RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Thanks Tim! I was looking for that one but couldn't find it. -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, October 03, 2017 10:03 AM To: dev@ctakes.apache.org Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] Here's the most recent publication, which describes the system in ctakes 4.0 and later: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.sciencedirect.com_science_article_pii_S1532046417300850=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=L05lBYR93doAn-IsnZW2HMb7Ev0Y_82_0CpE3FYzpEA=GohiPyZbSEWfBjnOtC6x3UNnzv-fOBTnPFaIBUnVjm8= Tim On Tue, 2017-10-03 at 13:52 +, Finan, Sean wrote: > > > > With the changes in Input, the co-reference between all the > > entities should still be preserved right? > No. One of the experts can better explain this, but the coreference > module works with "best match" chains. With one sentence of text, > term (Markable) A may have a best match with term B. As soon as you > add more text, you introduce the possibility that term A will have a > better best match with C and/or D, and the previous match to B will > be deemed less accurate and dropped. > In your case the coreference A - B seems to be lost in favor of one > using internal term A', and that is a little strange. It could be > that overlapping markables are being discarded? I will try to look > into this really quickly. > > You can look at some publications on coref if you search the > web. The one that probably best applies to the current coref module > (Tim, Dima, is this true?) is > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.aclweb.org_a > nthology_W12- > 2D2409=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup- > IbsIg9Q1TPOylpP9FE4GTK- > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=ceLOeKc31GMcMXRVqM_QfDAoSqTWnl > HbNcMy1vdWWTE=_CKDY58PHb_DWnHgx72vKozAAas7qI9k72hwfHU8Cik= > > Sean > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Tuesday, October 03, 2017 4:18 AM > To: dev@ctakes.apache.org > Subject: RE: Enabling drugner pipeline and identifying dates > [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > Hi Sean, I still have some doubts on this. If I run the piper file > with the complete text I sent earlier, I could see only superscript - > 4 for Thalomid and the co-reference of this to "treatment of > hepatocellular carcinoma" is still lost. Also I don’t see any > superscript with number-1 too. With the changes in Input, the co- > reference between all the entities should still be preserved right? > Do we have any more info or doc on this co-reference module to > understand its complexity better? > > Regards, > Gandhi > > > -Original Message- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Monday, October 02, 2017 8:36 PM > To: dev@ctakes.apache.org > Subject: RE: Enabling drugner pipeline and identifying dates > [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > Hi Tim, > > The coreference question (just a question) was for a different item > altogether. Sorry for any confusion. The reason that I CC:d you ... > > From Gandhi: > > > > Interestingly even I was able to generate [Sean's coref output] > > using piper GUI by having only that single line - " The patient > > started study treatment of Thalomid 200mg (days 1-21), and > > Epirubicin, 20 mg/m2 (days 1, 8, and 15) on 06/07/02 for the > > treatment of hepatocellular carcinoma. " in the input file. > > But when I change the input file content with the following > > lines: [Full paragraph (below), single-sentence in middle] The > > co-reference superscript is lost by then. > Sean's answer: > > > > Ctakes is a system with many moving parts. Things that precede or > > follow your original example sentence will change the evaluation of > > that sentence. > With the pipeline you are using and the full note, you should see a > number (mine is 4) next to the first "thalomid" in the original > example sentence. If you click that number you should see (to the > right) 4 instances of "thalomid". > > > > Tim can correct me here, but maybe the coreference module ranked > > the links between "thalomid" as much higher than the rank between > > "study treatment of thalomid 200mg" and "the treatment of > > hepatocellular carcinoma" and discarded the encapsulating treatment > >
Re: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
This is very informative. Thank you Tim Alex On Oct 3, 2017 10:06, "Miller, Timothy" < timothy.mil...@childrens.harvard.edu> wrote: > Here's the most recent publication, which describes the system in > ctakes 4.0 and later: > http://www.sciencedirect.com/science/article/pii/S1532046417300850 > Tim > > On Tue, 2017-10-03 at 13:52 +, Finan, Sean wrote: > > > > > > With the changes in Input, the co-reference between all the > > > entities should still be preserved right? > > No. One of the experts can better explain this, but the coreference > > module works with "best match" chains. With one sentence of text, > > term (Markable) A may have a best match with term B. As soon as you > > add more text, you introduce the possibility that term A will have a > > better best match with C and/or D, and the previous match to B will > > be deemed less accurate and dropped. > > In your case the coreference A - B seems to be lost in favor of one > > using internal term A', and that is a little strange. It could be > > that overlapping markables are being discarded? I will try to look > > into this really quickly. > > > > You can look at some publications on coref if you search the > > web. The one that probably best applies to the current coref module > > (Tim, Dima, is this true?) is > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.aclweb.org_a > > nthology_W12- > > 2D2409=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup- > > IbsIg9Q1TPOylpP9FE4GTK- > > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=ceLOeKc31GMcMXRVqM_QfDAoSqTWnl > > HbNcMy1vdWWTE=_CKDY58PHb_DWnHgx72vKozAAas7qI9k72hwfHU8Cik= > > > > Sean > > > > -Original Message----- > > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > > > Sent: Tuesday, October 03, 2017 4:18 AM > > To: dev@ctakes.apache.org > > Subject: RE: Enabling drugner pipeline and identifying dates > > [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > > > Hi Sean, I still have some doubts on this. If I run the piper file > > with the complete text I sent earlier, I could see only superscript - > > 4 for Thalomid and the co-reference of this to "treatment of > > hepatocellular carcinoma" is still lost. Also I don’t see any > > superscript with number-1 too. With the changes in Input, the co- > > reference between all the entities should still be preserved right? > > Do we have any more info or doc on this co-reference module to > > understand its complexity better? > > > > Regards, > > Gandhi > > > > > > -Original Message- > > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > > Sent: Monday, October 02, 2017 8:36 PM > > To: dev@ctakes.apache.org > > Subject: RE: Enabling drugner pipeline and identifying dates > > [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > > > Hi Tim, > > > > The coreference question (just a question) was for a different item > > altogether. Sorry for any confusion. The reason that I CC:d you ... > > > > From Gandhi: > > > > > > Interestingly even I was able to generate [Sean's coref output] > > > using piper GUI by having only that single line - " The patient > > > started study treatment of Thalomid 200mg (days 1-21), and > > > Epirubicin, 20 mg/m2 (days 1, 8, and 15) on 06/07/02 for the > > > treatment of hepatocellular carcinoma. " in the input file. > > > But when I change the input file content with the following > > > lines: [Full paragraph (below), single-sentence in middle] The > > > co-reference superscript is lost by then. > > Sean's answer: > > > > > > Ctakes is a system with many moving parts. Things that precede or > > > follow your original example sentence will change the evaluation of > > > that sentence. > > With the pipeline you are using and the full note, you should see a > > number (mine is 4) next to the first "thalomid" in the original > > example sentence. If you click that number you should see (to the > > right) 4 instances of "thalomid". > > > > > > Tim can correct me here, but maybe the coreference module ranked > > > the links between "thalomid" as much higher than the rank between > > > "study treatment of thalomid 200mg" and "the treatment of > > > hepatocellular carcinoma" and discarded the encapsulating treatment > > > texts from markables? It is probably more complex than that. > > Sean
Re: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Here's the most recent publication, which describes the system in ctakes 4.0 and later: http://www.sciencedirect.com/science/article/pii/S1532046417300850 Tim On Tue, 2017-10-03 at 13:52 +, Finan, Sean wrote: > > > > With the changes in Input, the co-reference between all the > > entities should still be preserved right? > No. One of the experts can better explain this, but the coreference > module works with "best match" chains. With one sentence of text, > term (Markable) A may have a best match with term B. As soon as you > add more text, you introduce the possibility that term A will have a > better best match with C and/or D, and the previous match to B will > be deemed less accurate and dropped. > In your case the coreference A - B seems to be lost in favor of one > using internal term A', and that is a little strange. It could be > that overlapping markables are being discarded? I will try to look > into this really quickly. > > You can look at some publications on coref if you search the > web. The one that probably best applies to the current coref module > (Tim, Dima, is this true?) is > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.aclweb.org_a > nthology_W12- > 2D2409=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup- > IbsIg9Q1TPOylpP9FE4GTK- > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=ceLOeKc31GMcMXRVqM_QfDAoSqTWnl > HbNcMy1vdWWTE=_CKDY58PHb_DWnHgx72vKozAAas7qI9k72hwfHU8Cik= > > Sean > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Tuesday, October 03, 2017 4:18 AM > To: dev@ctakes.apache.org > Subject: RE: Enabling drugner pipeline and identifying dates > [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > Hi Sean, I still have some doubts on this. If I run the piper file > with the complete text I sent earlier, I could see only superscript - > 4 for Thalomid and the co-reference of this to "treatment of > hepatocellular carcinoma" is still lost. Also I don’t see any > superscript with number-1 too. With the changes in Input, the co- > reference between all the entities should still be preserved right? > Do we have any more info or doc on this co-reference module to > understand its complexity better? > > Regards, > Gandhi > > > -Original Message- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Monday, October 02, 2017 8:36 PM > To: dev@ctakes.apache.org > Subject: RE: Enabling drugner pipeline and identifying dates > [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] > > Hi Tim, > > The coreference question (just a question) was for a different item > altogether. Sorry for any confusion. The reason that I CC:d you ... > > From Gandhi: > > > > Interestingly even I was able to generate [Sean's coref output] > > using piper GUI by having only that single line - " The patient > > started study treatment of Thalomid 200mg (days 1-21), and > > Epirubicin, 20 mg/m2 (days 1, 8, and 15) on 06/07/02 for the > > treatment of hepatocellular carcinoma. " in the input file. > > But when I change the input file content with the following > > lines: [Full paragraph (below), single-sentence in middle] The > > co-reference superscript is lost by then. > Sean's answer: > > > > Ctakes is a system with many moving parts. Things that precede or > > follow your original example sentence will change the evaluation of > > that sentence. > With the pipeline you are using and the full note, you should see a > number (mine is 4) next to the first "thalomid" in the original > example sentence. If you click that number you should see (to the > right) 4 instances of "thalomid". > > > > Tim can correct me here, but maybe the coreference module ranked > > the links between "thalomid" as much higher than the rank between > > "study treatment of thalomid 200mg" and "the treatment of > > hepatocellular carcinoma" and discarded the encapsulating treatment > > texts from markables? It is probably more complex than that. > Sean > > "This patient is participating in a Non-IND study; Protocol CG- > 000424: "Phase I/II of Thalidomide and Epirubicin in Patients with > Unresectable or Metastatic Hepatocellular Carcinoma".Information has > been received from the investigator regarding an 82 year-old male > patient who had gastrointestinal bleeding while on Thalomid, > Epirubicin, and Coumadin. He had a past medical history of > diverticulosis in 03/02 and a right atrial clot from intraventricular > catheter (IVC) for which he was started on Coumadin. During the > hospita
RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
> With the changes in Input, the co-reference between all the entities should > still be preserved right? No. One of the experts can better explain this, but the coreference module works with "best match" chains. With one sentence of text, term (Markable) A may have a best match with term B. As soon as you add more text, you introduce the possibility that term A will have a better best match with C and/or D, and the previous match to B will be deemed less accurate and dropped. In your case the coreference A - B seems to be lost in favor of one using internal term A', and that is a little strange. It could be that overlapping markables are being discarded? I will try to look into this really quickly. You can look at some publications on coref if you search the web. The one that probably best applies to the current coref module (Tim, Dima, is this true?) is https://www.aclweb.org/anthology/W12-2409 Sean -Original Message- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Tuesday, October 03, 2017 4:18 AM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] Hi Sean, I still have some doubts on this. If I run the piper file with the complete text I sent earlier, I could see only superscript - 4 for Thalomid and the co-reference of this to "treatment of hepatocellular carcinoma" is still lost. Also I don’t see any superscript with number-1 too. With the changes in Input, the co-reference between all the entities should still be preserved right? Do we have any more info or doc on this co-reference module to understand its complexity better? Regards, Gandhi -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Monday, October 02, 2017 8:36 PM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] Hi Tim, The coreference question (just a question) was for a different item altogether. Sorry for any confusion. The reason that I CC:d you ... From Gandhi: > Interestingly even I was able to generate [Sean's coref output] using piper > GUI by having only that single line - " The patient started study treatment > of Thalomid 200mg (days 1-21), and Epirubicin, 20 mg/m2 (days 1, 8, and 15) > on 06/07/02 for the treatment of hepatocellular carcinoma. " in the input > file. >But when I change the input file content with the following lines: [Full >paragraph (below), single-sentence in middle] The co-reference superscript is >lost by then. Sean's answer: > Ctakes is a system with many moving parts. Things that precede or follow > your original example sentence will change the evaluation of that sentence. With the pipeline you are using and the full note, you should see a number (mine is 4) next to the first "thalomid" in the original example sentence. If you click that number you should see (to the right) 4 instances of "thalomid". >Tim can correct me here, but maybe the coreference module ranked the links >between "thalomid" as much higher than the rank between "study treatment of >thalomid 200mg" and "the treatment of hepatocellular carcinoma" and discarded >the encapsulating treatment texts from markables? It is probably more complex >than that. Sean "This patient is participating in a Non-IND study; Protocol CG-000424: "Phase I/II of Thalidomide and Epirubicin in Patients with Unresectable or Metastatic Hepatocellular Carcinoma".Information has been received from the investigator regarding an 82 year-old male patient who had gastrointestinal bleeding while on Thalomid, Epirubicin, and Coumadin. He had a past medical history of diverticulosis in 03/02 and a right atrial clot from intraventricular catheter (IVC) for which he was started on Coumadin. During the hospitalization for a right atrial clot in 03/02 hepatocellular carcinoma was first noted and he was referred to an oncologist. The patient started study treatment of Thalomid 200mg (days 1-21), and Epirubicin, 20 mg/m2 (days 1, 8, and 15) on 06/07/02 for the treatment of hepatocellular carcinoma. He was concomitantly receiving Cardura, Ambien (for insomnia), Megace, Coumadin, and Oxycodone. This patient presented to the emergency room with the chief complaint of hematochezia. He reported noticing bright red blood and small clots mixed in with his stool. On 07/13/02, he was admitted due to gastrointestinal bleed. The physician ordered 2 large bore intravenous lines and planned to transfuse for hematocrit less than 30%. Due to the INR (international normalized ratio) level of 3.0, Coumadin was held. He was also noted to have bilateral lower extremity edema with dyspnea on exertion. On 07/13/02, he had a chest X-ray PA and l
RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hi Sean, I still have some doubts on this. If I run the piper file with the complete text I sent earlier, I could see only superscript - 4 for Thalomid and the co-reference of this to "treatment of hepatocellular carcinoma" is still lost. Also I don’t see any superscript with number-1 too. With the changes in Input, the co-reference between all the entities should still be preserved right? Do we have any more info or doc on this co-reference module to understand its complexity better? Regards, Gandhi -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Monday, October 02, 2017 8:36 PM To: dev@ctakes.apache.org Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] Hi Tim, The coreference question (just a question) was for a different item altogether. Sorry for any confusion. The reason that I CC:d you ... From Gandhi: > Interestingly even I was able to generate [Sean's coref output] using piper > GUI by having only that single line - " The patient started study treatment > of Thalomid 200mg (days 1-21), and Epirubicin, 20 mg/m2 (days 1, 8, and 15) > on 06/07/02 for the treatment of hepatocellular carcinoma. " in the input > file. >But when I change the input file content with the following lines: [Full >paragraph (below), single-sentence in middle] The co-reference superscript is >lost by then. Sean's answer: > Ctakes is a system with many moving parts. Things that precede or follow > your original example sentence will change the evaluation of that sentence. With the pipeline you are using and the full note, you should see a number (mine is 4) next to the first "thalomid" in the original example sentence. If you click that number you should see (to the right) 4 instances of "thalomid". >Tim can correct me here, but maybe the coreference module ranked the links >between "thalomid" as much higher than the rank between "study treatment of >thalomid 200mg" and "the treatment of hepatocellular carcinoma" and discarded >the encapsulating treatment texts from markables? It is probably more complex >than that. Sean "This patient is participating in a Non-IND study; Protocol CG-000424: "Phase I/II of Thalidomide and Epirubicin in Patients with Unresectable or Metastatic Hepatocellular Carcinoma".Information has been received from the investigator regarding an 82 year-old male patient who had gastrointestinal bleeding while on Thalomid, Epirubicin, and Coumadin. He had a past medical history of diverticulosis in 03/02 and a right atrial clot from intraventricular catheter (IVC) for which he was started on Coumadin. During the hospitalization for a right atrial clot in 03/02 hepatocellular carcinoma was first noted and he was referred to an oncologist. The patient started study treatment of Thalomid 200mg (days 1-21), and Epirubicin, 20 mg/m2 (days 1, 8, and 15) on 06/07/02 for the treatment of hepatocellular carcinoma. He was concomitantly receiving Cardura, Ambien (for insomnia), Megace, Coumadin, and Oxycodone. This patient presented to the emergency room with the chief complaint of hematochezia. He reported noticing bright red blood and small clots mixed in with his stool. On 07/13/02, he was admitted due to gastrointestinal bleed. The physician ordered 2 large bore intravenous lines and planned to transfuse for hematocrit less than 30%. Due to the INR (international normalized ratio) level of 3.0, Coumadin was held. He was also noted to have bilateral lower extremity edema with dyspnea on exertion. On 07/13/02, he had a chest X-ray PA and lateral done that showed no evidence of acute pneumonia or congestive heart failure. On 07/14/02, he underwent an ultrasound which was negative for deep vein thrombosis. This patient did not take Thalomid on the day of his admittance to the hospital, but resumed treatment shortly after with no return of symptoms. On 07/15/02, he was discharged in stable condition. There have been no further reports of bleeding at this time. Thedoctor has assessed the hematochezia as related to Coumadin treatment and previously diagnosed diverticulosis, and not to protocol therapy with Thalomid and Epirubicin.Additional information received from the investigator on 27Aug02 reveals that this male patient began on 07Jun02 two cycles of therapy with Thalidomide and Epirubicin. His post cycle two computed tomography scans revealed increase in size of liver lesion with development of multiple new satellite nodules. On 29Jul02, the investigator removed this patient from protocol for progressive disease and recommended hospice care. After seeking a second opinion from two other institutions, this patient was admitted to hospice on 05Aug02. On 20Aug02, the investigator noted that this patient w
RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Hi Tim, The coreference question (just a question) was for a different item altogether. Sorry for any confusion. The reason that I CC:d you ... From Gandhi: > Interestingly even I was able to generate [Sean's coref output] using piper > GUI by having only that single line - " The patient started study treatment > of Thalomid 200mg (days 1-21), and Epirubicin, 20 mg/m2 (days 1, 8, and 15) > on 06/07/02 for the treatment of hepatocellular carcinoma. " in the input > file. >But when I change the input file content with the following lines: [Full >paragraph (below), single-sentence in middle] The co-reference superscript is >lost by then. Sean's answer: > Ctakes is a system with many moving parts. Things that precede or follow > your original example sentence will change the evaluation of that sentence. With the pipeline you are using and the full note, you should see a number (mine is 4) next to the first "thalomid" in the original example sentence. If you click that number you should see (to the right) 4 instances of "thalomid". >Tim can correct me here, but maybe the coreference module ranked the links >between "thalomid" as much higher than the rank between "study treatment of >thalomid 200mg" and "the treatment of hepatocellular carcinoma" and discarded >the encapsulating treatment texts from markables? It is probably more complex >than that. Sean "This patient is participating in a Non-IND study; Protocol CG-000424: "Phase I/II of Thalidomide and Epirubicin in Patients with Unresectable or Metastatic Hepatocellular Carcinoma".Information has been received from the investigator regarding an 82 year-old male patient who had gastrointestinal bleeding while on Thalomid, Epirubicin, and Coumadin. He had a past medical history of diverticulosis in 03/02 and a right atrial clot from intraventricular catheter (IVC) for which he was started on Coumadin. During the hospitalization for a right atrial clot in 03/02 hepatocellular carcinoma was first noted and he was referred to an oncologist. The patient started study treatment of Thalomid 200mg (days 1-21), and Epirubicin, 20 mg/m2 (days 1, 8, and 15) on 06/07/02 for the treatment of hepatocellular carcinoma. He was concomitantly receiving Cardura, Ambien (for insomnia), Megace, Coumadin, and Oxycodone. This patient presented to the emergency room with the chief complaint of hematochezia. He reported noticing bright red blood and small clots mixed in with his stool. On 07/13/02, he was admitted due to gastrointestinal bleed. The physician ordered 2 large bore intravenous lines and planned to transfuse for hematocrit less than 30%. Due to the INR (international normalized ratio) level of 3.0, Coumadin was held. He was also noted to have bilateral lower extremity edema with dyspnea on exertion. On 07/13/02, he had a chest X-ray PA and lateral done that showed no evidence of acute pneumonia or congestive heart failure. On 07/14/02, he underwent an ultrasound which was negative for deep vein thrombosis. This patient did not take Thalomid on the day of his admittance to the hospital, but resumed treatment shortly after with no return of symptoms. On 07/15/02, he was discharged in stable condition. There have been no further reports of bleeding at this time. Thedoctor has assessed the hematochezia as related to Coumadin treatment and previously diagnosed diverticulosis, and not to protocol therapy with Thalomid and Epirubicin.Additional information received from the investigator on 27Aug02 reveals that this male patient began on 07Jun02 two cycles of therapy with Thalidomide and Epirubicin. His post cycle two computed tomography scans revealed increase in size of liver lesion with development of multiple new satellite nodules. On 29Jul02, the investigator removed this patient from protocol for progressive disease and recommended hospice care. After seeking a second opinion from two other institutions, this patient was admitted to hospice on 05Aug02. On 20Aug02, the investigator noted that this patient was suffering worsening fatigue and got tired getting out of his chair. On 25Aug02, this patient died due to disease progression. The investigator assessed the death as not related to study treatment and expected" -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Monday, October 02, 2017 10:36 AM To: dev@ctakes.apache.org Subject: Re: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] My bad, I didn't read too closely and thought this was going to be a coreference patch. I don't know this FSM code that well, so I am not an expert. My biggest concern at a glance is that these additions help find more true positives (as in your examples), can we verify that they won't creat
Re: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
It is a very busy time for me but this is on my todo list. Don't be afraid to ping in a week or so if you don't hear anything. Tim On Fri, 2017-09-29 at 14:04 +, Finan, Sean wrote: > Hi Gandhi, > > > > Did you mean that with the text I sent, the co-reference > > superscript-1 will be lost? > Yes. Well, to be more clear, the coreference that was resolved as #1 > in your original sentence alone will be lost. However, there are > eight or none coreference chains discovered in your full paragraph, > and one of those will have superscript 1s. > > > > > Could someone have a look and know your thoughts please? > Thank you for creating the jira and the patch. I am sure that > somebody will take a look. > > Thanks, > Sean > > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Friday, September 29, 2017 2:25 AM > To: dev@ctakes.apache.org > Subject: RE: Enabling drugner pipeline and identifying dates > [EXTERNAL] [SUSPICIOUS] > > Hi Sean, > > Thanks again for the response. I guess its mistake from my side that > I dint send the complete text. Did you mean that with the text I > sent, the co-reference superscript-1 will be lost? > > Also as per your advice, We have created an issue - https://urldefen > se.proofpoint.com/v2/url?u=https- > 3A__issues.apache.org_jira_browse_CTAKES- > 2D459=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67Gv > lGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=iyJsQ5ekdL7Vf_wcjADsUYBjMaVho > hpozRybEEpwNUg=KHAFRjKk4tjMJGHaIjrUuqk6XAtVFYP0sVuN5ODLs3Q= for > measurement FSM changes and attached the modified file changes. Could > someone have a look and know your thoughts please? > > Regards, > Gandhi > > > -Original Message- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Thursday, September 28, 2017 8:21 PM > To: dev@ctakes.apache.org > Cc: Miller, Timothy <timothy.mil...@childrens.harvard.edu> > Subject: RE: Enabling drugner pipeline and identifying dates > [EXTERNAL] [SUSPICIOUS] > > Hi Gandhi, > > I don't recall you sending me that entire snippet of text. I think > that I only had your single example sentence. > You have discovered one of the quirks of software: "change the data, > change the result." > Ctakes is a system with many moving parts. Things that precede or > follow your original example sentence will change the evaluation of > that sentence. > With the pipeline you are using and the full note, you should see a > number (mine is 4) next to the first "thalomid" in the original > example sentence. If you click that number you should see (to the > right) 4 instances of "thalomid". > Tim can correct me here, but maybe the coreference module ranked the > links between "thalomid" as much higher than the rank between "study > treatment of thalomid 200mg" and "the treatment of hepatocellular > carcinoma" and discarded the encapsulating treatment texts from > markables? It is probably more complex than that. > > > > > we have also made some code changes in MeasurementFSM.java to > > identify certain measurements like '20 mg/m2' which was not > > identified out of the box. Should we send the code changes to you > > so that you can consider the same to be productized ? Please > > advise." > I don't know if you've noticed the recent emails on the dev list > involving Alexandru Zbarcea. Alex has been creating or commenting on > Jira items and attaching code for fixes and enhancements. This is a > widely used process and is fairly easy to follow. I think that the > following links are relevant: > Working with issues: https://urldefense.proofpoint.com/v2/url?u=http > s-3A__confluence.atlassian.com_jiracoreserver073_working-2Dwith- > 2Dissues- > 2D861257307.html=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxe > FU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=iyJsQ5ekdL7Vf_wcjA > DsUYBjMaVhohpozRybEEpwNUg=2BFHffDc3fS5DTAXq3M5MsGBv_uG0t3MceVT38alp > 2Q= > Creating patches: https://urldefense.proofpoint.com/v2/url?u=https- > 3A__confluence.atlassian.com_crucible_creating-2Dpatch-2Dfiles-2Dfor- > 2Dpre-2Dcommit-2Dreviews- > 2D298977458.html=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxe > FU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=iyJsQ5ekdL7Vf_wcjA > DsUYBjMaVhohpozRybEEpwNUg=JXOJanO4pjISmYVdCpcTLHD72n0_wzJMa7xrYDT1G > yc= > Attaching files: https://urldefense.proofpoint.com/v2/url?u=https-3 > A__confluence.atlassian.com_jiracorecloud_attaching-2Dfiles-2Dand- > 2Dscreenshots-2Dto-2Dissues- > 2D765593805.html=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
