeing the prescription

- ASR : User clicks on the push-to-talk button to record an utterance

- listview_item_clicked : User clicks on the list to choose a drug

- listview_cancel_clicked : User clicks on the cancel button after seeing a list of drugs

- FREE_COMMENT_ADDED : User clicks and records a free-form utterance by clicking "add free comment" button

- EMPTY_UTTERANCE: Recording containing an empty utterance

- APP_CRASH : An application crash that happened in the dialogue turn

- EVAL_FINISH_APPROVED : User clicks on the final upload button to finish the experiment

- RESTART_CONVERSATION_SESSION : User clicks on the restart conversation button

- RESTART_CANCEL_CLICKED : User cancels the restart process by clicking on the cancel button

- EVAL_FINISH_CANCELED : User cancels the final upload process by clicking on the cancel button

** Free Comments: **

The users had the possibility of recording a speech-to-text message upon viewing a prescription.

These messages had not beed added to the dialogue state tracking but were visualized on the interface and saved in

the database. Users can find free comments by searching for FREE_COMMENT_ADDED events in the events.txt to find out

about these events.