Yleiskäyttöinen tekstinluokittelija suomenkielisille potilaskertomusteksteille

Medical texts are an underused source of data in clinical analytics. Extracting the relevant information from unstructured texts is difficult and while there are some tools available, they are often targeted for English texts. The situation is worse for smaller languages, such as Finnish. In this work, we reviewed literature in text mining and natural language processing fields in the scope of analyzing medical texts. Using the results of our literature review, we created an algorithm for information extraction from patient record texts. During this thesis work we created a decent text mining tool that works through text classification. This algorithm can be used detect medical conditions solely from medical texts. The usage of the algorithm is limited through the availability of large training data.Potilaskertomustekstejä käytetään kliinisessä analytiikassa huomattavan vähäisessä määrin. Olennaisen tiedon poimiminen tekstin joukosta on vaikeaa, ja vaikka siihen on työkaluja saatavilla, ovat ne useimmiten tehty englanninkielisille teksteille. Pienempien kielten, kuten suomen kohdalla tilanne on heikompi. Tässä työssä tehtiin kirjallisuuskatsaus tekstinlouhintaan ja luonnollisen kielen käsittelyyn liittyvään kirjallisuuteen, keskittyen erityisesti menetelmiin jotka soveltuvat lääketieteellisten tekstien analysointiin. Kirjallisuuskatsauksen pohjalta loimme algoritmin, joka soveltuu yleisesti lääketieteellisten tekstien luokitteluun. Tämän diplomityön osana luotiin tekstinlouhintatyökalu suomenkielisille lääketieteellisille teksteille. Kehitettyä algoritmia voidaan käyttää erilaisten tilojen tunnistamiseen potilaskertomusteksteistä. Algoritmin käyttöä kuitenkin rajoittaa tarve suurehkolle määrälle opetusdataa

Semi-Supervised Named Entity Recognition:\ud Learning to Recognize 100 Entity Types with Little Supervision\ud

Named Entity Recognition (NER) aims to extract and to classify rigid designators in text such as proper names, biological species, and temporal expressions. There has been growing interest in this field of research since the early 1990s. In this thesis, we document a trend moving away from handcrafted rules, and towards machine learning approaches. Still, recent machine learning approaches have a problem with annotated data availability, which is a serious shortcoming in building and maintaining large-scale NER systems. \ud \ud In this thesis, we present an NER system built with very little supervision. Human supervision is indeed limited to listing a few examples of each named entity (NE) type. First, we introduce a proof-of-concept semi-supervised system that can recognize four NE types. Then, we expand its capacities by improving key technologies, and we apply the system to an entire hierarchy comprised of 100 NE types. \ud \ud Our work makes the following contributions: the creation of a proof-of-concept semi-supervised NER system; the demonstration of an innovative noise filtering technique for generating NE lists; the validation of a strategy for learning disambiguation rules using automatically identified, unambiguous NEs; and finally, the development of an acronym detection algorithm, thus solving a rare but very difficult problem in alias resolution. \ud \ud We believe semi-supervised learning techniques are about to break new ground in the machine learning community. In this thesis, we show that limited supervision can build complete NER systems. On standard evaluation corpora, we report performances that compare to baseline supervised systems in the task of annotating NEs in texts. \u

Syntactic Frequency and Sentence Processing in Standard Indonesian:Data from agrammatic aphasia and ERP

Aphasia is a language impairment caused by focal brain damage affecting multiple channels of language. Studies have shown that one third of stroke patients show some form of aphasia. One of the key characteristics of aphasia is that in most types, patients show deficits in sentence processing. This is so much so that many aphasia assessment tools utilize sentence comprehension or production tasks to determine aphasia type or severity, or perhaps to provide a more detailed profile on the symptoms. Individuals with aphasia have been known to face difficulties in processing sentences with a derived or non-canonical structure, like the passive. While numerous studies have discussed the morphosyntactic basis of this deficit, other aspects of sentence processing such as frequency of the sentence structures are often neglected. There is considerable possibility of syntactic frequency affecting sentence processing, as a large body of research has shown the impact of word-level frequency towards language processing. Could the impairment of processing non-canonical sentences be related to the low frequency of these sentences?This thesis examines sentence processing in Standard Indonesian, a language where the passive occurs at a rate that is comparable to active sentences. Individuals with aphasia and controls were tested with sentence comprehension and production tasks, and an event-related potential study of sentence processing for healthy adults were conducted. We found the passive to be unimpaired for aphasic individuals, and we also did not find any observable processing differences between the active and the passive in the neuroimaging experiment

Front-Line Physicians' Satisfaction with Information Systems in Hospitals

Day-to-day operations management in hospital units is difficult due to continuously varying situations, several actors involved and a vast number of information systems in use. The aim of this study was to describe front-line physicians' satisfaction with existing information systems needed to support the day-to-day operations management in hospitals. A cross-sectional survey was used and data chosen with stratified random sampling were collected in nine hospitals. Data were analyzed with descriptive and inferential statistical methods. The response rate was 65 % (n = 111). The physicians reported that information systems support their decision making to some extent, but they do not improve access to information nor are they tailored for physicians. The respondents also reported that they need to use several information systems to support decision making and that they would prefer one information system to access important information. Improved information access would better support physicians' decision making and has the potential to improve the quality of decisions and speed up the decision making process.Peer reviewe

End of life care in nursing homes: Palliative drug prescribing and doctors' existential vulnerability

Nursing homes are the main arena for end-of-life (EOL) care in Norway. Patients, their informal caregivers and academics alike have called for doctors more involved in EOL care, but the nursing home doctor’s role has been given relatively little attention in research. This thesis explores the doctor’s work with EOL care in nursing homes from the perspectives of EOL prescription changes (paper I); the effectiveness and safety of palliative prescriptions (paper II); and from nursing home doctors’ own experiences and how their existential vulnerability impacts on their work (paper III). Paper I Methods. A historical cohort study, set in three urban nursing homes in Norway, between January 2008 and February 2013. Drug prescriptions, diagnoses, and demographic data were collected from electronic patient records. Results. 524 patients were included. On the day of death, almost all patients had active prescriptions; around three out of four patients were prescribed palliative drugs. Palliative drugs were associated with nursing home, length of stay >16 months, age, and a diagnosis of cancer. Initiations of palliative drugs and withdrawals of curative/preventive drugs most commonly took place on the day of death. Paper II Methods. A systematic search of the literature published before December 2016, including studies on safety or effectiveness of drug therapy in dying adults with at least one outcome on symptom control, adverse effects, or survival. Results. Of 5940 unique titles identified, 12 studies met the inclusion criteria. Five studies assessed anticholinergics for death rattle, providing no evidence that scopolamine hydrobromide or atropine were superior to placebo. Five studies examined drugs for dyspnea, anxiety, or terminal restlessness, providing some evidence supporting the use of morphine and midazolam. Two studies examined opioids for pain, providing some support for morphine, diamorphine and fentanyl. Eight studies included safety outcomes, revealing no important differences in adverse effects between the interventions, and no evidence for midazolam shortening survival. Paper III Methods. A qualitative study based on three focus group interviews with purposive samples of 17 nursing home doctors. The interviews were audio-recorded, transcribed, and analyzed with systematic text condensation (STC). Results. Nursing home doctors interviewed in paper III experienced having to balance treatment compromises in order to assist patients’ and families’ preparation for death, with their sense of professional conduct. This was an arduous process demanding patience and consideration. Existential vulnerability also manifested as powerlessness mastering issues of life and death and families’ expectations. Personal commitment was balanced with protective disengagement on the patient’s deathbed, triggering both feelings of wonder and guilt. Conclusion Palliative drug therapy and drug therapy changes are common for nursing home patients on the last day of life. Improvements in end-of-life care in nursing homes imply addressing prognostication and an earlier response to palliative needs. There is a lack of evidence concerning the effectiveness and safety of palliative drug treatment in dying patients, and the reviewed evidence provides limited guidance for clinicians. Anticholinergic agents are not supported for the treatment of death rattle. Existential vulnerability is experienced by nursing home doctors as a burden of powerlessness and guilt in difficult treatment compromises and in the need for protective disengagement, but also as a resource in communication and professional coping.Sykehjem er den fremste arena for terminalomsorg i Norge. Legens økte involvering i terminalomsorgen er etterspurt av pasientene, deres omsorgspersoner, og fagmiljøet, men har fått relativt liten oppmerksomhet i forskning. Denne avhandlingen utforsker sykehjemslegens arbeid i terminalomsorgen, fra tre forskjellige perspektiv: legemiddelendringer på sykehjem ved livets slutt (artikkel I), evidens for nytte og sikkerhet ved lindrende legemidler ved livets slutt (artikkel II), og sykehjemslegens egne erfaringer, og hvordan deres eksistensielle sårbarhet påvirker deres arbeid. Artikkel I Metode. En historisk kohort studie, gjennomført ved tre by-sykehjem i Norge, i perioden januar 2008 til februar 2013. Legemiddelforskrivninger, diagnoser, og demografiske data ble innsamlet fra elektronisk pasientjournal. Resultat. 524 pasienter ble inkludert. På dødsdagen hadde nær alle pasienter aktive legemiddel-forskrivninger; omkring 3 av 4 sto på lindrende legemidler. Lindrende legemidler var forbundet med sykehjem, oppholdsvarighet over 16 måneder, alder, og kreftdiagnose. Flest endringer av lindrende legemidler og seponeringer av kurativ/preventive legemidler skjedde på dødsdagen. Artikkel II Metode. Systematisk litteratursøk av publikasjoner frem til desember 2016 på effektivitet og sikkerhet av legemiddelbehandling av døende voksne pasienter med minst ett utfallsmål innen symptomkontroll, bivirkning eller overlevelse. Resultater. Av 5940 unike titler identifisert, møtte 12 inklusjonskriteriene. Fem studier omhandlet antikolinerge legemidler for dødsralling, og viste ingen evidens for at skopolamin hydrobromid eller atropin var bedre enn placebo. Fem studier undersøkte legemiddelbehandling av tungpust, angst, og terminal rastløshet/uro, og viste noestøtte for bruken av morfin og midazolam. To studier undersøkte opiater for smerte, og viste noe støtte for morfin, heroin, og fentanyl. Åtte studier undersøkte legemiddelsikkerhet, og viste ingen nevneverdige forskjeller i bivirkninger mellom intervensjoner, og uendret overlevelse ved bruk av midazolam. Artikkel III Metode. En kvalitativ studie basert på tre fokusgruppeintervju med strategisk utvalg av 17 sykehjemsleger. Intervjuene ble tatt opp, transkribert, og analysert med systematisk tekstkondensering. Resultater. Sykehjemslegene erfarte å balansere behandlingskompromisser for behjelpe pasient og pårørendes forberedelse til døden, med deres egen profesjonalitet. Dette var en prosess som krevde tålmodighet og omtanke. Eksistensiell sårbarhet ble også uttrykt som maktesløshet i å mestre liv og død, og pårørendes forventninger til legen. På pasientens dødsleie ble personlig nærhet avveid mot beskyttende distanse, og kunne utløse følelser både av skyld og ærefrykt. Konklusjon Lindrende legemiddelbehandling og endringer i legemidler er vanlige ved livets slutt for sykehjemspasienter. Forbedringer i terminalomsorgen innebærer bedre prognostisering av døden, og en tidligere respons på palliative behov. Det er mangel på evidens for effekt og sikkerhet av lindrende legemiddelbehandling av dødende pasienter, og gjennomgått evidens alene gir lite veiledning for klinikere. Antikolinerge medikamenter støttes ikke for behandling av dødsralling. Eksistensiell sårbarhet erfares av sykehjemsleger både som en byrde av maktesløshet og skyldfølelse ved vanskelige behandlingskompromiss, og i behovet for beskyttende distanse fra pasientsituasjoner, men også som en ressurs i kommunikasjon og profesjonell mestring

Reading skills in mental illness: A multimodal analysis

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London.Reading is a complex process involving multiple skills – i.e., phonological processing, comprehension, and word recognition. It is also a significant predictor of socio-economic status, academic achievement, and has vast importance in everyday functioning. Reading deficits can lead to maladaptive behaviour and consequently increase the risk of incarceration. Severe reading skills deficits are present in schizophrenia, and to some extent in people with psychopathy and forensic populations (Chapter 2 – systematic review and meta-analysis). Considering the overlap between discreet clinical diagnoses and the presence of symptoms and psychopathology-related traits in non-clinical populations, this thesis aimed to examine the behavioural and neurofunctional associations between reading skills and dimensional psychopathology-related traits in the general and clinical populations. To address these aims, three empirical investigations were carried out: i) behavioural studies (Chapters 4 and 5) investigating the relationship between reading-related skills, as indexed by performance on a lexical decision task (LDT) requiring word-nonword recognition, and a range of psychopathologyrelated traits (schizotypy, psychopathy, impulsivity, and affective traits) in a general population sample (N = 78), ii) a functional magnetic resonance imaging (fMRI) study (Chapter 6) investigating the neural correlates of this relationship (N = 22), and iii) a preliminary clinical study (Chapter 7) investigating the relationship between reading skills of phonological processing and comprehension, dimensional psychopathology, and cognition (verbal learning and memory, IQ, and executive functioning) in a forensic psychiatric sample (N = 15). The findings suggest that traits of positive schizotypy (Unusual Experiences), fearless dominance (Meanness) and callous aggression (Boldness) in psychopathy, and motor impulsivity can modulate behavioural responses in word-nonword recognition (LDT performance) in the general population. Higher motor impulsivity was the trait most strongly associated with lower LDT performance accuracy in non-native speakers. At the neural level also, motor impulsivity was most consistently associated with lower activity in some of the brain areas that are crucial for word recognition, namely the fusiform and inferior frontal gyri (IFG). In the forensic psychiatric sample, 13/15 patients were diagnosed with a psychotic disorder and all reading skills were significantly below their age norms and showed some association with executive function and verbal learning. In this sample, Lifestyle psychopathy was significantly associated with poor LDT performance, especially in low-frequency words recognition and Cognitive Perceptual aspect of positive schizotypy with severe deficits in reading comprehension, overall reading ability, and poor low-frequency word recognition. In conclusion, positive schizotypy and psychosis seem to be associated with poor reading skills. Higher psychopathy and motor impulsivity traits seem to predict of poor reading skills across the general and clinical populations and modulate neural activity during correct word-nonword recognition. These findings provide insight into the relationship between dimensional psychopathology-related traits, their comorbidities, and reading skills in clinical and non-clinical populations, and suggest that poor reading skills in clinical populations should be considered as important treatment targets

Development and transfer in reading ability: a study of Zairean EFL learners.

In general, educational practices in Zairean secondary schools point to a\ud positivistic orientation to literacy, in spite of the fact that one of the stated aims of\ud secondary education is to encourage independent thinking in students.\ud For this reason, one of the aims of the present study was to promote greater\ud independence in students by presenting a humanistic-interpretive approach to\ud reading, as demonstrated by the practice of sustained silent reading. For this\ud purpose, some of the students involved in the study (the experimental subjects)\ud were presented with graded readers in English, in a 20h (1h/week) experimental\ud reading programme. Moreover, in keeping with the view of reading as a unitary\ud process, transferable across languages, a second aim of the study was to explore\ud the possibility of transfer in reading ability between French as a L2 and English as\ud a FL.\ud Data were supplied by experimental and control subjects from questionnaires and\ud cloze passages in French, and in English, that were administered before and after\ud the reading programme. These data failed to provide unequivocal evidence for the\ud expected transfer and improvement, and reasons are offered for this outcome.\ud Nonetheless, the experimental subjects performed as well as the control subjects\ud at the second administration of the measurement instruments. In other terms, one\ud hour of sustained silent reading in English, along with 4 hours of traditional EFL\ud teaching, appeared to be as educationally beneficial as the usual 5 hours/week\ud orally driven, teacher-directed EFL classroom practice