Update README.md

README.md

@@ -87,19 +87,34 @@ The system prompt was: Imagine you are a useful medical assistant that is trying
 
 The user prompt was: Now provide a 3–5 sentence summary for the doctor's note written for a patient's understanding.
 
+Example Doctor's Note for Prompt:
+
+A 70-year-old woman presented in November 2017 to the Emergency Department at Skåne University Hospital, Sweden, due to the rapid onset of fever, shivers, and a suspected skin infection. She had a previous medical history of left-sided ductal breast cancer with lymph node involvement in 1999, which was treated chronologically with neoadjuvant chemotherapy, partial mastectomy, axillary lymph node dissection, and radiation therapy. In addition, in 2001, a right-sided localised ductal breast cancer in situ was identified and was treated surgically with a partial mastectomy. Secondary to her lymph node dissection, she developed lymphoedema of her left arm, which had been continuously treated with compression stockings. The patient was on treatment with an ACE inhibitor and a beta-blocker due to hypertension, and in addition, she had a known systolic murmur, characterized as physiological, as transthoracic echocardiographs in 2011 and 2017 were normal. Since her surgery in 1999, on a total of six occasions prior to her last and seventh visit, of which the first episode occurred in 2008, she had been treated for erysipelas in her left upper arm. The presentation had always been sudden with spiking fever and erythema spreading in approximately the same localisation. Interestingly, on all three out of the three occasions where a blood culture has been drawn on presentation with erysipelas, the cultures have shown growth of a bacterium belonging to the S. mitis group. These first two isolates also had similar MIC values for penicillin of 0.064 and 0.125 mg/L, for vancomycin of 0.25 and 0.5 mg/L, and for gentamicin of 2 and 2 mg/L (). In addition, they were both sensitive to clindamycin.\\nOn the present visit, she once again had a sharply demarcated, warm, swollen, and painful erythema measuring approximately 7 × 15 cm in the lymphoedematous area on her left upper arm. No local portal of bacterial entry was found. Vital parameters showed a temperature of 38.0°C, respiratory rate of 16 breaths/min, O2 saturation of 96% on room air, heart rate of 80 beats/min, and blood pressure of 120/70 mmHg. On physical examination, a grade II systolic murmur was heard with punctum maximum I2 dexter. She had no signs of septic emboli, oral examination showed no signs of infection, and examination of lymph nodes was normal. Possibly due to her quick presentation, that is, less than 6 hours from the onset of symptoms, her laboratory results were normal with a white blood cell count of 8.4 ∗ 109/L, platelets of 263 ∗ 109/L, and hemoglobin of 147 g/L. Her CRP was 12 mg/L. She was clinically diagnosed with erysipelas, and due to previous bacteraemia with the S. mitis group in relation to erysipelas and the presence of a systolic murmur, blood cultures were drawn and she was treated with one dose of intravenous penicillin (3g≈5 million IU) followed by an oral penicillin (1g≈1.6 million IU) three times daily, for seven days. Once again, now for the third time, the two blood cultures showed growth of a bacterium belonging to the S. mitis group. The MIC value for penicillin was 0.125 mg/L, for vancomycin 1 mg/L, and for gentamicin 16 mg/L (). Similar to the two previous isolates, it was also sensitive to clindamycin. Her treatment was prolonged for 10 days, and a follow-up visit was arranged. Repeat blood cultures were drawn 14 days after discontinuation of antibiotics and they were negative. To prevent further infections, she has once again been referred to the lymphoedema outpatient clinic as well as to the dentist office. On follow-up, thereafter, the patient had no sequelae to her infection, and she gave informed consent for this case report to be published.\\nThe three blood isolates, one analysed in 2015 and two in 2017 (15 and 8 months apart), were initially subgrouped to S. mitis/S. oralis/S. pseudopneumoniae of the S. mitis group by combining the MALDI-TOF MS results (MALDI Biotyper, Bruker) with the information that the three stains were resistant to optochin. To allow a more detailed comparison, the three stored isolates were reanalysed and now ethanol/formic acid extractions were performed on the strains, and the updated and improved Bruker MALDI Biotyper database (DB-7311 MSP Library) was used for the MALDI Biotyper analysis. In addition to the standard log (score), weighted list (scores) was also calculated []. S. mitis was the best match for both the first and second isolates when both log (score) and list (score) were calculated. For the third isolate, the best match was S. oralis for both types of scores (). Next, the mass spectra of the three isolates were inspected manually. All three strains showed the specific peak 6839.1 m/z which is associated with S mitis and S. oralis strains, but only the third isolate showed the specific peak 5822.5 m/z which is associated with S. oralis () []. In addition, no peak profiles typical for S. pneumoniae and S. pseudopneumoniae could be detected in the three isolates [, ]. These results further support that the first two isolates are S. mitis and the third isolate is S. oralis. Many differences were seen in the mass spectra of the third isolate (S. oralis) compared to the first two (S. mitis). On the other hand, no clear differences in the spectra between the first and second isolate could be seen, and one can therefore not exclude that they belong to the same clone.
+
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 ## Expected Output Format
 
-The expected output format is 3-5 sentence summary 
+The expected output format is 3-5 sentence summary that uses patient-friendly and layman language for ease of understanding. The output will keep key information from the doctor's notes to ensure that critical details regarding the patient's health are still disclosed, but are interpretable.
 
-## Limitations
+Below is an example of the expected output format for a summary: 
 
+```
+A 70-year-old woman was admitted to the hospital because she had a sudden fever, chills, and a skin infection on her arm. She had a history of breast cancer and had experienced similar skin infections several times before. Blood tests showed that the infection was caused by a bacteria from the S. mitis group, which had caused problems in the past. She was treated with antibiotics, and after a few weeks, the infection cleared up. To prevent future infections, she was referred to specialists for her lymphoedema and to the dentist.
+```
+
+## Limitations
 
+Some limitations of this model include:
 
+1. This model does not provide medical advice. It just summarizes given doctor's notes into more readable summaries for patients. So, only doctor's notes should be given as input to get an accurate and properly formatted output.
+  
+2. The model was trained to keep key details, but remove overwhelming medical jargon. In this process, it is important to note that all "key" details may not be retained in the output summary. It is important to use the output summary to understand the doctor's note better, but should not be used to make medical decisions. In short, the summary does not replace the doctor's note.
 
+3. For any niche conditions/diagnoses that weren't covered in the training data, there is a risk of hallucination as the model may not be specialized enough to accurately output a summary.
 
+4. Since the model just focuses on summarization, ensure that the doctor's notes are redacted of any highly personal information. The model itself will not store this data, but to ensure privacy in the output summary, it is important to take out names or other personal information in the input. The model was trained on anonymous doctor's notes. 
 
 ## Citation [optional]