arXiv subjects

Stefan Kramer

Publications and source records attributed to Stefan Kramer.

At least 37 records · Page 2Linked to original sources

arXiv2022

Invariant Representations with Stochastically Quantized Neural Networks

Representation learning algorithms offer the opportunity to learn invariant representations of the input data with regard to nuisance factors. Many authors have leveraged such strategies to learn fair representations, i.e., vectors where information about sensitive attributes is removed. These methods are attractive as they may be interpreted as minimizing the mutual information between a neural layer's activations and a sensitive attribute. However, the theoretical grounding of such methods relies either on the computation of infinitely accurate adversaries or on minimizing a variational upper bound of a mutual information estimate. In this paper, we propose a methodology for direct computation of the mutual information between a neural layer and a sensitive attribute. We employ stochastically-activated binary neural networks, which lets us treat neurons as random variables. We are then able to compute (not bound) the mutual information between a layer and a sensitive attribute and use this information as a regularization factor during gradient descent. We show that this method compares favorably with the state of the art in fair representation learning and that the learned representations display a higher level of invariance compared to full-precision neural networks.

cs.LG↗

arXiv2022

Neural RELAGGS

Multi-relational databases are the basis of most consolidated data collections in science and industry today. Most learning and mining algorithms, however, require data to be represented in a propositional form. While there is a variety of specialized machine learning algorithms that can operate directly on multi-relational data sets, propositionalization algorithms transform multi-relational databases into propositional data sets, thereby allowing the application of traditional machine learning and data mining algorithms without their modification. One prominent propositionalization algorithm is RELAGGS by Krogel and Wrobel, which transforms the data by nested aggregations. We propose a new neural network based algorithm in the spirit of RELAGGS that employs trainable composite aggregate functions instead of the static aggregate functions used in the original approach. In this way, we can jointly train the propositionalization with the prediction model, or, alternatively, use the learned aggegrations as embeddings in other algorithms. We demonstrate the increased predictive performance by comparing N-RELAGGS with RELAGGS and multiple other state-of-the-art algorithms.

cs.LG↗

arXiv2022

A Fair Experimental Comparison of Neural Network Architectures for Latent Representations of Multi-Omics for Drug Response Prediction

Recent years have seen a surge of novel neural network architectures for the integration of multi-omics data for prediction. Most of the architectures include either encoders alone or encoders and decoders, i.e., autoencoders of various sorts, to transform multi-omics data into latent representations. One important parameter is the depth of integration: the point at which the latent representations are computed or merged, which can be either early, intermediate, or late. The literature on integration methods is growing steadily, however, close to nothing is known about the relative performance of these methods under fair experimental conditions and under consideration of different use cases. We developed a comparison framework that trains and optimizes multi-omics integration methods under equal conditions. We incorporated early integration and four recently published deep learning methods: MOLI, Super.FELT, OmiEmbed, and MOMA. Further, we devised a novel method, Omics Stacking, that combines the advantages of intermediate and late integration. Experiments were conducted on a public drug response data set with multiple omics data (somatic point mutations, somatic copy number profiles and gene expression profiles) that was obtained from cell lines, patient-derived xenografts, and patient samples. Our experiments confirmed that early integration has the lowest predictive performance. Overall, architectures that integrate triplet loss achieved the best results. Statistical differences can, overall, rarely be observed, however, in terms of the average ranks of methods, Super.FELT is consistently performing best in a cross-validation setting and Omics Stacking best in an external test set setting. The source code of all experiments is available under \url{https://github.com/kramerlab/Multi-Omics_analysis}

cs.LG↗

arXiv2022

Fair Interpretable Representation Learning with Correction Vectors

Neural network architectures have been extensively employed in the fair representation learning setting, where the objective is to learn a new representation for a given vector which is independent of sensitive information. Various representation debiasing techniques have been proposed in the literature. However, as neural networks are inherently opaque, these methods are hard to comprehend, which limits their usefulness. We propose a new framework for fair representation learning that is centered around the learning of "correction vectors", which have the same dimensionality as the given data vectors. Correction vectors may be computed either explicitly via architectural constraints or implicitly by training an invertible model based on Normalizing Flows. We show experimentally that several fair representation learning models constrained in such a way do not exhibit losses in ranking or classification performance. Furthermore, we demonstrate that state-of-the-art results can be achieved by the invertible model. Finally, we discuss the law standing of our methodology in light of recent legislation in the European Union.

cs.LG↗

arXiv2022

Fair Group-Shared Representations with Normalizing Flows

The issue of fairness in machine learning stems from the fact that historical data often displays biases against specific groups of people which have been underprivileged in the recent past, or still are. In this context, one of the possible approaches is to employ fair representation learning algorithms which are able to remove biases from data, making groups statistically indistinguishable. In this paper, we instead develop a fair representation learning algorithm which is able to map individuals belonging to different groups in a single group. This is made possible by training a pair of Normalizing Flow models and constraining them to not remove information about the ground truth by training a ranking or classification model on top of them. The overall, ``chained'' model is invertible and has a tractable Jacobian, which allows to relate together the probability densities for different groups and ``translate'' individuals from one group to another. We show experimentally that our methodology is competitive with other fair representation learning algorithms. Furthermore, our algorithm achieves stronger invariance w.r.t. the sensitive attribute.

cs.LG↗

arXiv2022

Fair Interpretable Learning via Correction Vectors

Neural network architectures have been extensively employed in the fair representation learning setting, where the objective is to learn a new representation for a given vector which is independent of sensitive information. Various "representation debiasing" techniques have been proposed in the literature. However, as neural networks are inherently opaque, these methods are hard to comprehend, which limits their usefulness. We propose a new framework for fair representation learning which is centered around the learning of "correction vectors", which have the same dimensionality as the given data vectors. The corrections are then simply summed up to the original features, and can therefore be analyzed as an explicit penalty or bonus to each feature. We show experimentally that a fair representation learning problem constrained in such a way does not impact performance.

cs.LG↗

arXiv2021

Secure Sum Outperforms Homomorphic Encryption in (Current) Collaborative Deep Learning

Deep learning (DL) approaches are achieving extraordinary results in a wide range of domains, but often require a massive collection of private data. Hence, methods for training neural networks on the joint data of different data owners, that keep each party's input confidential, are called for. We address a specific setting in federated learning, namely that of deep learning from horizontally distributed data with a limited number of parties, where their vulnerable intermediate results have to be processed in a privacy-preserving manner. This setting can be found in medical and healthcare as well as industrial applications. The predominant scheme for this is based on homomorphic encryption (HE), and it is widely considered to be without alternative. In contrast to this, we demonstrate that a carefully chosen, less complex and computationally less expensive secure sum protocol in conjunction with default secure channels exhibits superior properties in terms of both collusion-resistance and runtime. Finally, we discuss several open research questions in the context of collaborative DL, especially regarding privacy risks caused by joint intermediate results.

cs.CR↗

arXiv2021

Fast Private Parameter Learning and Inference for Sum-Product Networks

A sum-product network (SPN) is a graphical model that allows several types of inferences to be drawn efficiently. There are two types of learning for SPNs: Learning the architecture of the model, and learning the parameters. In this paper, we tackle the second problem: We show how to learn the weights for the sum nodes, assuming the architecture is fixed, and the data is horizontally partitioned between multiple parties. The computations will preserve the privacy of each participant. Furthermore, we will use secret sharing instead of (homomorphic) encryption, which allows fast computations and requires little computational resources. To this end, we use a novel integer division to compute approximate real divisions. We also show how simple and private inferences can be performed using the learned SPN.

cs.LG↗

arXiv2021

Pattern Sampling for Shapelet-based Time Series Classification

Subsequence-based time series classification algorithms provide accurate and interpretable models, but training these models is extremely computation intensive. The asymptotic time complexity of subsequence-based algorithms remains a higher-order polynomial, because these algorithms are based on exhaustive search for highly discriminative subsequences. Pattern sampling has been proposed as an effective alternative to mitigate the pattern explosion phenomenon. Therefore, we employ pattern sampling to extract discriminative features from discretized time series data. A weighted trie is created based on the discretized time series data to sample highly discriminative patterns. These sampled patterns are used to identify the shapelets which are used to transform the time series classification problem into a feature-based classification problem. Finally, a classification model can be trained using any off-the-shelf algorithm. Creating a pattern sampler requires a small number of patterns to be evaluated compared to an exhaustive search as employed by previous approaches. Compared to previously proposed algorithms, our approach requires considerably less computational and memory resources. Experiments demonstrate how the proposed approach fares in terms of classification accuracy and runtime performance.

cs.LG↗

arXiv2021

Focusing Knowledge-based Graph Argument Mining via Topic Modeling

Decision-making usually takes five steps: identifying the problem, collecting data, extracting evidence, identifying pro and con arguments, and making decisions. Focusing on extracting evidence, this paper presents a hybrid model that combines latent Dirichlet allocation and word embeddings to obtain external knowledge from structured and unstructured data. We study the task of sentence-level argument mining, as arguments mostly require some degree of world knowledge to be identified and understood. Given a topic and a sentence, the goal is to classify whether a sentence represents an argument in regard to the topic. We use a topic model to extract topic- and sentence-specific evidence from the structured knowledge base Wikidata, building a graph based on the cosine similarity between the entity word vectors of Wikidata and the vector of the given sentence. Also, we build a second graph based on topic-specific articles found via Google to tackle the general incompleteness of structured knowledge bases. Combining these graphs, we obtain a graph-based model which, as our evaluation shows, successfully capitalizes on both structured and unstructured data.

cs.IR↗

arXiv2021

Deep Neural Networks to Recover Unknown Physical Parameters from Oscillating Time Series

Deep neural networks (DNNs) are widely used in pattern-recognition tasks for which a human comprehensible, quantitative description of the data-generating process, e.g., in the form of equations, cannot be achieved. While doing so, DNNs often produce an abstract (entangled and non-interpretable) representation of the data-generating process. This is one of the reasons why DNNs are not extensively used in physics-signal processing: physicists generally require their analyses to yield quantitative information about the studied systems. In this article we use DNNs to disentangle components of oscillating time series, and recover meaningful information. We show that, because DNNs can find useful abstract feature representations, they can be used when prior knowledge about the signal-generating process exists, but is not complete, as it is particularly the case in "new-physics" searches. To this aim, we train our DNN on synthetic oscillating time series to perform two tasks: a regression of the signal latent parameters and signal denoising by an Autoencoder-like architecture. We show that the regression and denoising performance is similar to those of least-square curve fittings (LS-fit) with true latent parameters' initial guesses, in spite of the DNN needing no initial guesses at all. We then explore applications in which we believe our architecture could prove useful for time-series processing in physics, when prior knowledge is incomplete. As an example, we employ DNNs as a tool to inform LS-fits when initial guesses are unknown. We show that the regression can be performed on some latent parameters, while ignoring the existence of others. Because the Autoencoder needs no prior information about the physical model, the remaining unknown latent parameters can still be captured, thus making use of partial prior knowledge, while leaving space for data exploration and discoveries.

cs.LG↗

arXiv2020

Deep Unsupervised Identification of Selected SNPs between Adapted Populations on Pool-seq Data

The exploration of selected single nucleotide polymorphisms (SNPs) to identify genetic diversity between different sequencing population pools (Pool-seq) is a fundamental task in genetic research. As underlying sequence reads and their alignment are error-prone and univariate statistical solutions only take individual positions of the genome into account, the identification of selected SNPs remains a challenging process. Deep learning models like convolutional neural networks (CNNs) are able to consider large input areas in their decisions. We suggest an unsupervised pipeline to be independent of a rarely known ground truth. We train a supervised discriminator CNN to distinguish alignments from different populations and utilize the model for unsupervised SNP calling by applying explainable artificial intelligence methods. Our proposed multivariate method is based on two main assumptions: We assume (i) that instances having a high predictive certainty of being distinguishable are likely to contain genetic variants, and (ii) that selected SNPs are located at regions with input features having the highest influence on the model's decision process. We directly compare our method with statistical results on two different Pool-seq datasets and show that our solution is able to extend statistical results.

q-bio.GN↗

arXiv2020

Rule Extraction from Binary Neural Networks with Convolutional Rules for Model Validation

Most deep neural networks are considered to be black boxes, meaning their output is hard to interpret. In contrast, logical expressions are considered to be more comprehensible since they use symbols that are semantically close to natural language instead of distributed representations. However, for high-dimensional input data such as images, the individual symbols, i.e. pixels, are not easily interpretable. We introduce the concept of first-order convolutional rules, which are logical rules that can be extracted using a convolutional neural network (CNN), and whose complexity depends on the size of the convolutional filter and not on the dimensionality of the input. Our approach is based on rule extraction from binary neural networks with stochastic local search. We show how to extract rules that are not necessarily short, but characteristic of the input, and easy to visualize. Our experiments show that the proposed approach is able to model the functionality of the neural network while at the same time producing interpretable logical rules.

cs.LG↗

arXiv2020

Ranking Creative Language Characteristics in Small Data Scenarios

The ability to rank creative natural language provides an important general tool for downstream language understanding and generation. However, current deep ranking models require substantial amounts of labeled data that are difficult and expensive to obtain for different domains, languages and creative characteristics. A recent neural approach, the DirectRanker, promises to reduce the amount of training data needed but its application to text isn't fully explored. We therefore adapt the DirectRanker to provide a new deep model for ranking creative language with small data. We compare DirectRanker with a Bayesian approach, Gaussian process preference learning (GPPL), which has previously been shown to work well with sparse data. Our experiments with sparse training data show that while the performance of standard neural ranking approaches collapses with small training datasets, DirectRanker remains effective. We find that combining DirectRanker with GPPL increases performance across different settings by leveraging the complementary benefits of both models. Our combined approach outperforms the previous state-of-the-art on humor and metaphor novelty tasks, increasing Spearman's $ρ$ by 14% and 16% on average.

cs.CL↗

arXiv2020

Towards Probability-based Safety Verification of Systems with Components from Machine Learning

Machine learning (ML) has recently created many new success stories. Hence, there is a strong motivation to use ML technology in software-intensive systems, including safety-critical systems. This raises the issue of safety verification of MLbased systems, which is currently thought to be infeasible or, at least, very hard. We think that it requires taking into account specific properties of ML technology such as: (i) Most ML approaches are inductive, which is both their power and their source of error. (ii) Neural networks (NN) resulting from deep learning are at the current state of the art not transparent. Consequently, there will always be errors remaining and, at least for deep NNs (DNNs), verification of their internal structure is extremely hard. In general, safety engineering cannot provide full guarantees that no harm will ever occur. That is why probabilities are used, e.g., for specifying a risk or a Tolerable Hazard Rate (THR). In this vision paper, we propose verification based on probabilities of errors both estimated by controlled experiments and output by the inductively learned classifier itself. Generalization error bounds may propagate to the probabilities of a hazard, which must not exceed a THR. As a result, the quantitatively determined bound on the probability of a classification error of an ML component in a safety-critical system contributes in a well-defined way to the latter's overall safety verification.

cs.SE↗

arXiv2019

Pairwise Learning to Rank by Neural Networks Revisited: Reconstruction, Theoretical Analysis and Practical Performance

We present a pairwise learning to rank approach based on a neural net, called DirectRanker, that generalizes the RankNet architecture. We show mathematically that our model is reflexive, antisymmetric, and transitive allowing for simplified training and improved performance. Experimental results on the LETOR MSLR-WEB10K, MQ2007 and MQ2008 datasets show that our model outperforms numerous state-of-the-art methods, while being inherently simpler in structure and using a pairwise approach only.

cs.IR↗

arXiv2018

Online Multi-Label Classification: A Label Compression Method

Many modern applications deal with multi-label data, such as functional categorizations of genes, image labeling and text categorization. Classification of such data with a large number of labels and latent dependencies among them is a challenging task, and it becomes even more challenging when the data is received online and in chunks. Many of the current multi-label classification methods require a lot of time and memory, which make them infeasible for practical real-world applications. In this paper, we propose a fast linear label space dimension reduction method that transforms the labels into a reduced encoded space and trains models on the obtained pseudo labels. Additionally, it provides an analytical method to update the decoding matrix which maps the labels into the original space and is used during the test phase. Experimental results show the effectiveness of this approach in terms of running times and the prediction performance over different measures.

cs.LG↗

arXiv2017

Ensembles of Randomized Time Series Shapelets Provide Improved Accuracy while Reducing Computational Costs

Shapelets are discriminative time series subsequences that allow generation of interpretable classification models, which provide faster and generally better classification than the nearest neighbor approach. However, the shapelet discovery process requires the evaluation of all possible subsequences of all time series in the training set, making it extremely computation intensive. Consequently, shapelet discovery for large time series datasets quickly becomes intractable. A number of improvements have been proposed to reduce the training time. These techniques use approximation or discretization and often lead to reduced classification accuracy compared to the exact method. We are proposing the use of ensembles of shapelet-based classifiers obtained using random sampling of the shapelet candidates. Using random sampling reduces the number of evaluated candidates and consequently the required computational cost, while the classification accuracy of the resulting models is also not significantly different than that of the exact algorithm. The combination of randomized classifiers rectifies the inaccuracies of individual models because of the diversity of the solutions. Based on the experiments performed, it is shown that the proposed approach of using an ensemble of inexpensive classifiers provides better classification accuracy compared to the exact method at a significantly lesser computational cost.

cs.LG↗