Breast mass segmentation from mammograms with deep transfer learning

Abstract. Mammography is an x-ray imaging method used in breast cancer screening, which is a time consuming process. Many different computer assisted diagnosis have been created to hasten the image analysis. Deep learning is the use of multilayered neural networks for solving different tasks. Deep learning methods are becoming more advanced and popular for segmenting images. One deep transfer learning method is to use these neural networks with pretrained weights, which typically improves the neural networks performance. In this thesis deep transfer learning was used to segment cancerous masses from mammography images. The convolutional neural networks used were pretrained and fine-tuned, and they had an an encoder-decoder architecture. The ResNet22 encoder was pretrained with mammography images, while the ResNet34 encoder was pretrained with various color images. These encoders were paired with either a U-Net or a Feature Pyramid Network decoder. Additionally, U-Net model with random initialization was also tested. The five different models were trained and tested on the Oulu Dataset of Screening Mammography (9204 images) and on the Portuguese INbreast dataset (410 images) with two different loss functions, binary cross-entropy loss with soft Jaccard loss and a loss function based on focal Tversky index. The best models were trained on the Oulu Dataset of Screening Mammography with the focal Tversky loss. The best segmentation result achieved was a Dice similarity coefficient of 0.816 on correctly segmented masses and a classification accuracy of 88.7% on the INbreast dataset. On the Oulu Dataset of Screening Mammography, the best results were a Dice score of 0.763 and a classification accuracy of 83.3%. The results between the pretrained models were similar, and the pretrained models had better results than the non-pretrained models. In conclusion, deep transfer learning is very suitable for mammography mass segmentation and the choice of loss function had a large impact on the results.Rinnan massojen segmentointi mammografiakuvista syvä- ja siirto-oppimista hyödyntäen. Tiivistelmä. Mammografia on röntgenkuvantamismenetelmä, jota käytetään rintäsyövän seulontaan. Mammografiakuvien seulonta on aikaa vievää ja niiden analysoimisen avuksi on kehitelty useita tietokoneavusteisia ratkaisuja. Syväoppimisella tarkoitetaan monikerroksisten neuroverkkojen käyttöä eri tehtävien ratkaisemiseen. Syväoppimismenetelmät ovat ajan myötä kehittyneet ja tulleet suosituiksi kuvien segmentoimiseen. Yksi tapa yhdistää syvä- ja siirtooppimista on hyödyntää neuroverkkoja esiopetettujen painojen kanssa, mikä auttaa parantamaan neuroverkkojen suorituskykyä. Tässä diplomityössä tutkittiin syvä- ja siirto-oppimisen käyttöä syöpäisten massojen segmentoimiseen mammografiakuvista. Käytetyt konvoluutioneuroverkot olivat esikoulutettuja ja hienosäädettyjä. Lisäksi niillä oli enkooderi-dekooderi arkkitehtuuri. ResNet22 enkooderi oli esikoulutettu mammografia kuvilla, kun taas ResNet34 enkooderi oli esikoulutettu monenlaisilla värikuvilla. Näihin enkoodereihin yhdistettiin joko U-Net:n tai piirrepyramidiverkon dekooderi. Lisäksi käytettiin U-Net mallia ilman esikoulutusta. Nämä viisi erilaista mallia koulutettiin ja testattiin sekä Oulun Mammografiaseulonta Datasetillä (9204 kuvaa) että portugalilaisella INbreast datasetillä (410 kuvaa) käyttäen kahta eri tavoitefunktiota, jotka olivat binääriristientropia yhdistettynä pehmeällä Jaccard-indeksillä ja fokaaliin Tversky indeksiin perustuva tavoitefunktiolla. Parhaat mallit olivat koulutettu Oulun datasetillä fokaalilla Tversky tavoitefunktiolla. Parhaat tulokset olivat 0,816 Dice kerroin oikeissa positiivisissa segmentaatioissa ja 88,7 % luokittelutarkkuus INbreast datasetissä. Esikoulutetut mallit antoivat parempia tuloksia kuin mallit joita ei esikoulutettu. Oulun datasetillä parhaat tulokset olivat 0,763:n Dice kerroin ja 83,3 % luokittelutarkkuus. Tuloksissa ei ollut suurta eroa esikoulutettujen mallien välillä. Tulosten perusteella syvä- ja siirto-oppiminen soveltuvat hyvin massojen segmentoimiseen mammografiakuvista. Lisäksi tavoitefunktiovalinnalla saatiin suuri vaikutus tuloksiin

Being creative is mandatory:experiences of communication in game development from the perspective of creative employees

Abstract. Although game development is a form of software development, it cannot be compared directly to traditional software development. The audio-visual elements of games and their fundamental requirement to be “fun” make them exceptionally challenging to implement. Traditional software development has been extensively studied for decades, but research on game development is still in its early stages. More research is needed on game development because traditional software development processes and methods may not directly fit the needs of the gaming industry or may even be harmful. This thesis answers the question of how professionals who work in creative jobs in the gaming industry experience communication and feedback in the game development process and what factors they consider to be obstacles to the process. An interview study was conducted with six Finnish game developers as part of this thesis. Many of the interviewees also worked as leaders of creative workers. The interview material was subjected to a qualitative content analysis, and the results were compared with literature. The analysis revealed that creative workers consider communication and its quality to be an important part of their work. It was a source of encouragement and motivation for them, as well as a tool for ensuring the quality of their work and guidance. It was noteworthy that communication difficulties, such as those related to work instructions or feedback, were considered by the interviewees to be obstacles that slowed down the game development process. Other obstacles included poor project management and planning. Good communication is one of the most important pillars of the game development process. It helps ideas to grow by sharing a common vision and navigating through the toughest challenges. If we better understand what game development team members see, experience, and feel, we can help them thrive and persevere in their work. This can produce better games, successful companies, and happier people behind them

Impact of pasireotide on postoperative pancreatic fistulas following distal resections

Purpose Postoperative pancreatic fistula (POPF), a difficult complication after surgery, can cause peripancreatic fluid collection and infections in the operative area. In addition, pancreatic fluid is corrosive and can lead to postoperative bleeding. Clinically significant grade B and C fistulas (CR-POPF) increase postoperative morbidity, resulting in a prolonged hospital stay. Delaying adjuvant therapy due to fistula formation in cancer patients can affect their prognosis. In this study, we aimed to determine if pasireotide affects fistula formation, and the severity of other complications in patients following pancreatic distal resections. Data and methods Between 2000 and 2016, 258 distal pancreatectomies were performed at Helsinki University Hospital and were included in our analysis. Pasireotide was administered to patients undergoing distal resections between July 2014 and December 2016. Patients received 900-mu g pasireotide administered twice daily perioperatively. Other patients who received octreotide treatment were analyzed separately. Complications such as fistulas (POPF), delayed gastric emptying (DGE), postpancreatectomy hemorrhage (PPH), reoperations, and mortality were recorded and analyzed 90 days postoperatively. Results Overall, 47 (18%) patients received pasireotide and 31 (12%) octreotide, while 180 patients (70%) who received neither constituted the control group. There were 40 (16%) clinically relevant grade B and C POPFs: seven (15%) in the pasireotide group, three (10%) in the octreotide group, and 30 (17%) in the control group (p = 0.739). Severe complications categorized as Clavien-Dindo grade III or IV were recorded in 64 (25%) patients: 17 (27%) in the pasireotide group, 4 (6%) in the octreotide group, and 43 (67%) in the control group (p = 0.059). We found no 90-day mortality. Conclusions In this study, pasireotide did not reduce clinically relevant POPFs or severe complications following pancreatic distal resection.Peer reviewe

Sensory profiles in women with neuropathic pain after breast cancer surgery

Purpose We performed a detailed analysis of sensory function in patients with chronic post-surgical neuropathic pain (NP) after breast cancer treatments by quantitative sensory testing (QST) with DFNS (German Research Network on Neuropathic Pain) protocol and bed side examination (BE). The nature of sensory changes in peripheral NP may reflect distinct pathophysiological backgrounds that can guide the treatment choices. NP with sensory gain (i.e., hyperesthesia, hyperalgesia, allodynia) has been shown to respond to Na+-channel blockers (e.g., oxcarbazepine). Methods 104 patients with at least "probable" NP in the surgical area were included. All patients had been treated for breast cancer 4-9 years ago and the handling of the intercostobrachial nerve (ICBN) was verified by the surgeon. QST was conducted at the site of NP in the surgical or nearby area and the corresponding contralateral area. BE covered the upper body and sensory abnormalities were marked on body maps and digitalized for area calculation. The outcomes of BE and QST were compared to assess the value of QST in the sensory examination of this patient group. Results Loss of function in both small and large fibers was a prominent feature in QST in the area of post-surgical NP. QST profiles did not differ between spared and resected ICBN. In BE, hypoesthesia on multiple modalities was highly prevalent. The presence of sensory gain in BE was associated with more intense pain. Conclusions Extensive sensory loss is characteristic for chronic post-surgical NP several years after treatment for breast cancer. These patients are unlikely to respond to Na+-channel blockers.Peer reviewe

Prognostic and diagnostic value of REG4 serum and tissue expression in pancreatic ductal adenocarcinoma

Expression of regenerating islet-derived protein 4 (REG4), a secretory protein involved in cell differentiation and proliferation, is upregulated in inflammatory bowel diseases and in many gastrointestinal malignancies. The prognostic significance of its expression in pancreatic ductal adenocarcinoma is unknown. Our aim was to investigate tumor tissue and serum REG4 expression in pancreatic ductal adenocarcinoma patients. We also evaluated as a control the diagnostic value of serum REG4 level in patients with chronic pancreatitis. Immunohistochemical expression of REG4 was evaluated in 154 surgical specimens and serum REG4 level in 130 samples from pancreatic ductal adenocarcinoma patients treated at Helsinki University Hospital, Finland, in 2000–2011. REG4 tissue and serum expression was assessed in relation to clinicopathological parameters and patient survival. A chronic pancreatitis control group comprised 34 patients who underwent pancreatic resection because of suspicion of malignancy. Significant survival differences were detectable in subgroups: in tumor stages IA–IIA, high serum REG4 level predicted worse survival (p=0.046). In patients with grade I tumor, positive tissue REG4 expression predicted better survival (p=0.006). In multivariate analysis, neither tissue nor serum REG4 expression was independent prognostic factors. Serum REG4 levels were higher in pancreatic ductal adenocarcinoma than in chronic pancreatitis (p=0.002), with diagnostic sensitivity of 45% and specificity of 91%. In logistic regression analysis, a multivariate model with REG4, CA19-9, and age provided sensitivity of 82% and specificity of 79%. REG4 tissue expression is a prognostic marker in subgroups of pancreatic ductal adenocarcinoma patients. Serum REG4 level might be useful in differential diagnosis between pancreatic ductal adenocarcinoma and chronic pancreatitis. © 2018, © The Author(s) 2018.Peer reviewe

Effect And Predictive Value Of Routine Preoperative Laboratory Testing For Endoscopic Retrograde Cholangiopancreatography

Background and Aims: Several studies and guidelines are questioning routine preoperative laboratory tests in surgical and endoscopic procedures. Their effect in endoscopic retrograde cholangiopancreatography is not currently known. This study was carried out to evaluate the risk of adverse effects in endoscopic retrograde cholangiopancreatography and their association with preoperative lab tests. Materials and Methods: A single-center, prospective observational study on all 956 patients undergoing 1196 endoscopic retrograde cholangiopancreatographies in the Endoscopy Unit of Helsinki University Central Hospital from 1 March 2012 to 28 February 2013. Routine preoperative laboratory test results (basic blood count, creatinine, potassium, sodium, international normalized ratio/thromboplastin time, and amylase), health status, medication, and demographic information of all patients were analyzed in relation to adverse effects related to endoscopic retrograde cholangiopancreatography and procedural sedation. Results: Multivariate analysis showed post-endoscopic retrograde cholangiopancreatography pancreatitis (43 cases, 3.6%) to have no association with abnormal routine preoperative laboratory tests. Respiratory depression caused by sedation (128 cases, 11%) was not associated with abnormal routine preoperative laboratory tests, and anemia was found to be a slightly protecting factor. Cardiovascular depression caused by sedation was associated with thrombocytopenia (odds ratio = 1.87, p = 0.025) and, in male patients, hyponatremia (odds ratio = 3.66, p <0.001). Incidence of other adverse effects was too low for statistical analysis. Conclusion: Routine universal preoperative lab testing was not found to be successful in predicting adverse effects in endoscopic retrograde cholangiopancreatography procedures. Laboratory testing should be done focusing on each patient's individual needs.Peer reviewe

Efficacy of 5-day parenteral versus intramammary benzylpenicillin for treatment of clinical mastitis caused by gram-positive bacteria susceptible to penicillin in vitro

Peer reviewe