Name Variants for Improving Entity Discovery and Linking

Identifying all names that refer to a particular set of named entities is a challenging task, as quite often we need to consider many features that include a lot of variation like abbreviations, aliases, hypocorism, multilingualism or partial matches. Each entity type can also have specific rules for name variances: people names can include titles, country and branch names are sometimes removed from organization names, while locations are often plagued by the issue of nested entities. The lack of a clear strategy for collecting, processing and computing name variants significantly lowers the recall of tasks such as Named Entity Linking and Knowledge Base Population since name variances are frequently used in all kind of textual content. This paper proposes several strategies to address these issues. Recall can be improved by combining knowledge repositories and by computing additional variances based on algorithmic approaches. Heuristics and machine learning methods then analyze the generated name variances and mark ambiguous names to increase precision. An extensive evaluation demonstrates the effects of integrating these methods into a new Named Entity Linking framework and confirms that systematically considering name variances yields significant performance improvements

On the Importance of Drill-Down Analysis for Assessing Gold Standards and Named Entity Linking Performance

Rigorous evaluations and analyses of evaluation results are key towards improving Named Entity Linking systems. Nevertheless, most current evaluation tools are focused on benchmarking and comparative evaluations. Therefore, they only provide aggregated statistics such as precision, recall and F1-measure to assess system performance and no means for conducting detailed analyses up to the level of individual annotations. This paper addresses the need for transparent benchmarking and fine-grained error analysis by introducing Orbis, an extensible framework that supports drill-down analysis, multiple annotation tasks and resource versioning. Orbis complements approaches like those deployed through the GERBIL and TAC KBP tools and helps developers to better understand and address shortcomings in their Named Entity Linking tools. We present three uses cases in order to demonstrate the usefulness of Orbis for both research and production systems: (i)improving Named Entity Linking tools; (ii) detecting gold standard errors; and (iii) performing Named Entity Linking evaluations with multiple versions of the included resources

Evaluation of a prostate cancer e-health-tutorial

Hintergrund: Angesichts verschiedener Behandlungsoptionen ist die Information und Therapieentscheidung beim lokalisierten Prostatakarzinom eine Herausforderung. Die digitale Informationstechnologie bietet im Vergleich zu gedruckten Informationen mehr Möglichkeiten, die Information und die Patientenkommunikation bedarfsgerecht zu gestalten. Ziele: Zur Unterstützung der Therapieentscheidung und der Kommunikation mit Patienten ist in der deutschsprachigen Schweiz ein Online-Tutorial in einem systematischen Prozess entwickelt und in einer Pilotstudie getestet worden. In der Evaluation interessierten die Nutzerzufriedenheit, die Erfüllung der Informationsbedürfnisse, die Vorbereitung auf die Therapieentscheidung und deren subjektive Qualität. Material und Methoden: Die Plattform wurde in einem iterativen Prozess mittels Fokusgruppen mit Ärzten und Patienten auf der Grundlage von Informationen aus bestehenden Broschüren entwickelt. Für den Test der Plattform wurden in 8 urologischen Kliniken 87 Patienten zur Teilnahme eingeladen. Die 56 Nutzer wurden 4 Wochen nach dem Login und 3 Monate nach dem Therapieentscheid online befragt, 48 Nutzer füllten beide Befragungen aus. Eingesetzte Instrumente waren die Preparation for Decision Making Scale (PDMS), die Decisional Conflict Scale (DCS) und die Decisional Regret Scale (DRS). Ergebnisse und Diskussion: Die Nutzenden sind mit der Plattform sehr zufrieden und finden ihre Informationsbedürfnisse gut erfüllt. Sie zeigen 3 Monate nach dem Entscheid eine gute Vorbereitung auf die Entscheidung (MW PDMS 75, SD 23) und berichten über niedrigen Entscheidungskonflikt (MW DCS 9.6, SD 11) und kaum Bedauern über die Entscheidung (MW DRS 6.4, SD 9.6). Basierend auf diesen Erkenntnissen kann die Plattform zur weiteren Nutzung empfohlen werden.Background: Due to the multitude of therapy options the treatment decision after diagnosis of a localised prostate cancer is challenging. Compared to printed booklets, web based information technology offers more possibilities to tailor information to patients’ individual needs. Objectives: To support the decision making process as well as the communication with patients we developed an online tutorial in a systematic process in the German speaking part of Switzerland and then tested it in a pilot study. The study investigated users’ satisfaction, the coverage of information needs, the preparation for decision making and the subjective quality of the decision. Materials and methods: Based on already existing information material the online tutorial was developed in an iterative process using focus groups with patients and urologists. For the following evaluation in eight clinics a total of 87 patients were invited to access the platform and participate in the study. From these patients 56 used the tutorial and 48 answered both surveys (the first one 4 weeks after the first login and the second one 3 months after treatment decision). The surveys used the Preparation for Decision Making Scale (PDMS), the Decisional Conflict Scale (DCS), and the Decisional Regret Scale (DRS). Results and Conclusion: Satisfaction with the tutorial is very high among patients with newly diagnosed localized prostate cancer. Users find their information needs sufficiently covered. Three months after the decision they felt that they were well prepared for the decision making (Mean PDMS 75, SD 23), they had low decisional conflict (Mean DCS 9.6, SD 11) and almost no decisional regret (Mean DRS 6.4, SD 9.6). Based on these findings the further use of the tutorial can be recommended

A phase II study evaluating neo-/adjuvant EIA chemotherapy, surgical resection and radiotherapy in high-risk soft tissue sarcoma

<p>Abstract</p> <p>Background</p> <p>The role of chemotherapy in high-risk soft tissue sarcoma is controversial. Though many patients undergo initial curative resection, distant metastasis is a frequent event, resulting in 5-year overall survival rates of only 50-60%. Neo-adjuvant and adjuvant chemotherapy (CTX) has been applied to achieve pre-operative cytoreduction, assess chemosensitivity, and to eliminate occult metastasis. Here we report on the results of our non-randomized phase II study on neo-adjuvant treatment for high-risk STS.</p> <p>Method</p> <p>Patients with potentially curative high-risk STS (size ≥ 5 cm, deep/extracompartimental localization, tumor grades II-III [FNCLCC]) were included. The protocol comprised 4 cycles of neo-adjuvant chemotherapy (EIA, etoposide 125 mg/m²iv days 1 and 4, ifosfamide 1500 mg/m²iv days 1 - 4, doxorubicin 50 mg/m²day 1, pegfilgrastim 6 mg sc day 5), definitive surgery with intra-operative radiotherapy, adjuvant radiotherapy and 4 adjuvant cycles of EIA.</p> <p>Result</p> <p>Between 06/2005 and 03/2010 a total of 50 subjects (male = 33, female = 17, median age 50.1 years) were enrolled. Median follow-up was 30.5 months. The majority of primary tumors were located in the extremities or trunk (92%), 6% originated in the abdomen/retroperitoneum. Response by RECIST criteria to neo-adjuvant CTX was 6% CR (n = 3), 24% PR (n = 12), 62% SD (n = 31) and 8% PD (n = 4). Local recurrence occurred in 3 subjects (6%). Distant metastasis was observed in 12 patients (24%). Overall survival (OS) and disease-free survival (DFS) at 2 years was 83% and 68%, respectively. Multivariate analysis failed to prove influence of resection status or grade of histological necrosis on OS or DFS. Severe toxicities included neutropenic fever (4/50), cardiac toxicity (2/50), and CNS toxicity (4/50) leading to CTX dose reductions in 4 subjects. No cases of secondary leukemias were observed so far.</p> <p>Conclusion</p> <p>The current protocol is feasible for achieving local control rates, as well as OS and DFS comparable to previously published data on neo-/adjuvant chemotherapy in this setting. However, the definitive role of chemotherapy remains unclear in the absence of large, randomized trials. Therefore, the current regimen can only be recommended within a clinical study, and a possibly increased risk of secondary leukemias has to be taken into account.</p> <p>Trial registration</p> <p>ClinicalTrials.gov <a href="http://www.clinicaltrials.gov/ct2/show/NCT01382030">NCT01382030</a>, EudraCT 2004-002501-72</p

Improved Survival in Osteosarcoma Patients with Atypical Low Vascularization.

BACKGROUND: Osteosarcoma is considered a highly vascularized bone tumor with early metastatic dissemination through intratumoral blood vessels mostly into the lung. Novel targets for therapy such as tumor vascularization are highly warranted since little progress has been achieved in the last 30 years. However, proof of relevance for vascularization as a major prognostic parameter has been hampered by tumor heterogeneity, difficulty in detecting microvessels by immunohistochemistry, and small study cohorts. Most recently, we demonstrated that highly standardized whole-slide imaging could overcome these limitations (Kunz et al., PloS One 9(3):e90727, 2014). In this study, we applied this method to a multicenter cohort of 131 osteosarcoma patients to test osteosarcoma vascularization as a prognostic determinant. METHODS: Computer-assisted whole-slide analysis, together with enzymatic epitope retrieval, was used for CD31-based microvessel quantification in 131 pretreatment formalin-fixed and paraffin-embedded biopsies from three bone tumor centers. Kaplan-Meier-estimated survival and chemoresponse were determined and multivariate analysis was performed. Conventional hot-spot-based microvessel density (MVD) determination was compared with whole-slide imaging. RESULTS: We detected high estimated overall (p </= 0.008) and relapse-free (p </= 0.004) survival in 25 % of osteosarcoma patients with low osteosarcoma vascularization in contrast to other patient groups. Furthermore, all patients with low osteosarcoma vascularization showed a good response to neoadjuvant chemotherapy. Comparison of conventional MVD determination with whole-slide imaging suggests false high quantification or even exclusion of samples with low osteosarcoma vascularization due to difficult CD31 detection in previous studies. CONCLUSION: Low intratumoral vascularization at the time of diagnosis is a strong predictor for prolonged survival and good response to neoadjuvant chemotherapy in osteosarcoma