Update README.md

README.md

@@ -18,3 +18,395 @@ The model was fine-tuned and evaluated as detailed in [this notebook](https://co
 
 The model achieves a **Rouge-2** score of 19.33 on Pubmed which is competitive to state-of-the-art models.
 
+## Usage
+
+The model can be used as follows:
+
+```python 
+LONG_ARTICLE = """"anxiety affects quality of life in those living
+with parkinson 's disease ( pd ) more so than
+overall cognitive status , motor deficits , apathy
+, and depression [ 13 ] . although anxiety and
+depression are often related and coexist in pd
+patients , recent research suggests that anxiety
+rather than depression is the most prominent and
+prevalent mood disorder in pd [ 5 , 6 ] . yet ,
+our current understanding of anxiety and its
+impact on cognition in pd , as well as its neural
+basis and best treatment practices , remains
+meager and lags far behind that of depression .
+overall , neuropsychiatric symptoms in pd have
+been shown to be negatively associated with
+cognitive performance . for example , higher
+depression scores have been correlated with lower
+scores on the mini - mental state exam ( mmse ) [
+8 , 9 ] as well as tests of memory and executive
+functions ( e.g. , attention ) [ 1014 ] . likewise
+, apathy and anhedonia in pd patients have been
+associated with executive dysfunction [ 10 , 1523
+] . however , few studies have specifically
+investigated the relationship between anxiety and
+cognition in pd . one study showed a strong
+negative relationship between anxiety ( both state
+and trait ) and overall cognitive performance (
+measured by the total of the repeatable battery
+for the assessment of neuropsychological status
+index ) within a sample of 27 pd patients .
+furthermore , trait anxiety was negatively
+associated with each of the cognitive domains
+assessed by the rbans ( i.e. , immediate memory ,
+visuospatial construction , language , attention ,
+and delayed memory ) . two further studies have
+examined whether anxiety differentially affects
+cognition in patients with left - sided dominant
+pd ( lpd ) versus right - sided dominant pd ( rpd
+) ; however , their findings were inconsistent .
+the first study found that working memory
+performance was worse in lpd patients with anxiety
+compared to rpd patients with anxiety , whereas
+the second study reported that , in lpd , apathy
+but not anxiety was associated with performance on
+nonverbally mediated executive functions and
+visuospatial tasks ( e.g. , tmt - b , wms - iii
+spatial span ) , while in rpd , anxiety but not
+apathy significantly correlated with performance
+on verbally mediated tasks ( e.g. , clock reading
+test and boston naming test ) . furthermore ,
+anxiety was significantly correlated with
+neuropsychological measures of attention and
+executive and visuospatial functions . taken
+together , it is evident that there are limited
+and inconsistent findings describing the
+relationship between anxiety and cognition in pd
+and more specifically how anxiety might influence
+particular domains of cognition such as attention
+and memory and executive functioning . it is also
+striking that , to date , no study has examined
+the influence of anxiety on cognition in pd by
+directly comparing groups of pd patients with and
+without anxiety while excluding depression . given
+that research on healthy young adults suggests
+that anxiety reduces processing capacity and
+impairs processing efficiency , especially in the
+central executive and attentional systems of
+working memory [ 26 , 27 ] , we hypothesized that
+pd patients with anxiety would show impairments in
+attentional set - shifting and working memory
+compared to pd patients without anxiety .
+furthermore , since previous work , albeit limited
+, has focused on the influence of symptom
+laterality on anxiety and cognition , we also
+explored this relationship . seventeen pd patients
+with anxiety and thirty - three pd patients
+without anxiety were included in this study ( see
+table 1 ) . the cross - sectional data from these
+participants was taken from a patient database
+that has been compiled over the past 8 years (
+since 2008 ) at the parkinson 's disease research
+clinic at the brain and mind centre , university
+of sydney . inclusion criteria involved a
+diagnosis of idiopathic pd according to the united
+kingdom parkinson 's disease society brain bank
+criteria   and were confirmed by a neurologist (
+sjgl ) . patients also had to have an adequate
+proficiency in english and have completed a full
+neuropsychological assessment . ten patients in
+this study ( 5 pd with anxiety ; 5 pd without
+anxiety ) were taking psychotropic drugs ( i.e. ,
+benzodiazepine or selective serotonin reuptake
+inhibitor ) . patients were also excluded if they
+had other neurological disorders , psychiatric
+disorders other than affective disorders ( such as
+anxiety ) , or if they reported a score greater
+than six on the depression subscale of the
+hospital anxiety and depression scale ( hads ) .
+thus , all participants who scored within a
+depressed  ( hads - d > 6 ) range were excluded
+from this study , in attempt to examine a refined
+sample of pd patients with and without anxiety in
+order to determine the independent effect of
+anxiety on cognition . this research was approved
+by the human research ethics committee of the
+university of sydney , and written informed
+consent was obtained from all participants . self
+- reported hads was used to assess anxiety in pd
+and has been previously shown to be a useful
+measure of clinical anxiety in pd . a cut - off
+score of > 8 on the anxiety subscale of the hads (
+hads - a ) was used to identify pd cases with
+anxiety ( pda+ ) , while a cut - off score of < 6
+on the hads - a was used to identify pd cases
+without anxiety ( pda ) . this criterion was more
+stringent than usual ( > 7 cut - off score ) , in
+effort to create distinct patient groups . the
+neurological evaluation rated participants
+according to hoehn and yahr ( h&y ) stages   and
+assessed their motor symptoms using part iii of
+the revised mds task force unified parkinson 's
+disease rating scale ( updrs ) . in a similar way
+this was determined by calculating a total left
+and right score from rigidity items 3035 ,
+voluntary movement items 3643 , and tremor items
+5057 from the mds - updrs part iii ( see table 1 )
+. processing speed was assessed using the trail
+making test , part a ( tmt - a , z - score ) .
+attentional set - shifting was measured using the
+trail making test , part b ( tmt - b , z - score )
+. working memory was assessed using the digit span
+forward and backward subtest of the wechsler
+memory scale - iii ( raw scores ) . language was
+assessed with semantic and phonemic verbal fluency
+via the controlled oral word associated test (
+cowat animals and letters , z - score ) . the
+ability to retain learned verbal memory was
+assessed using the logical memory subtest from the
+wechsler memory scale - iii ( lm - i z - score ,
+lm - ii z - score , % lm retention z - score ) .
+the mini - mental state examination ( mmse )
+demographic , clinical , and neuropsychological
+variables were compared between the two groups
+with the independent t - test or mann  whitney u
+test , depending on whether the variable met
+parametric assumptions . chi - square tests were
+used to examine gender and symptom laterality
+differences between groups . all analyses employed
+an alpha level of p < 0.05 and were two - tailed .
+spearman correlations were performed separately in
+each group to examine associations between anxiety
+and/or depression ratings and cognitive functions
+. as expected , the pda+ group reported
+significant greater levels of anxiety on the hads
+- a ( u = 0 , p < 0.001 ) and higher total score
+on the hads ( u = 1 , p < 0.001 ) compared to the
+pda group ( table 1 ) . groups were matched in age
+( t(48 ) = 1.31 , p = 0.20 ) , disease duration (
+u = 259 , p = 0.66 ) , updrs - iii score ( u =
+250.5 , p = 0.65 ) , h&y ( u = 245 , p = 0.43 ) ,
+ledd ( u = 159.5 , p = 0.80 ) , and depression (
+hads - d ) ( u = 190.5 , p = 0.06 ) . additionally
+, all groups were matched in the distribution of
+gender (  = 0.098 , p = 0.75 ) and side - affected
+(  = 0.765 , p = 0.38 ) . there were no group
+differences for tmt - a performance ( u = 256 , p
+= 0.62 ) ( table 2 ) ; however , the pda+ group
+had worse performance on the trail making test
+part b ( t(46 ) = 2.03 , p = 0.048 ) compared to
+the pda group ( figure 1 ) . the pda+ group also
+demonstrated significantly worse performance on
+the digit span forward subtest ( t(48 ) = 2.22 , p
+= 0.031 ) and backward subtest ( u = 190.5 , p =
+0.016 ) compared to the pda group ( figures 2(a )
+and 2(b ) ) . neither semantic verbal fluency (
+t(47 ) = 0.70 , p = 0.49 ) nor phonemic verbal
+fluency ( t(47 ) = 0.39 , p = 0.70 ) differed
+between groups . logical memory i immediate recall
+test ( u = 176 , p = 0.059 ) showed a trend that
+the pda+ group had worse new verbal learning and
+immediate recall abilities than the pda group .
+however , logical memory ii test performance ( u =
+219 , p = 0.204 ) and logical memory % retention (
+u = 242.5 , p = 0.434 ) did not differ between
+groups . there were also no differences between
+groups in global cognition ( mmse ) ( u = 222.5 ,
+p = 0.23 ) . participants were split into lpd and
+rpd , and then further group differences were
+examined between pda+ and pda. importantly , the
+groups remained matched in age , disease duration
+, updrs - iii , dde , h&y stage , and depression
+but remained significantly different on self -
+reported anxiety . lpda+ demonstrated worse
+performance on the digit span forward test ( t(19
+) = 2.29 , p = 0.033 ) compared to lpda , whereas
+rpda+ demonstrated worse performance on the digit
+span backward test ( u = 36.5 , p = 0.006 ) , lm -
+i immediate recall ( u = 37.5 , p = 0.008 ) , and
+lm - ii ( u = 45.0 , p = 0.021 ) but not lm %
+retention ( u = 75.5 , p = 0.39 ) compared to
+rpda. this study is the first to directly compare
+cognition between pd patients with and without
+anxiety . the findings confirmed our hypothesis
+that anxiety negatively influences attentional set
+- shifting and working memory in pd . more
+specifically , we found that pd patients with
+anxiety were more impaired on the trail making
+test part b which assessed attentional set -
+shifting , on both digit span tests which assessed
+working memory and attention , and to a lesser
+extent on the logical memory test which assessed
+memory and new verbal learning compared to pd
+patients without anxiety . taken together , these
+findings suggest that anxiety in pd may reduce
+processing capacity and impair processing
+efficiency , especially in the central executive
+and attentional systems of working memory in a
+similar way as seen in young healthy adults [ 26 ,
+27 ] . although the neurobiology of anxiety in pd
+remains unknown , many researchers have postulated
+that anxiety disorders are related to
+neurochemical changes that occur during the early
+, premotor stages of pd - related degeneration [
+37 , 38 ] such as nigrostriatal dopamine depletion
+, as well as cell loss within serotonergic and
+noradrenergic brainstem nuclei ( i.e. , raphe
+nuclei and locus coeruleus , resp . , which
+provide massive inputs to corticolimbic regions )
+. over time , chronic dysregulation of
+adrenocortical and catecholamine functions can
+lead to hippocampal damage as well as
+dysfunctional prefrontal neural circuitries [ 39 ,
+40 ] , which play a key role in memory and
+attention . recent functional neuroimaging work
+has suggested that enhanced hippocampal activation
+during executive functioning and working memory
+tasks may represent compensatory processes for
+impaired frontostriatal functions in pd patients
+compared to controls . therefore , chronic stress
+from anxiety , for example , may disrupt
+compensatory processes in pd patients and explain
+the cognitive impairments specifically in working
+memory and attention seen in pd patients with
+anxiety . it has also been suggested that
+hyperactivation within the putamen may reflect a
+compensatory striatal mechanism to maintain normal
+working memory performance in pd patients ;
+however , losing this compensatory activation has
+been shown to contribute to poor working memory
+performance . anxiety in mild pd has been linked
+to reduced putamen dopamine uptake which becomes
+more extensive as the disease progresses . this
+further supports the notion that anxiety may
+disrupt compensatory striatal mechanisms as well ,
+providing another possible explanation for the
+cognitive impairments observed in pd patients with
+anxiety in this study . noradrenergic and
+serotonergic systems should also be considered
+when trying to explain the mechanisms by which
+anxiety may influence cognition in pd . although
+these neurotransmitter systems are relatively
+understudied in pd cognition , treating the
+noradrenergic and serotonergic systems has shown
+beneficial effects on cognition in pd . selective
+serotonin reuptake inhibitor , citalopram , was
+shown to improve response inhibition deficits in
+pd , while noradrenaline reuptake blocker ,
+atomoxetine , has been recently reported to have
+promising effects on cognition in pd [ 45 , 46 ] .
+overall , very few neuroimaging studies have been
+conducted in pd in order to understand the neural
+correlates of pd anxiety and its underlying neural
+pathology . future research should focus on
+relating anatomical changes and neurochemical
+changes to neural activation in order to gain a
+clearer understanding on how these pathologies
+affect anxiety in pd . to further understand how
+anxiety and cognitive dysfunction are related ,
+future research should focus on using advanced
+structural and function imaging techniques to
+explain both cognitive and neural breakdowns that
+are associated with anxiety in pd patients .
+research has indicated that those with amnestic
+mild cognitive impairment who have more
+neuropsychiatric symptoms have a greater risk of
+developing dementia compared to those with fewer
+neuropsychiatric symptoms . future studies should
+also examine whether treating neuropsychiatric
+symptoms might impact the progression of cognitive
+decline and improve cognitive impairments in pd
+patients . previous studies have used pd symptom
+laterality as a window to infer asymmetrical
+dysfunction of neural circuits . for example , lpd
+patients have greater inferred right hemisphere
+pathology , whereas rpd patients have greater
+inferred left hemisphere pathology . thus ,
+cognitive domains predominantly subserved by the
+left hemisphere ( e.g. , verbally mediated tasks
+of executive function and verbal memory ) might be
+hypothesized to be more affected in rpd than lpd ;
+however , this remains controversial . it has also
+been suggested that since anxiety is a common
+feature of left hemisphere involvement [ 48 , 49 ]
+, cognitive domains subserved by the left
+hemisphere may also be more strongly related to
+anxiety . results from this study showed selective
+verbal memory deficits in rpd patients with
+anxiety compared to rpd without anxiety , whereas
+lpd patients with anxiety had greater attentional
+/ working memory deficits compared to lpd without
+anxiety . although these results align with
+previous research , interpretations of these
+findings should be made with caution due to the
+small sample size in the lpd comparison
+specifically . recent work has suggested that the
+hads questionnaire may underestimate the burden of
+anxiety related symptomology and therefore be a
+less sensitive measure of anxiety in pd [ 30 , 50
+] . in addition , our small sample size also
+limited the statistical power for detecting
+significant findings . based on these limitations
+, our findings are likely conservative and
+underrepresent the true impact anxiety has on
+cognition in pd . additionally , the current study
+employed a very brief neuropsychological
+assessment including one or two tests for each
+cognitive domain . future studies are encouraged
+to collect a more complex and comprehensive
+battery from a larger sample of pd participants in
+order to better understand the role anxiety plays
+on cognition in pd . another limitation of this
+study was the absence of diagnostic interviews to
+characterize participants ' psychiatric symptoms
+and specify the type of anxiety disorders included
+in this study . future studies should perform
+diagnostic interviews with participants ( e.g. ,
+using dsm - v criteria ) rather than relying on
+self - reported measures to group participants ,
+in order to better understand whether the type of
+anxiety disorder ( e.g. , social anxiety , phobias
+, panic disorders , and generalized anxiety )
+influences cognitive performance differently in pd
+. one advantage the hads questionnaire provided
+over other anxiety scales was that it assessed
+both anxiety and depression simultaneously and
+allowed us to control for coexisting depression .
+although there was a trend that the pda+ group
+self - reported higher levels of depression than
+the pda group , all participants included in the
+study scored < 6 on the depression subscale of the
+hads . controlling for depression while assessing
+anxiety has been identified as a key shortcoming
+in the majority of recent work . considering many
+previous studies have investigated the influence
+of depression on cognition in pd without
+accounting for the presence of anxiety and the
+inconsistent findings reported to date , we
+recommend that future research should try to
+disentangle the influence of anxiety versus
+depression on cognitive impairments in pd .
+considering the growing number of clinical trials
+for treating depression , there are few if any for
+the treatment of anxiety in pd . anxiety is a key
+contributor to decreased quality of life in pd and
+greatly requires better treatment options .
+moreover , anxiety has been suggested to play a
+key role in freezing of gait ( fog ) , which is
+also related to attentional set - shifting [ 52 ,
+53 ] . future research should examine the link
+between anxiety , set - shifting , and fog , in
+order to determine whether treating anxiety might
+be a potential therapy for improving fog ."""
+
+from transformers import LEDForConditionalGeneration, LEDTokenizer
+
+tokenizer = LEDTokenizer.from_pretrained("patrickvonplaten/led-large-16384-pubmed")
+
+input_ids = tokenizer(LONG_ARTICLE).input_ids.to("cuda")
+global_attention_mask = torch.zeros_like(input_ids)
+# set global_attention_mask on first token
+global_attention_mask[:, 0] = 1
+
+model = LEDForConditionalGeneration.from_pretrained("patrickvonplaten/led-large-16384-pubmed", return_dict_in_generate=True).to("cuda")
+
+sequences = model.generate(input_ids, global_attention_mask=global_attention_mask).sequences
+
+summary = tokenizer.batch_decode(sequences)
+```