Clinical time series are known for irregular, highly-sporadic and strongly-complex structures, and are consequently difficult to model by traditional state-space models. In this blog, we provide a summary of a recently conducted study [1] on employing variational recurrent neural networks (VRNNs) [2] for forecasting clinical time series, extracted from the electronic health records (EHRs) of patients. Variational recurrent neural networks (VRNNs) combine recurrent neural networks (RNNs) [3] and variational inference (VI) [4], and are state-of-the-art methods to model highly-variable sequential data such as text, speech, time series and multimedia signals in a generative fashion. This study focused on incorporating multiple correlated time series to improve the forecasting of VRNNs. The selection of those correlated time series is based on the similarity of the supplementary medical information e.g., disease diagnostics, ethnicity and age etc., between the patients. The effectiveness of utilizing such supplementary information was measured with root mean square error (RMSE), on clinical benchmark data-set “Medical Information Mart for Intensive Care (MIMIC III)” for multi-step-ahead prediction. In addition, a subjective analysis to highlight the effects of the similarity of the supplementary medical information on individual temporal features e.g., Systolic Blood Pressure (SBP), Heart Rate (HR) etc., of the patients from the same data-set was performed. The results of this research demonstrated that incorporating the correlated time series based on the supplementary medical information can help improving the accuracy of the VRNNs for clinical time series forecasting.
A variational recurrent neural network (VRNN) [2] is the extension of a standard Variational Autoencoder (VAE) [4] to the cases with sequential data. It is a combination of a Recurrent Neural Network (RNN) and a VAE. More specifically, a VRNN employs a VAE at each time-step. However, the prior on the latent variable of this VAE is assumed to be a multivariate Gaussian whose parameters are computed from the previous hidden state of the RNN. The detailed discussion on VRNN and VAE is provided in [2] and [4] respectively. In this study [1], the VRNN is extended in the sense that the multiple correlated temporal signals are also included in the input which improvises the robustness of the model. This is since the model i.e., VRNN, is now forced to learn the additional local patterns of the data space, when conditioned on the additional correlated temporal signals i.e., time series, of the related patients.
An empirical investigation was carried out to quantify the effectiveness of this approach on a clinical benchmark data set “MIMIC III”. However, MIMIC III is a highly complicated data set involving millions of events for approximately 60,000 patients in Intensive Care Units (ICUs). As such, a baseline approach [5] was followed to pre-process the data. After following [5], the resulting pre-processed data set was used to build four models: VRNN, VRNN-I, VRNN-S and VRNN-I-S. The first two models belong to the family of VRNNs whereas the last two models are the extensions of the first two models using this approach. As such, VRNN and VRNN-I act as the baseline models whereas VRNN-S and VRNN-I-S are their improved variations using this approach. All four models are tested for multi-step-ahead predictions with RMSE.
The Average (i.e., for all the temporal variables) RMSE on the test data-set for multi-step-ahead forecasting are presented in Table I. In this table, the first column displays the step size for forecasting. The next four columns present the RMSE with rounded standard deviations using VRNN (M1), VRNN-I (M2), VRNN-S (M3), and VRNN-I-S (M4). The last two columns share the p values resulting from the Mann-Whitney U test. These tests have the alternative hypotheses RMSE (VRNN-S) < RMSE (VRNN) and RMSE (VRNN-I-S) < RMSE (VRNN-I) respectively i.e., these tests find if the improved variations VRNN-S and VRNN-I-S are significantly better than their respective baseline VRNN and VRNN-I. From this table, it can be observed that VRNN-I-S achieves the lowest values of RMSE in all the ten cases. Furthermore, VRNN-S achieves the second lowest error in all the ten cases. From the last two columns in Table I, we find out that in 6/10 cases; at-least one of VRNN-S and VRNN-I-S performs significantly better than the respective baseline as indicated by the p values.
We further perform a simple qualitative analysis to highlight the importance of correlated temporal signals in robust and improved forecasting of VRNNs. We select three patients in the test data-set where VRNN-S and VRNN-I-S both achieve the lowest RMSE. For each of these patients, we select three most similar patients based on disease diagnostics and report the information about the set of common diseases between our selected patients and their corresponding most similar patients in Table II. In this table, the first column shows the identity of each of the three selected patients. The second column reports the number of common diseases between that patient and its three most similar patients. The third column shares the International Classification of Diseases, Ninth Revision (ICD9) codes for the corresponding diseases. The last column categorizes the respective ICD9 codes to the most appropriate disease family (i.e., Heart, Blood Pressure, Kidney, Respiratory) for better interpretation and analysis. After reporting the information about the common diseases, we plot the predictions of all four models on our patients of interest in figure 1. This figure shares the one-step-ahead predicted values (re-scaled) for all six temporal variables for these patients. Considering the first patient (P1) in figure 1; we observe that VRNN-S and VRNN-I-S outperform the baselines on Heart Rate (HR), which is related to the category of the most common diseases for that patient in Table II. Similarly analysing the second patient (P2); we observe that VRNNS and VRNN-I-S outperform the baselines on Systolic Blood Pressure (SBP) which is strongly related to high blood pressure related diseases. Finally, the same analysis is performed for third patient (P3) where VRNN-S and VRNN-I-S achieve superior predictions on Respiratory Rate (RR) and Systolic Blood Pressure (SBP). From figure 1, we verify that incorporating correlated temporal signals indeed helps improving the forecasting accuracy of the VRNNs for clinical time series. This is especially true for the temporal features which are related to the set of the common diseases between the patients.
In this paper, we evaluate the effectiveness of utilizing multiple correlated time series in clinical time series forecasting tasks. Such correlated time series can be extracted from a set of similar patients; where the similarity can be computed on the basis of the supplementary domain information such as disease diagnostics, age and ethnicity etc. As our baselines, we choose VRNN and its variant, which are state-of-the-art deep-generative models for sequential data-sets. From the findings in section V, we believe that the performance of Variational Recurrent models can be improved by including the correlated temporal signals. This is since in 6/10 cases considered in Table I; at-least one of VRNN-S and VRNN-I-S performs significantly better than the baselines as indicated by the p values resulting from the statistical tests. Additionally, it can be observed from figure 1 that the incorporation of multiple correlated time series helps recovering the temporal features related to the common diseases between the patients. On the basis of the points discussed above, it can be argued that discarding such supplementary domain information while analysing clinical data-sets may not be an optimal strategy, since such information may be used to improve the generalization.
[1] Ullah, Sibghat, et al. “Exploring Clinical Time Series Forecasting with Meta-Features in Variational Recurrent Models.” To appear in, 2020 International Joint Conference on Neural Networks (IJCNN).
[2] Chung, Junyoung, et al. “A recurrent latent variable model for sequential data.” Advances in neural information processing systems. 2015.
[3] LeCun, Yann, Yoshua Bengio, and Geoffrey Hinton. “Deep learning.” nature 521.7553 (2015): 436-444.
[4] Kingma, Diederik P., and Max Welling. “Stochastic gradient VB and the variational auto-encoder.” Second International Conference on Learning Representations, ICLR.
[5] Harutyunyan, Hrayr, et al. “Multitask learning and benchmarking with clinical time series data.” Sci Data 6, 96 (2019). https://doi.org/10.1038/s41597-019-0103-9.
The topic of my research is “Multi-criteria Preference Aware Design Optimization”, which is one of the projects of this ECOLE doctoral training program. The main aim of my research is to develop a system which can learn from user experience of designing and support the user by giving multiple suggestions from which the user can choose.
There are several designing frameworks for assisting users like SketchRNN [1], Shadow Draw [2], etc. Regardless of how efficient 2D design tools are, there is a lack of efficient tools for 3D counterparts. But in engineering applications, we mainly need to deal with 3D models for designing. It is more difficult to model a 3D shape of high dimensionality for the complexity of its shape. The design process in the engineering domain is complex, i.e., there are many possible paths leading through the design space and the design space is too large to be navigated by the human designer. So, through my research, we aim to design a system that supports the designer in searching and suggesting for applications in engineering design.
Machine learning and deep learning approaches are the backbones of automated analytical models. But all these approaches are data-driven approaches. So, one of the key aspects of training machine learning models is to gather potential large dataset to train the model. There is existing dataset for 2D sketches [1,2], but for 3D shapes there is no existing dataset to understand the design process.
A key part of my research is to understand the human user-centric design process for engineering applications. Conducting research with human participants in an essential part to understand the human designing process. The most challenging part involves human study as it is time-consuming and difficult with a high number of human participants, which is essential for the system to suggest the multiple options for the designer to choose from. Starting with a simpler idea, we did initial experimental setup to understand human behavior of the design process and categorized them into distinct groups. To overcome the limitations, we propose to use target shape matching optimization whose hyper parameters can be tuned to match human user modification data. For a more detailed explanation, the link below [3] refers.
By tuning the hyperparameters of the target shape optimization we can create a digital analogy for human user interactive shape modification. Previous research on sequential modelling approach like Recurrent Neural Networks (RNNs) has been used to model sequences from 2D design tasks, such as human drawing [2]. So, we further experimented on using RNNs to learn the past changes gathered from optimizations data and predict the next possible steps in engineering design application. Below is an example from our model predictions of next possible change in the design (Figure 1).
We only include a basic idea of a design assistance system and why it is necessary for engineering applications and then verified our initial approach to come up with a suitable model. I will keep you informed about our work in my future blog.
[1] Y. J. Lee, C. L. Zitnick, and M. F. Cohen, “ShadowDraw: real-time user guidance for freehand drawing,” 2011.
[2] D. Ha and D. Eck, “A neural representation of sketch drawings,” in 6th International Conference on Learning Representations, ICLR 2018, Vancouver, BC, Canada, April 30 – May 3, 2018, Conference Track Proceedings, 2018.
[3] Saha, S., Rios, T.., Minku, L.L., Yao, X., Xu, Z., Sendhoff, B., “Optimal Evolutionary Optimization Hyper-parameters to Mimic Human User Behavior,” 2019 IEEE Symposium Series on Computational Intelligence (SSCI), Xiamen, China, 2019, pp. 858-866
[4] S. Saha., Rios, T.D., Sendhoff, B., Menzel, S., Bäck, T., Yao, X., Xu, Z., & Wollstadt, P., “Learning Time-Series Data of Industrial Design Optimization using Recurrent Neural Networks,” 2019 International Conference on Data Mining Workshops (ICDMW), Beijing, China, 2019, pp. 785-792.
During the PhD we are constantly challenged to find solutions for technical problems and push the knowledge frontier in our fields a little further ahead. As a measure to support controlling the current COVID-19 epidemic, many of us started working in home office a couple of weeks ago and, therefore, we face new sorts of problems, such as staying healthy, connected and focused on our work [1,2]. Hence, we wrote down a few pros and cons of working from home in our notepads, as well as some tips to “survive” the home office season, which we are sharing with you in this post.
Working from home can be very pleasant and fruitful. Apart from tasks that require special hardware, for example, running chemistry experiments in a lab, we usually can do a lot with a notebook, access to the internet and remote access to our workstation in the office. Furthermore:
Working at home can be very convenient, however, it has some drawbacks, especially in the long term. In such cases, it’s common to feel isolated and less productive [1], because:
Staying healthy is now the priority, so going back to the office is not yet an option, so all we can do is focus on improving our home-office experience by minimizing the cons in our list. Here is a short list of tips we came up with for tackling the drawbacks of working during the quarantine:
Finally, we hope our impressions and tips help you to go through this exceptional working conditions. It is not ideal for many of us, but it is temporary and very important to contain the epidemic. Let’s do our part and help keeping our communities safe.
[1] B. Lufkin, “Coronavirus: How to work from home, the right way”, bbc.com, 2020. [Online]. Available: https://www.bbc.com/worklife/article/20200312-coronavirus-covid-19-update-work-from-home-in-a-pandemic. [Accessed: 30- Mar- 2020].
[2] S. Philipp and J. Bexten, “Home Office: Das sind die wichtigsten Vor- und Nachteile – ingenieur.de”, ingenieur.de – Jobbörse und Nachrichtenportal für Ingenieure, 2020. [Online]. Available: https://www.ingenieur.de/karriere/arbeitsleben/alltag/home-office-das-wichtigsten-vorteile-nachteile/. [Accessed: 30- Mar- 2020].
It has been during my Master’s thesis internship when I first heard about the Early Stage Researcher (ESR) figure. PhD student and industry researcher at the same time, I thought it was the perfect mix for my future development. Thus, after been graduated, I started looking for a job and finally, I found the one I was interested in: Machine Learning ESR. I applied for this position, did the interview and got hired… The beginning of a new phase of my life, within the ECOLE project.
Nowadays, we are living in the digital era and the amount of user-generated data is exponentially growing every day. In this context, users usually explain what they like, dislike or think in the form of textual comments (e.g. tweets, social media posts, reviews). Leveraging the rich latent information contained in the user-generated data available can be crucial for many purposes. For example, an automobile company can launch a face-lift car that would satisfy customers more than before, by mining history order and users’ feedback [1]. Recently, research in the manufacturing industry focuses on developing advanced text mining approaches to discover hidden patterns, to predict market trends and to learn customer preferences and unknown relations, for improving their competitiveness and productivity. Keeping this in mind, my objective within ECOLE is on developing statistical machine learning and probabilistic models for preference learning. The focus will be not only on obtaining good results but also on getting interpretability of the outputs and on providing a measure of confidence about them. ECOLE aims at solving a series of related optimisation problems, instead of treating each problem instance in isolation, thus the learned information could be integrated to include preference constraints in multi-criteria optimization frameworks (e.g. product design, where structural, aerodynamics and aesthetic constraints have to be considered simultaneously).
Now, it has been more than a year since I have been involved in ECOLE. During this period, I had the possibility to know and to work with the other ESRs, to learn a lot from the experienced supervisors (from academia and industry), and to travel and visit several countries for attending summer schools, workshops, conferences. The mixture of different cultures, backgrounds and the collaboration between academia and industry has created an inspiring and motivating environment to improve either soft-skills, technical skills and grow as a researcher.
[1] Ray Y Zhong, Xun Xu, Eberhard Klotz, and Stephen T Newman. Intelligent manufacturing in the context of industry 4.0: a review. Engineering, 3(5):616–630, 2017.
Dynamic multi-objective optimization problems (DMOPs) involve multiple conflicting and time-varying objectives, which widely exist in real-world problems. Evolutionary algorithms are broadly applied to solve DMOPs due to their competent ability in handling highly complex and non-linear problems and most importantly solving those problems that cannot be addressed by traditional optimization methods.
Without generality, the minimization problem is considered here and a DMOP [1] can be mathematically formulated as follows:
Evolutionary algorithms for solving DMOPs are called dynamic multi-objective evolutionary algorithms (DMOEAs) [2]. In the development of DMO, a mature framework of DMOEAs [3] has been proposed by researchers, as shown in Fig. 1.
The detailed steps of the framework of DMOEAs are as follows:
Most existing work in DMO mainly focus on how to improve the effectiveness of response mechanisms.
[1]. M. Farina, K. Deb, P. Amato, Dynamic multiobjective optimization problems: test cases, approximations, and applications, IEEE Trans. Evolut. Comput. 8 (5) (2004) 425–442.
[2]. S. Yang and X. Yao, Evolutionary Computation for Dynamic Optimization Problems. Springer, 2013, vol. 490.
[3]. G. Ruan, G. Yu, J. Zheng, J. Zou, and S. Yang, “The effect of diversity maintenance on prediction in dynamic multi-objective optimization,” Applied Soft Computing, vol. 58, pp. 631–647, 2017.
Time flies fast. It has been almost over one year since I joined ECOLE. And it has been an exciting year. Travelling between Birmingham, Warsaw, Leiden, Berlin, Coimbra and Xiamen. Listening to talks in state of the art on research in Evolutionary Computation and Machine Learning. Attending workshops in the research institutions of two world-known tech companies. The opportunities promised and given by the Innovative Training Network have not fallen short. But aside from all the excitement and activities, who am I, what do I do and what is that drove me to ECOLE in the first place?
Well, my prior academic pursuits were in Theoretical Nuclear Physics at the Technical University Darmstadt. And while I of course enjoyed studying the field and gaining understanding into the inner subnuclear workings of the world, I felt at times the research self was missing out in some way on my initial fascinations which took me too it. So, where to go else? Stumbling upon ECOLE was to be honest a bit of a lucky coincidence. I was working prior at software company while looking for PhD and residency programs, when a friend of mine was recommending me the posting for an Early Stage Researcher position he found at one of the partner institutions. I applied, was interviewed and subsequentially have been offered the position. It has been a bit unusual for me to travel this much for the Marie Curie Fellowship, but I am happy to have found a new home. And with Computational Intelligence research being situated at the intersection between Natural Computation and Artificial Intelligence, there is still plenty of space for me to philosophize about nature, while keeping in touch with reality through real-world problems.
ECOLE is especially great in regards of opportunities to learn, grow and try out new things. I particularly had a lot of fun (but also stress) with preparing and giving a short keynote-style public talk on nature-inspired artificial intelligence for the popular science segment of the Z2X festival in Berlin last August. The talk was luckily to be held lightweight and in front of a small audience. I decided to talk about the history and inspirations behind current popular methods and highlight evolutionary approaches as a means for creative problem-solving. While part of the audience seemed to have got lost with some of the bare technicalities, the main ideas sticked. Which was the most important thing for me. I was thus more than happy to have received and interesting questions in return. By the way: I am planning to put my practice slides online soon, if you are interested, feel free to take a look. The actual talk was given completely in oral form, as I was informed one day prior that the beamer was missing, but it worked out.
So, what’s up for the future? Currently, I work on model-based approaches as a means to tackle the transfer learning problem in continuous optimisation. A bit of a complicated idea, but I find this notion to be intuive and interesting to explore. In any way, I will keep you updated about my work in a future blog post. Until then, everyone keep up with the good work! 🙂
The adaptive synthetic (ADASYN) sampling technique is a method that aims to adaptively generate minority samples according to their distributions [5]. The main improvement compared to SMOTE is the samples which are harder to learn are given higher importance and will be oversampled more often in ADASYN. The general idea of ADASYN is shown in Figure 3.
[1]. He, H. and Garcia, E.A., 2009. Learning from imbalanced data. IEEE Transactions on knowledge and data engineering, 21(9), pp.1263-1284
[2]. Ganganwar, V., 2012. An overview of classification algorithms for imbalanced datasets. International Journal of Emerging Technology and Advanced Engineering, 2(4), pp.42-47.
[3]. Santos, M.S., Soares, J.P., Abreu, P.H., Araujo, H. and Santos, J., 2018. Cross-validation for imbalanced datasets: Avoiding overoptimistic and overfitting approaches [research frontier]. ieee ComputatioNal iNtelligeNCe magaziNe, 13(4), pp.59-76.
[4]. Chawla, N.V., Bowyer, K.W., Hall, L.O. and Kegelmeyer, W.P., 2002. SMOTE: synthetic minority over-sampling technique. Journal of artificial intelligence research, 16, pp.321-357.
[5]. He, H., Bai, Y., Garcia, E.A. and Li, S., 2008, June. ADASYN: Adaptive synthetic sampling approach for imbalanced learning. In 2008 IEEE International Joint Conference on Neural Networks (IEEE World Congress on Computational Intelligence) (pp. 1322-1328). IEEE.
[1] Lütkepohl, Helmut. New introduction to multiple time series analysis. Springer Science & Business Media, 2005.
[2] LeCun, Yann, Yoshua Bengio, and Geoffrey Hinton. “Deep learning.” nature 521.7553 (2015): 436-444.
[3] Williams, Ronald J., and David Zipser. “A learning algorithm for continually running fully recurrent neural networks.” Neural computation 1.2 (1989): 270-280.
[4] Rangapuram, Syama Sundar, et al. “Deep state space models for time series forecasting.” Advances in Neural Information Processing Systems. 2018.
[5] Qiu, Jinwen, S. Rao Jammalamadaka, and Ning Ning. “Multivariate Bayesian Structural Time Series Model.” Journal of Machine Learning Research 19.68 (2018): 1-33.
[6] Harutyunyan, Hrayr, et al. “Multitask learning and benchmarking with clinical time series data.” arXiv preprint arXiv:1703.07771 (2017).
[7] Guo, Tian, et al. “Robust online time series prediction with recurrent neural networks.” 2016 IEEE International Conference on Data Science and Advanced Analytics (DSAA). Ieee, 2016.
Innovative Training Networks (ITN) drive scientific excellence and innovation. They bring together universities, research institutes and other sectors from across the world to train researchers to doctorate level.
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