Prognosis of prostate gland morphology study using artificial neural network

The research goal is to optimize the management of patients with serum PSA level falling in the range of 4-10 ng/ ml by designing and educating of an artificial neural network, which may be used to predict prostate gland morphology basing on clinical, laboratory and imaging data. Material and methods. Data of 254 patients, who were admitted to the oncological Department of S. R. Mirotvortsev Clinical hospital for transrectal prostate biopsy, was collected to construct several artificial neural networks with different architecture. External validation was performed on 27 patients, who had prostate biopsy in January-February 2014. Results. One-layer network, consisting of 11 input, 9 hidden and 3 output neurons, was determined to be the most successful: in 92.6% cases it was correct in predicting prostate cancer or its absence. Input factors were evaluated according to their relative importance, from more important to less important: prostate volume, serum PSA, patient's age, prostate consistency, PSA velocity, prostate symmetry, previous negative biopsy, free serum PSA, intake of 5-alpha-reductase inhibitors. Conclusion. Artificial neural networks may be used to predict morphological findings in prostate biopsy. High PSA density and firm prostate consistency should cause suspicion of prostate cancer

Artificial neural networks for selection of pulsar candidates from the radio continuum surveys

Pulsar search with time-domain observation is very computationally expensive and data volume will be enormous with the next generation telescopes such as the Square Kilometre Array. We apply artificial neural networks (ANNs), a machine learning method, for efficient selection of pulsar candidates from radio continuum surveys, which are much cheaper than time-domain observation. With observed quantities such as radio fluxes, sky position and compactness as inputs, our ANNs output the "score" that indicates the degree of likeliness of an object to be a pulsar. We demonstrate ANNs based on existing survey data by the TIFR GMRT Sky Survey (TGSS) and the NRAO VLA Sky Survey (NVSS) and test their performance. Precision, which is the ratio of the number of pulsars classified correctly as pulsars to that of any objects classified as pulsars, is about 96$\%$. Finally, we apply the trained ANNs to unidentified radio sources and our fiducial ANN with five inputs (the galactic longitude and latitude, the TGSS and NVSS fluxes and compactness) generates 2,436 pulsar candidates from 456,866 unidentified radio sources. These candidates need to be confirmed if they are truly pulsars by time-domain observations. More information such as polarization will narrow the candidates down further.Comment: 11 pages, 13 figures, 3 tables, accepted for publication in MNRA

The Relativistic Hopfield network: rigorous results

The relativistic Hopfield model constitutes a generalization of the standard Hopfield model that is derived by the formal analogy between the statistical-mechanic framework embedding neural networks and the Lagrangian mechanics describing a fictitious single-particle motion in the space of the tuneable parameters of the network itself. In this analogy the cost-function of the Hopfield model plays as the standard kinetic-energy term and its related Mattis overlap (naturally bounded by one) plays as the velocity. The Hamiltonian of the relativisitc model, once Taylor-expanded, results in a P-spin series with alternate signs: the attractive contributions enhance the information-storage capabilities of the network, while the repulsive contributions allow for an easier unlearning of spurious states, conferring overall more robustness to the system as a whole. Here we do not deepen the information processing skills of this generalized Hopfield network, rather we focus on its statistical mechanical foundation. In particular, relying on Guerra's interpolation techniques, we prove the existence of the infinite volume limit for the model free-energy and we give its explicit expression in terms of the Mattis overlaps. By extremizing the free energy over the latter we get the generalized self-consistent equations for these overlaps, as well as a picture of criticality that is further corroborated by a fluctuation analysis. These findings are in full agreement with the available previous results.Comment: 11 pages, 1 figur

Non-Rigid Liver Registration for Laparoscopy using Data-Driven Biomechanical Models

During laparoscopic liver resection, the limited access to the organ, the small field of view and lack of palpation can obstruct a surgeon’s workflow. Automatic navigation systems could use the images from preoperative volumetric organ scans to help the surgeons find their target (tumors) and risk-structures (vessels) more efficiently. This requires the preoperative data to be fused (or registered) with the intraoperative scene in order to display information at the correct intraoperative position. One key challenge in this setting is the automatic estimation of the organ’s current intra-operative deformation, which is required in order to predict the position of internal structures. Parameterizing the many patient-specific unknowns (tissue properties, boundary conditions, interactions with other tissues, direction of gravity) is very difficult. Instead, this work explores how to employ deep neural networks to solve the registration problem in a data-driven manner. To this end, convolutional neural networks are trained on synthetic data to estimate an organ’s intraoperative displacement field and thus its current deformation. To drive this estimation, visible surface cues from the intraoperative camera view must be supplied to the networks. Since reliable surface features are very difficult to find, the networks are adapted to also find correspondences between the pre- and intraoperative liver geometry automatically. This combines the search for correspondences with the biomechanical behavior estimation and allows the networks to tackle the full non-rigid registration problem in one single step. The result is a model which can quickly predict the volume deformation of a liver, given only sparse surface information. The model combines the advantages of a physically accurate biomechanical simulation with the speed and powerful feature extraction capabilities of deep neural networks. To test the method intraoperatively, a registration pipeline is developed which constructs a map of the liver and its surroundings from the laparoscopic video and then uses the neural networks to fuse the preoperative volume data into this map. The deformed organ volume can then be rendered as an overlay directly onto the laparoscopic video stream. The focus of this pipeline is to be applicable to real surgery, where everything should be quick and non-intrusive. To meet these requirements, a SLAM system is used to localize the laparoscopic camera (avoiding setup of an external tracking system), various neural networks are used to quickly interpret the scene and semi-automatic tools let the surgeons guide the system. Beyond the concrete advantages of the data-driven approach for intraoperative registration, this work also demonstrates general benefits of training a registration system preoperatively on synthetic data. The method lets the engineer decide which values need to be known explicitly and which should be estimated implicitly by the networks, which opens the door to many new possibilities.:1 Introduction 1.1 Motivation 1.1.1 Navigated Liver Surgery 1.1.2 Laparoscopic Liver Registration 1.2 Challenges in Laparoscopic Liver Registration 1.2.1 Preoperative Model 1.2.2 Intraoperative Data 1.2.3 Fusion/Registration 1.2.4 Data 1.3 Scope and Goals of this Work 1.3.1 Data-Driven, Biomechanical Model 1.3.2 Data-Driven Non-Rigid Registration 1.3.3 Building a Working Prototype 2 State of the Art 2.1 Rigid Registration 2.2 Non-Rigid Liver Registration 2.3 Neural Networks for Simulation and Registration 3 Theoretical Background 3.1 Liver 3.2 Laparoscopic Liver Resection 3.2.1 Staging Procedure 3.3 Biomechanical Simulation 3.3.1 Physical Balance Principles 3.3.2 Material Models 3.3.3 Numerical Solver: The Finite Element Method (FEM) 3.3.4 The Lagrangian Specification 3.4 Variables and Data in Liver Registration 3.4.1 Observable 3.4.2 Unknowns 4 Generating Simulations of Deforming Organs 4.1 Organ Volume 4.2 Forces and Boundary Conditions 4.2.1 Surface Forces 4.2.2 Zero-Displacement Boundary Conditions 4.2.3 Surrounding Tissues and Ligaments 4.2.4 Gravity 4.2.5 Pressure 4.3 Simulation 4.3.1 Static Simulation 4.3.2 Dynamic Simulation 4.4 Surface Extraction 4.4.1 Partial Surface Extraction 4.4.2 Surface Noise 4.4.3 Partial Surface Displacement 4.5 Voxelization 4.5.1 Voxelizing the Liver Geometry 4.5.2 Voxelizing the Displacement Field 4.5.3 Voxelizing Boundary Conditions 4.6 Pruning Dataset - Removing Unwanted Results 4.7 Data Augmentation 5 Deep Neural Networks for Biomechanical Simulation 5.1 Training Data 5.2 Network Architecture 5.3 Loss Functions and Training 6 Deep Neural Networks for Non-Rigid Registration 6.1 Training Data 6.2 Architecture 6.3 Loss 6.4 Training 6.5 Mesh Deformation 6.6 Example Application 7 Intraoperative Prototype 7.1 Image Acquisition 7.2 Stereo Calibration 7.3 Image Rectification, Disparity- and Depth- estimation 7.4 Liver Segmentation 7.4.1 Synthetic Image Generation 7.4.2 Automatic Segmentation 7.4.3 Manual Segmentation Modifier 7.5 SLAM 7.6 Dense Reconstruction 7.7 Rigid Registration 7.8 Non-Rigid Registration 7.9 Rendering 7.10 Robotic Operating System 8 Evaluation 8.1 Evaluation Datasets 8.1.1 In-Silico 8.1.2 Phantom Torso and Liver 8.1.3 In-Vivo, Human, Breathing Motion 8.1.4 In-Vivo, Human, Laparoscopy 8.2 Metrics 8.2.1 Mean Displacement Error 8.2.2 Target Registration Error (TRE) 8.2.3 Champfer Distance 8.2.4 Volumetric Change 8.3 Evaluation of the Synthetic Training Data 8.4 Data-Driven Biomechanical Model (DDBM) 8.4.1 Amount of Intraoperative Surface 8.4.2 Dynamic Simulation 8.5 Volume to Surface Registration Network (V2S-Net) 8.5.1 Amount of Intraoperative Surface 8.5.2 Dependency on Initial Rigid Alignment 8.5.3 Registration Accuracy in Comparison to Surface Noise 8.5.4 Registration Accuracy in Comparison to Material Stiffness 8.5.5 Champfer-Distance vs. Mean Displacement Error 8.5.6 In-vivo, Human Breathing Motion 8.6 Full Intraoperative Pipeline 8.6.1 Intraoperative Reconstruction: SLAM and Intraoperative Map 8.6.2 Full Pipeline on Laparoscopic Human Data 8.7 Timing 9 Discussion 9.1 Intraoperative Model 9.2 Physical Accuracy 9.3 Limitations in Training Data 9.4 Limitations Caused by Difference in Pre- and Intraoperative Modalities 9.5 Ambiguity 9.6 Intraoperative Prototype 10 Conclusion 11 List of Publications List of Figures Bibliograph

Siamese hierarchical attention networks for extractive summarization

[EN] In this paper, we present an extractive approach to document summarization based on Siamese Neural Networks. Specifically, we propose the use of Hierarchical Attention Networks to select the most relevant sentences of a text to make its summary. We train Siamese Neural Networks using document-summary pairs to determine whether the summary is appropriated for the document or not. By means of a sentence-level attention mechanism the most relevant sentences in the document can be identified. Hence, once the network is trained, it can be used to generate extractive summaries. The experimentation carried out using the CNN/DailyMail summarization corpus shows the adequacy of the proposal. In summary, we propose a novel end-to-end neural network to address extractive summarization as a binary classification problem which obtains promising results in-line with the state-of-the-art on the CNN/DailyMail corpus.This work has been partially supported by the Spanish MINECO and FEDER founds under project AMIC (TIN2017-85854-C4-2-R). Work of Jose-Angel Gonzalez is also financed by Universitat Politecnica de Valencia under grant PAID-01-17.González-Barba, JÁ.; Segarra Soriano, E.; García-Granada, F.; Sanchís Arnal, E.; Hurtado Oliver, LF. (2019). Siamese hierarchical attention networks for extractive summarization. Journal of Intelligent & Fuzzy Systems. 36(5):4599-4607. https://doi.org/10.3233/JIFS-179011S45994607365N. Begum , M. Fattah , and F. Ren . Automatic text summarization using support vector machine 5(7) (2009), 1987–1996.J. Cheng and M. Lapata . Neural summarization by extracting sentences and words. In Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics, ACL 2016, August 7-12, 2016, Berlin, Germany, Volume 1: Long Papers, 2016.K.M. Hermann , T. Kocisky , E. Grefenstette , L. Espeholt , W. Kay , M. Suleyman , and P. Blunsom . Teaching machines to read and comprehend, CoRR, abs/1506.03340, 2015.D.P. Kingma and J. Ba . Adam: A method for stochastic optimization. CoRR, abs/1412.6980, 2014.Lloret, E., & Palomar, M. (2011). Text summarisation in progress: a literature review. Artificial Intelligence Review, 37(1), 1-41. doi:10.1007/s10462-011-9216-zLouis, A., & Nenkova, A. (2013). Automatically Assessing Machine Summary Content Without a Gold Standard. Computational Linguistics, 39(2), 267-300. doi:10.1162/coli_a_00123Miao, Y., & Blunsom, P. (2016). Language as a Latent Variable: Discrete Generative Models for Sentence Compression. Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing. doi:10.18653/v1/d16-1031R. Mihalcea and P. Tarau . Textrank: Bringing order into text. In Proceedings of the 2004 Conference on Empirical Methods in Natural Language Processing, 2004.T. Mikolov , K. Chen , G. S. Corrado , and J. Dean . Efficient estimation of word representations in vector space, CoRR, abs/1301.3781, 2013.Minaee, S., & Liu, Z. (2017). Automatic question-answering using a deep similarity neural network. 2017 IEEE Global Conference on Signal and Information Processing (GlobalSIP). doi:10.1109/globalsip.2017.8309095R. Paulus , C. Xiong , and R. Socher , A deep reinforced model for abstractive summarization. CoRR, abs/1705.04304, 2017.Schuster, M., & Paliwal, K. K. (1997). Bidirectional recurrent neural networks. IEEE Transactions on Signal Processing, 45(11), 2673-2681. doi:10.1109/78.650093See, A., Liu, P. J., & Manning, C. D. (2017). Get To The Point: Summarization with Pointer-Generator Networks. Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). doi:10.18653/v1/p17-1099Takase, S., Suzuki, J., Okazaki, N., Hirao, T., & Nagata, M. (2016). Neural Headline Generation on Abstract Meaning Representation. Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing. doi:10.18653/v1/d16-1112G. Tur and R. De Mori . Spoken language understanding: Systems for extracting semantic information from speech, John Wiley & Sons, 2011

Optimization the initial weights of artificial neural networks via genetic algorithm applied to hip bone fracture prediction

This paper aims to find the optimal set of initial weights to enhance the accuracy of artificial neural networks (ANNs) by using genetic algorithms (GA). The sample in this study included 228 patients with first low-trauma hip fracture and 215 patients without hip fracture, both of them were interviewed with 78 questions. We used logistic regression to select 5 important factors (i.e., bone mineral density, experience of fracture, average hand grip strength, intake of coffee, and peak expiratory flow rate) for building artificial neural networks to predict the probabilities of hip fractures. Three-layer (one hidden layer) ANNs models with back-propagation training algorithms were adopted. The purpose in this paper is to find the optimal initial weights of neural networks via genetic algorithm to improve the predictability. Area under the ROC curve (AUC) was used to assess the performance of neural networks. The study results showed the genetic algorithm obtained an AUC of 0.858±0.00493 on modeling data and 0.802 ± 0.03318 on testing data. They were slightly better than the results of our previous study (0.868±0.00387 and 0.796±0.02559, resp.). Thus, the preliminary study for only using simple GA has been proved to be effective for improving the accuracy of artificial neural networks.This research was supported by the National Science Council (NSC) of Taiwan (Grant no. NSC98-2915-I-155-005), the Department of Education grant of Excellent Teaching Program of Yuan Ze University (Grant no. 217517) and the Center for Dynamical Biomarkers and Translational Medicine supported by National Science Council (Grant no. NSC 100- 2911-I-008-001)