Randolf Scholz

Nghia Duong-Trung, Stefan Born, Jong Woo Kim et al.

Machine learning (ML) is becoming increasingly crucial in many fields of engineering but has not yet played out its full potential in bioprocess engineering. While experimentation has been accelerated by increasing levels of lab automation, experimental planning and data modeling are still largerly depend on human intervention. ML can be seen as a set of tools that contribute to the automation of the whole experimental cycle, including model building and practical planning, thus allowing human experts to focus on the more demanding and overarching cognitive tasks. First, probabilistic programming is used for the autonomous building of predictive models. Second, machine learning automatically assesses alternative decisions by planning experiments to test hypotheses and conducting investigations to gather informative data that focus on model selection based on the uncertainty of model predictions. This review provides a comprehensive overview of ML-based automation in bioprocess development. On the one hand, the biotech and bioengineering community should be aware of the potential and, most importantly, the limitation of existing ML solutions for their application in biotechnology and biopharma. On the other hand, it is essential to identify the missing links to enable the easy implementation of ML and Artificial Intelligence (AI) tools in valuable solutions for the bio-community.

Christian Klötergens, Vijaya Krishna Yalavarthi, Randolf Scholz et al.

State-of-the-art methods for forecasting irregularly sampled time series with missing values predominantly rely on just four datasets and a few small toy examples for evaluation. While ordinary differential equations (ODE) are the prevalent models in science and engineering, a baseline model that forecasts a constant value outperforms ODE-based models from the last five years on three of these existing datasets. This unintuitive finding hampers further research on ODE-based models, a more plausible model family. In this paper, we develop a methodology to generate irregularly sampled multivariate time series (IMTS) datasets from ordinary differential equations and to select challenging instances via rejection sampling. Using this methodology, we create Physiome-ODE, a large and sophisticated benchmark of IMTS datasets consisting of 50 individual datasets, derived from real-world ordinary differential equations from research in biology. Physiome-ODE is the first benchmark for IMTS forecasting that we are aware of and an order of magnitude larger than the current evaluation setting of four datasets. Using our benchmark Physiome-ODE, we show qualitatively completely different results than those derived from the current four datasets: on Physiome-ODE ODE-based models can play to their strength and our benchmark can differentiate in a meaningful way between different IMTS forecasting models. This way, we expect to give a new impulse to research on ODE-based time series modeling.

Vijaya Krishna Yalavarthi, Randolf Scholz, Stefan Born et al.

Probabilistic forecasting of irregularly sampled multivariate time series with missing values is an important problem in many fields, including health care, astronomy, and climate. State-of-the-art methods for the task estimate only marginal distributions of observations in single channels and at single timepoints, assuming a fixed-shape parametric distribution. In this work, we propose a novel model, ProFITi, for probabilistic forecasting of irregularly sampled time series with missing values using conditional normalizing flows. The model learns joint distributions over the future values of the time series conditioned on past observations and queried channels and times, without assuming any fixed shape of the underlying distribution. As model components, we introduce a novel invertible triangular attention layer and an invertible non-linear activation function on and onto the whole real line. We conduct extensive experiments on four datasets and demonstrate that the proposed model provides $4$ times higher likelihood over the previously best model.

Vijaya Krishna Yalavarthi, Randolf Scholz, Christian Kloetergens et al.

Probabilistic forecasting models for joint distributions of targets in irregular time series with missing values are a heavily under-researched area in machine learning, with, to the best of our knowledge, only two Models have been researched so far: The Gaussian Process Regression model, and ProFITi. While ProFITi, thanks to using multivariate normalizing flows, is very expressive, leading to better predictive performance, it suffers from marginalization inconsistency: It does not guarantee that the marginal distributions of a subset of variables in its predictive distributions coincide with the directly predicted distributions of these variables. When asked to directly predict marginal distributions, they are often vastly inaccurate. We propose MOSES (Marginalization Consistent Mixture of Separable Flows), a model that parametrizes a stochastic process through a mixture of several latent multivariate Gaussian Processes combined with separable univariate Normalizing Flows. In particular, MOSES can be analytically marginalized, allowing it to directly answer a wider range of probabilistic queries than most competitors. Experiments on four datasets show that MOSES achieves both accurate joint and marginal predictions, surpassing all other marginalization consistent baselines, while only trailing slightly behind ProFITi in joint prediction, but vastly superior when predicting marginal distributions.

Raaghav Radhakrishnan, Jan Fabian Schmid, Randolf Scholz et al.

Ground texture based localization methods are potential prospects for low-cost, high-accuracy self-localization solutions for robots. These methods estimate the pose of a given query image, i.e. the current observation of the ground from a downward-facing camera, in respect to a set of reference images whose poses are known in the application area. In this work, we deal with the initial localization task, in which we have no prior knowledge about the current robot positioning. In this situation, the localization method would have to consider all available reference images. However, in order to reduce computational effort and the risk of receiving a wrong result, we would like to consider only those reference images that are actually overlapping with the query image. For this purpose, we propose a deep metric learning approach that retrieves the most similar reference images to the query image. In contrast to existing approaches to image retrieval for ground images, our approach achieves significantly better recall performance and improves the localization performance of a state-of-the-art ground texture based localization method.

Mesay Samuel Gondere, Lars Schmidt-Thieme, Durga Prasad Sharma et al.

Handwritten digit recognition is one of the extensively studied area in machine learning. Apart from the wider research on handwritten digit recognition on MNIST dataset, there are many other research works on various script recognition. However, it is not very common for multi-script digit recognition which encourage the development of robust and multipurpose systems. Additionally working on multi-script digit recognition enables multi-task learning, considering the script classification as a related task for instance. It is evident that multi-task learning improves model performance through inductive transfer using the information contained in related tasks. Therefore, in this study multi-script handwritten digit recognition using multi-task learning will be investigated. As a specific case of demonstrating the solution to the problem, Amharic handwritten character recognition will also be experimented. The handwritten digits of three scripts including Latin, Arabic and Kannada are studied to show that multi-task models with reformulation of the individual tasks have shown promising results. In this study a novel way of using the individual tasks predictions was proposed to help classification performance and regularize the different loss for the purpose of the main task. This finding has outperformed the baseline and the conventional multi-task learning models. More importantly, it avoided the need for weighting the different losses of the tasks, which is one of the challenges in multi-task learning.

Sebastian Pineda-Arango, David Obando-Paniagua, Alperen Dedeoglu et al.

In deep learning models, learning more with less data is becoming more important. This paper explores how neural networks with normalized Radial Basis Function (RBF) kernels can be trained to achieve better sample efficiency. Moreover, we show how this kind of output layer can find embedding spaces where the classes are compact and well-separated. In order to achieve this, we propose a two-phase method to train those type of neural networks on classification tasks. Experiments on CIFAR-10 and CIFAR-100 show that networks with normalized kernels as output layer can achieve higher sample efficiency, high compactness and well-separability through the presented method in comparison to networks with SoftMax output layer.

Lukas Brinkmeyer, Rafael Rego Drumond, Randolf Scholz et al.

Parametric models, and particularly neural networks, require weight initialization as a starting point for gradient-based optimization. Recent work shows that a specific initial parameter set can be learned from a population of supervised learning tasks. Using this initial parameter set enables a fast convergence for unseen classes even when only a handful of instances is available (model-agnostic meta-learning). Currently, methods for learning model initializations are limited to a population of tasks sharing the same schema, i.e., the same number, order, type, and semantics of predictor and target variables. In this paper, we address the problem of meta-learning parameter initialization across tasks with different schemas, i.e., if the number of predictors varies across tasks, while they still share some variables. We propose Chameleon, a model that learns to align different predictor schemas to a common representation. In experiments on 23 datasets of the OpenML-CC18 benchmark, we show that Chameleon can successfully learn parameter initializations across tasks with different schemas, presenting, to the best of our knowledge, the first cross-dataset few-shot classification approach for unstructured data.

Josif Grabocka, Randolf Scholz, Lars Schmidt-Thieme

The minimization of loss functions is the heart and soul of Machine Learning. In this paper, we propose an off-the-shelf optimization approach that can minimize virtually any non-differentiable and non-decomposable loss function (e.g. Miss-classification Rate, AUC, F1, Jaccard Index, Mathew Correlation Coefficient, etc.) seamlessly. Our strategy learns smooth relaxation versions of the true losses by approximating them through a surrogate neural network. The proposed loss networks are set-wise models which are invariant to the order of mini-batch instances. Ultimately, the surrogate losses are learned jointly with the prediction model via bilevel optimization. Empirical results on multiple datasets with diverse real-life loss functions compared with state-of-the-art baselines demonstrate the efficiency of learning surrogate losses.