Łukasz Maziarka

Łukasz Kuciński, Witold Drzewakowski, Mateusz Olko et al.

Time series methods are of fundamental importance in virtually any field of science that deals with temporally structured data. Recently, there has been a surge of deterministic transformer models with time series-specific architectural biases. In this paper, we go in a different direction by introducing tsGT, a stochastic time series model built on a general-purpose transformer architecture. We focus on using a well-known and theoretically justified rolling window backtesting and evaluation protocol. We show that tsGT outperforms the state-of-the-art models on MAD and RMSE, and surpasses its stochastic peers on QL and CRPS, on four commonly used datasets. We complement these results with a detailed analysis of tsGT's ability to model the data distribution and predict marginal quantile values.

Łukasz Maziarka, Dawid Majchrowski, Tomasz Danel et al.

Self-supervised learning holds promise to revolutionize molecule property prediction - a central task to drug discovery and many more industries - by enabling data efficient learning from scarce experimental data. Despite significant progress, non-pretrained methods can be still competitive in certain settings. We reason that architecture might be a key bottleneck. In particular, enriching the backbone architecture with domain-specific inductive biases has been key for the success of self-supervised learning in other domains. In this spirit, we methodologically explore the design space of the self-attention mechanism tailored to molecular data. We identify a novel variant of self-attention adapted to processing molecules, inspired by the relative self-attention layer, which involves fusing embedded graph and distance relationships between atoms. Our main contribution is Relative Molecule Attention Transformer (R-MAT): a novel Transformer-based model based on the developed self-attention layer that achieves state-of-the-art or very competitive results across a~wide range of molecule property prediction tasks.

Łukasz Maziarka, Aleksandra Nowak, Maciej Wołczyk et al.

One of the main arguments behind studying disentangled representations is the assumption that they can be easily reused in different tasks. At the same time finding a joint, adaptable representation of data is one of the key challenges in the multi-task learning setting. In this paper, we take a closer look at the relationship between disentanglement and multi-task learning based on hard parameter sharing. We perform a thorough empirical study of the representations obtained by neural networks trained on automatically generated supervised tasks. Using a set of standard metrics we show that disentanglement appears naturally during the process of multi-task neural network training.

Maciej Wołczyk, Magdalena Proszewska, Łukasz Maziarka et al.

Modern generative models achieve excellent quality in a variety of tasks including image or text generation and chemical molecule modeling. However, existing methods often lack the essential ability to generate examples with requested properties, such as the age of the person in the photo or the weight of the generated molecule. Incorporating such additional conditioning factors would require rebuilding the entire architecture and optimizing the parameters from scratch. Moreover, it is difficult to disentangle selected attributes so that to perform edits of only one attribute while leaving the others unchanged. To overcome these limitations we propose PluGeN (Plugin Generative Network), a simple yet effective generative technique that can be used as a plugin to pre-trained generative models. The idea behind our approach is to transform the entangled latent representation using a flow-based module into a multi-dimensional space where the values of each attribute are modeled as an independent one-dimensional distribution. In consequence, PluGeN can generate new samples with desired attributes as well as manipulate labeled attributes of existing examples. Due to the disentangling of the latent representation, we are even able to generate samples with rare or unseen combinations of attributes in the dataset, such as a young person with gray hair, men with make-up, or women with beards. We combined PluGeN with GAN and VAE models and applied it to conditional generation and manipulation of images and chemical molecule modeling. Experiments demonstrate that PluGeN preserves the quality of backbone models while adding the ability to control the values of labeled attributes.

Marcin Sendera, Marek Śmieja, Łukasz Maziarka et al.

We propose FlowSVDD -- a flow-based one-class classifier for anomaly/outliers detection that realizes a well-known SVDD principle using deep learning tools. Contrary to other approaches to deep SVDD, the proposed model is instantiated using flow-based models, which naturally prevents from collapsing of bounding hypersphere into a single point. Experiments show that FlowSVDD achieves comparable results to the current state-of-the-art methods and significantly outperforms related deep SVDD methods on benchmark datasets.

Agnieszka Pocha, Tomasz Danel, Łukasz Maziarka

Graph neural networks have recently become a standard method for analysing chemical compounds. In the field of molecular property prediction, the emphasis is now put on designing new model architectures, and the importance of atom featurisation is oftentimes belittled. When contrasting two graph neural networks, the use of different atom features possibly leads to the incorrect attribution of the results to the network architecture. To provide a better understanding of this issue, we compare multiple atom representations for graph models and evaluate them on the prediction of free energy, solubility, and metabolic stability. To the best of our knowledge, this is the first methodological study that focuses on the relevance of atom representation to the predictive performance of graph neural networks.

Tomasz Danel, Marek Śmieja, Łukasz Struski et al.

We investigate the problem of training neural networks from incomplete images without replacing missing values. For this purpose, we first represent an image as a graph, in which missing pixels are entirely ignored. The graph image representation is processed using a spatial graph convolutional network (SGCN) -- a type of graph convolutional networks, which is a proper generalization of classical CNNs operating on images. On one hand, our approach avoids the problem of missing data imputation while, on the other hand, there is a natural correspondence between CNNs and SGCN. Experiments confirm that our approach performs better than analogical CNNs with the imputation of missing values on typical classification and reconstruction tasks.

Łukasz Maziarka, Marek Śmieja, Marcin Sendera et al.

We propose OneFlow - a flow-based one-class classifier for anomaly (outlier) detection that finds a minimal volume bounding region. Contrary to density-based methods, OneFlow is constructed in such a way that its result typically does not depend on the structure of outliers. This is caused by the fact that during training the gradient of the cost function is propagated only over the points located near to the decision boundary (behavior similar to the support vectors in SVM). The combination of flow models and a Bernstein quantile estimator allows OneFlow to find a parametric form of bounding region, which can be useful in various applications including describing shapes from 3D point clouds. Experiments show that the proposed model outperforms related methods on real-world anomaly detection problems.

Łukasz Maziarka, Tomasz Danel, Sławomir Mucha et al.

Designing a single neural network architecture that performs competitively across a range of molecule property prediction tasks remains largely an open challenge, and its solution may unlock a widespread use of deep learning in the drug discovery industry. To move towards this goal, we propose Molecule Attention Transformer (MAT). Our key innovation is to augment the attention mechanism in Transformer using inter-atomic distances and the molecular graph structure. Experiments show that MAT performs competitively on a diverse set of molecular prediction tasks. Most importantly, with a simple self-supervised pretraining, MAT requires tuning of only a few hyperparameter values to achieve state-of-the-art performance on downstream tasks. Finally, we show that attention weights learned by MAT are interpretable from the chemical point of view.

Tomasz Danel, Przemysław Spurek, Jacek Tabor et al.

Graph Convolutional Networks (GCNs) have recently become the primary choice for learning from graph-structured data, superseding hash fingerprints in representing chemical compounds. However, GCNs lack the ability to take into account the ordering of node neighbors, even when there is a geometric interpretation of the graph vertices that provides an order based on their spatial positions. To remedy this issue, we propose Spatial Graph Convolutional Network (SGCN) which uses spatial features to efficiently learn from graphs that can be naturally located in space. Our contribution is threefold: we propose a GCN-inspired architecture which (i) leverages node positions, (ii) is a proper generalization of both GCNs and Convolutional Neural Networks (CNNs), (iii) benefits from augmentation which further improves the performance and assures invariance with respect to the desired properties. Empirically, SGCN outperforms state-of-the-art graph-based methods on image classification and chemical tasks.

Przemysław Spurek, Aleksandra Nowak, Jacek Tabor et al.

Non-linear source separation is a challenging open problem with many applications. We extend a recently proposed Adversarial Non-linear ICA (ANICA) model, and introduce Cramer-Wold ICA (CW-ICA). In contrast to ANICA we use a simple, closed--form optimization target instead of a discriminator--based independence measure. Our results show that CW-ICA achieves comparable results to ANICA, while foregoing the need for adversarial training.

Sylwester Klocek, Łukasz Maziarka, Maciej Wołczyk et al.

Motivated by the human way of memorizing images we introduce their functional representation, where an image is represented by a neural network. For this purpose, we construct a hypernetwork which takes an image and returns weights to the target network, which maps point from the plane (representing positions of the pixel) into its corresponding color in the image. Since the obtained representation is continuous, one can easily inspect the image at various resolutions and perform on it arbitrary continuous operations. Moreover, by inspecting interpolations we show that such representation has some properties characteristic to generative models. To evaluate the proposed mechanism experimentally, we apply it to image super-resolution problem. Despite using a single model for various scaling factors, we obtained results comparable to existing super-resolution methods.

Bartosz Wójcik, Łukasz Maziarka, Jacek Tabor

In this paper, we propose a simple, fast and easy to implement algorithm LOSSGRAD (locally optimal step-size in gradient descent), which automatically modifies the step-size in gradient descent during neural networks training. Given a function $f$, a point $x$, and the gradient $\nabla_x f$ of $f$, we aim to find the step-size $h$ which is (locally) optimal, i.e. satisfies: $$ h=arg\,min_{t \geq 0} f(x-t \nabla_x f). $$ Making use of quadratic approximation, we show that the algorithm satisfies the above assumption. We experimentally show that our method is insensitive to the choice of initial learning rate while achieving results comparable to other methods.

Łukasz Maziarka, Agnieszka Pocha, Jan Kaczmarczyk et al.

Designing a molecule with desired properties is one of the biggest challenges in drug development, as it requires optimization of chemical compound structures with respect to many complex properties. To augment the compound design process we introduce Mol-CycleGAN - a CycleGAN-based model that generates optimized compounds with high structural similarity to the original ones. Namely, given a molecule our model generates a structurally similar one with an optimized value of the considered property. We evaluate the performance of the model on selected optimization objectives related to structural properties (presence of halogen groups, number of aromatic rings) and to a physicochemical property (penalized logP). In the task of optimization of penalized logP of drug-like molecules our model significantly outperforms previous results.

Łukasz Maziarka, Marek Śmieja, Aleksandra Nowak et al.

Global pooling, such as max- or sum-pooling, is one of the key ingredients in deep neural networks used for processing images, texts, graphs and other types of structured data. Based on the recent DeepSets architecture proposed by Zaheer et al. (NIPS 2017), we introduce a Set Aggregation Network (SAN) as an alternative global pooling layer. In contrast to typical pooling operators, SAN allows to embed a given set of features to a vector representation of arbitrary size. We show that by adjusting the size of embedding, SAN is capable of preserving the whole information from the input. In experiments, we demonstrate that replacing global pooling layer by SAN leads to the improvement of classification accuracy. Moreover, it is less prone to overfitting and can be used as a regularizer.