Peter, That sounds really useful! Were you able to benchmark it for runtime on a reasonably sized sample of your notes? Just curious because I wouldn't have expected regex to be that much of a bottleneck. Tim
On Tue, 2022-01-04 at 17:36 -0800, Peter Abramowitsch wrote: * External Email - Caution * Thank you for the fulsome and humorous response. Yes, I understand perfectly. We definitely think along the same lines. One of the drawbacks of static and simple to understand utility functions like JCasUtil's is that one can just slap things together without getting to grips with the wastage of resources that sometimes occur. This brings me to the topic of Negex. I've done a lot of improvements to it, also after I sent you that version last year. It has been well tested in over 100 million notes so i think I can check it in. But back to performance - it used to execute 200+ regular expressions multiple times on every sentence covering an identified annotation regardless of whether there was any hope of any of them matching. My solution was to build an inverted index of the compiled expressions keyed on unique words found in the expressions, so based on the sentence, I could look up and execute only the expressions that might match. This might cut the number of regex operations down to 5 or 10 and sometimes none at all. There were many other changes that related to negation detection, of course. For instance - handling sentences that switch between negating and non negating phrases within the same sentence. Peter On Tue, Jan 4, 2022 at 10:47 AM Finan, Sean < <mailto:sean.fi...@childrens.harvard.edu> sean.fi...@childrens.harvard.edu > wrote: Great question. The package name "windowed" isn't helpfully self-descriptive. It contains yet another bit of code that I wrote as quickly as possible to help somebody in real-time with a problem. * There is only a 'procedural' difference between the two. The models and methods are the same. The assertion engine has a bunch of objects delegating to objects delegating to more objects. Each object calls one or more JCasUtil.select() frequently for the same types. They also redundantly call JCasUtil.selectCovered() and selectCovering() for the same types. process( jcas ) { Collection<..> sentences = ...select(..); delegateA.do( sentences ); } class DelegateA { void do( Collection<..> sentences ) { for ( Sentence sentence : sentences ) { Collection<Token> tokens = JCasUtil.selectCovered( jcas, Token.class, sentence ); delegateB.use( tokens ); } } class DelegateB { void use( Collection<..> tokens ) { Collection<Sentence> sentence = JCasUtil.selectCovering( jcas, Sentece.class, tokens ); ... } } The above isn't an exact representation, but you get the point. The problem with code like this is repeated traversal of the (object) array in the cas. Every JCasUtil.select* pours through the whole thing. For a small document with a small cas (or early in a pipeline), that array may be small and the traversal fast. However, when people are (unadvisably) processing a single document that sizes in the gigabyte range, repeatedly going through the cas takes a long time. So, what I did was create a single container object that holds Collections of the types of interest and their covering relationships, populate all that stuff once per process( jcas ) and pass that container through to each delegate object. Basically, a jcas lite. The biggest culprit in the assertion engines was repeatedly iterating over the array for covered and covering windows, hence the subpackage name "windowed". Is it faster for smaller docs? Not so much. Does it instantaneously process the Encyclopedia Brittanica as one text? Of course not. Is it orders of magnitudes faster on such onerous docs? In my tests, yes. Going through my delegating example above, the end delegate is the same. Hence the processing is the same and repeatable. In my tests on both small and gargantuan documents the windowed version and the original version produced the same output. Sean ________________________________________ From: Peter Abramowitsch < <mailto:pabramowit...@gmail.com> pabramowit...@gmail.com > Sent: Tuesday, January 4, 2022 11:39 AM To: <mailto:dev@ctakes.apache.org> dev@ctakes.apache.org Subject: Re: Performance of the cleartk history module [EXTERNAL] * External Email - Caution * Hi Sean Ok.. I was confused whether I was meant to find it in the sources. But while you're reading this, is there a brief way to describe the difference between the older:package org.apache.ctakes.assertion.medfacts.cleartk; and org.apache.ctakes.assertion.medfacts.cleartk.windowed Peter On Tue, Jan 4, 2022 at 7:47 AM Finan, Sean < <mailto:sean.fi...@childrens.harvard.edu> sean.fi...@childrens.harvard.edu > wrote: Hi Peter, I created a second engine that just used text matching or regular expressions given the discovered events. It also uses covering section types, formatted text and other things, but the text match might be the most impactful item. You are an accomplished developer so the email scratch below is for the benefit of others who search archives. class LazyHistoryFinder extends JCasAnnotator_ImplBase { String[] HISTORY = { "history of", "h/o", "h / o" }; boolean isHistory( EventMention event ) { text = e.getCoveredText().toLowerCase(); return Arrays.stream( HISTORY ).anyMatch( text::startsWith ); } void process( JCas jcas ) throws Analysis*Ex { JCasUtil.select( jcas, EventMention.class ) .stream() .filter( this::isHistory ) .foreach( e -> e.setHistoryOf( CONST.NE_HISTORY_OF_PRESENT ) ); } } It requires a stroll through the monstrous cas array and it certainly isn't sexy, but it gets the job done. Sean ________________________________________ From: Peter Abramowitsch < <mailto:pabramowit...@gmail.com> pabramowit...@gmail.com > Sent: Monday, January 3, 2022 10:23 PM To: <mailto:dev@ctakes.apache.org> dev@ctakes.apache.org Subject: Re: Performance of the cleartk history module [EXTERNAL] * External Email - Caution * Thanks Sean By "following engine", you mean a second instance of the history engine that uses only the event spans, or you modified the current one to traverse the event-span within the context window? I see you made some source changes in that area and will check tomorrow. Peter On Mon, Jan 3, 2022 at 2:26 PM Finan, Sean < <mailto:sean.fi...@childrens.harvard.edu> sean.fi...@childrens.harvard.edu > wrote: Hi Peter, I have noticed this and just added a following engine that recognized text within event spans. It is a lazy solution, but it fit my needs and available time. Sean ________________________________________ From: Peter Abramowitsch < <mailto:pabramowit...@gmail.com> pabramowit...@gmail.com > Sent: Monday, January 3, 2022 5:03 PM To: <mailto:dev@ctakes.apache.org> dev@ctakes.apache.org Subject: Performance of the cleartk history module [EXTERNAL] * External Email - Caution * Hi All I've noticed that the HistoryCleartkAnalysisEngine misses many common forms of subject history including the obvious "h/o" prefix. Looking into the distribution, there's a model.jar and what appears to be a weights file containing trigger words: resources/org/apache/ctakes/assertion/models/history.txt where h, o, / are all given their own weights. But I'm not sure that they're actually used in this way: see below. However, there's also a tiny file: /org/apache/ctakes/assertion/semantic_classes/history.txt which does contain a few entries including "h/o" which I assume is used for training but is never referred to anywhere. Here's the behavior I'm seeing: example input condition term found history feature marked range text history of pregnancies "history of" included in the cu_term and prefterm yes no history of pregnancies history of adenopathy "history of" not included in the cu_term or prefterm yes yes adenopathy H/O postpartum psychosis "h/o" not included in the prefterm or cu_term yes yes postpartum psychosis H/O: postpartum psychosis "h/o" not included in the prefterm or cu_term yes no postpartum psychosis H/O pregnancies "h/o" included in the cu_term yes no h/o pregnancies You can see that it is quite perverse - there is a pattern suggesting that if the concept definition occupies the history words, then they cannot be seen by the history annotation engine. Has anyone else noticed this - and have they done anything about it? Peter
