Stanisław Jastrzębski

Jungkyu Park, Jakub Chłędowski, Stanisław Jastrzębski et al.

3D imaging enables accurate diagnosis by providing spatial information about organ anatomy. However, using 3D images to train AI models is computationally challenging because they consist of 10x or 100x more pixels than their 2D counterparts. To be trained with high-resolution 3D images, convolutional neural networks resort to downsampling them or projecting them to 2D. We propose an effective alternative, a neural network that enables efficient classification of full-resolution 3D medical images. Compared to off-the-shelf convolutional neural networks, our network, 3D Globally-Aware Multiple Instance Classifier (3D-GMIC), uses 77.98%-90.05% less GPU memory and 91.23%-96.02% less computation. While it is trained only with image-level labels, without segmentation labels, it explains its predictions by providing pixel-level saliency maps. On a dataset collected at NYU Langone Health, including 85,526 patients with full-field 2D mammography (FFDM), synthetic 2D mammography, and 3D mammography, 3D-GMIC achieves an AUC of 0.831 (95% CI: 0.769-0.887) in classifying breasts with malignant findings using 3D mammography. This is comparable to the performance of GMIC on FFDM (0.816, 95% CI: 0.737-0.878) and synthetic 2D (0.826, 95% CI: 0.754-0.884), which demonstrates that 3D-GMIC successfully classified large 3D images despite focusing computation on a smaller percentage of its input compared to GMIC. Therefore, 3D-GMIC identifies and utilizes extremely small regions of interest from 3D images consisting of hundreds of millions of pixels, dramatically reducing associated computational challenges. 3D-GMIC generalizes well to BCS-DBT, an external dataset from Duke University Hospital, achieving an AUC of 0.848 (95% CI: 0.798-0.896).

Mikołaj Sacha, Mikołaj Błaż, Piotr Byrski et al.

The central challenge in automated synthesis planning is to be able to generate and predict outcomes of a diverse set of chemical reactions. In particular, in many cases, the most likely synthesis pathway cannot be applied due to additional constraints, which requires proposing alternative chemical reactions. With this in mind, we present Molecule Edit Graph Attention Network (MEGAN), an end-to-end encoder-decoder neural model. MEGAN is inspired by models that express a chemical reaction as a sequence of graph edits, akin to the arrow pushing formalism. We extend this model to retrosynthesis prediction (predicting substrates given the product of a chemical reaction) and scale it up to large datasets. We argue that representing the reaction as a sequence of edits enables MEGAN to efficiently explore the space of plausible chemical reactions, maintaining the flexibility of modeling the reaction in an end-to-end fashion, and achieving state-of-the-art accuracy in standard benchmarks. Code and trained models are made available online at https://github.com/molecule-one/megan.

Mikołaj Sacha, Michał Sadowski, Piotr Kozakowski et al.

Retrosynthesis involves determining a sequence of reactions to synthesize complex molecules from simpler precursors. As this poses a challenge in organic chemistry, machine learning has offered solutions, particularly for predicting possible reaction substrates for a given target molecule. These solutions mainly fall into template-based and template-free categories. The former is efficient but relies on a vast set of predefined reaction patterns, while the latter, though more flexible, can be computationally intensive and less interpretable. To address these issues, we introduce METRO (Molecule-Edit Templates for RetrOsynthesis), a machine-learning model that predicts reactions using minimal templates - simplified reaction patterns capturing only essential molecular changes - reducing computational overhead and achieving state-of-the-art results on standard benchmarks.

Nan Wu, Stanisław Jastrzębski, Kyunghyun Cho et al.

We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, ModelNet40, and NVIDIA Dynamic Hand Gesture.

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.

Cheng-Hao Liu, Maksym Korablyov, Stanisław Jastrzębski et al.

De novo molecule generation often results in chemically unfeasible molecules. A natural idea to mitigate this problem is to bias the search process towards more easily synthesizable molecules using a proxy for synthetic accessibility. However, using currently available proxies still results in highly unrealistic compounds. We investigate the feasibility of training deep graph neural networks to approximate the outputs of a retrosynthesis planning software, and their use to bias the search process. We evaluate our method on a benchmark involving searching for drug-like molecules with antibiotic properties. Compared to enumerating over five million existing molecules from the ZINC database, our approach finds molecules predicted to be more likely to be antibiotics while maintaining good drug-like properties and being easily synthesizable. Importantly, our deep neural network can successfully filter out hard to synthesize molecules while achieving a $10^5$ times speed-up over using the retrosynthesis planning software.

Luke Darlow, Stanisław Jastrzębski, Amos Storkey

Collider bias is a harmful form of sample selection bias that neural networks are ill-equipped to handle. This bias manifests itself when the underlying causal signal is strongly correlated with other confounding signals due to the training data collection procedure. In the situation where the confounding signal is easy-to-learn, deep neural networks will latch onto this and the resulting model will generalise poorly to in-the-wild test scenarios. We argue herein that the cause of failure is a combination of the deep structure of neural networks and the greedy gradient-driven learning process used - one that prefers easy-to-compute signals when available. We show it is possible to mitigate against this by generating bias-decoupled training data using latent adversarial debiasing (LAD), even when the confounding signal is present in 100% of the training data. By training neural networks on these adversarial examples,we can improve their generalisation in collider bias settings. Experiments show state-of-the-art performance of LAD in label-free debiasing with gains of 76.12% on background coloured MNIST, 35.47% on fore-ground coloured MNIST, and 8.27% on corrupted CIFAR-10.

Farah E. Shamout, Yiqiu Shen, Nan Wu et al.

During the coronavirus disease 2019 (COVID-19) pandemic, rapid and accurate triage of patients at the emergency department is critical to inform decision-making. We propose a data-driven approach for automatic prediction of deterioration risk using a deep neural network that learns from chest X-ray images and a gradient boosting model that learns from routine clinical variables. Our AI prognosis system, trained using data from 3,661 patients, achieves an area under the receiver operating characteristic curve (AUC) of 0.786 (95% CI: 0.745-0.830) when predicting deterioration within 96 hours. The deep neural network extracts informative areas of chest X-ray images to assist clinicians in interpreting the predictions and performs comparably to two radiologists in a reader study. In order to verify performance in a real clinical setting, we silently deployed a preliminary version of the deep neural network at New York University Langone Health during the first wave of the pandemic, which produced accurate predictions in real-time. In summary, our findings demonstrate the potential of the proposed system for assisting front-line physicians in the triage of COVID-19 patients.

Witold Oleszkiewicz, Taro Makino, Stanisław Jastrzębski et al.

Deep neural networks (DNNs) show promise in breast cancer screening, but their robustness to input perturbations must be better understood before they can be clinically implemented. There exists extensive literature on this subject in the context of natural images that can potentially be built upon. However, it cannot be assumed that conclusions about robustness will transfer from natural images to mammogram images, due to significant differences between the two image modalities. In order to determine whether conclusions will transfer, we measure the sensitivity of a radiologist-level screening mammogram image classifier to four commonly studied input perturbations that natural image classifiers are sensitive to. We find that mammogram image classifiers are also sensitive to these perturbations, which suggests that we can build on the existing literature. We also perform a detailed analysis on the effects of low-pass filtering, and find that it degrades the visibility of clinically meaningful features called microcalcifications. Since low-pass filtering removes semantically meaningful information that is predictive of breast cancer, we argue that it is undesirable for mammogram image classifiers to be invariant to it. This is in contrast to natural images, where we do not want DNNs to be sensitive to low-pass filtering due to its tendency to remove information that is human-incomprehensible.

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.

Michał Zając, Konrad Zolna, Stanisław Jastrzębski

Recent work has shown that using unlabeled data in semi-supervised learning is not always beneficial and can even hurt generalization, especially when there is a class mismatch between the unlabeled and labeled examples. We investigate this phenomenon for image classification on the CIFAR-10 and the ImageNet datasets, and with many other forms of domain shifts applied (e.g. salt-and-pepper noise). Our main contribution is Split Batch Normalization (Split-BN), a technique to improve SSL when the additional unlabeled data comes from a shifted distribution. We achieve it by using separate batch normalization statistics for unlabeled examples. Due to its simplicity, we recommend it as a standard practice. Finally, we analyse how domain shift affects the SSL training process. In particular, we find that during training the statistics of hidden activations in late layers become markedly different between the unlabeled and the labeled examples.

Nan Wu, Jason Phang, Jungkyu Park et al.

We present a deep convolutional neural network for breast cancer screening exam classification, trained and evaluated on over 200,000 exams (over 1,000,000 images). Our network achieves an AUC of 0.895 in predicting whether there is a cancer in the breast, when tested on the screening population. We attribute the high accuracy of our model to a two-stage training procedure, which allows us to use a very high-capacity patch-level network to learn from pixel-level labels alongside a network learning from macroscopic breast-level labels. To validate our model, we conducted a reader study with 14 readers, each reading 720 screening mammogram exams, and find our model to be as accurate as experienced radiologists when presented with the same data. Finally, we show that a hybrid model, averaging probability of malignancy predicted by a radiologist with a prediction of our neural network, is more accurate than either of the two separately. To better understand our results, we conduct a thorough analysis of our network's performance on different subpopulations of the screening population, model design, training procedure, errors, and properties of its internal representations.

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.

Stanisław Jastrzębski, Quentin de Laroussilhe, Mingxing Tan et al.

Neural Architecture Search (NAS) enabled the discovery of state-of-the-art architectures in many domains. However, the success of NAS depends on the definition of the search space. Current search spaces are defined as a static sequence of decisions and a set of available actions for each decision. Each possible sequence of actions defines an architecture. We propose a more expressive class of search space: directed graphs. In our formalism, each decision is a vertex and each action is an edge. This allows us to model iterative and branching architecture design decisions. We demonstrate in simulation, and on image classification experiments, basic iterative and branching search structures, and show that the graph representation improves sample efficiency.

Wojciech Tarnowski, Piotr Warchoł, Stanisław Jastrzębski et al.

We demonstrate that in residual neural networks (ResNets) dynamical isometry is achievable irrespectively of the activation function used. We do that by deriving, with the help of Free Probability and Random Matrix Theories, a universal formula for the spectral density of the input-output Jacobian at initialization, in the large network width and depth limit. The resulting singular value spectrum depends on a single parameter, which we calculate for a variety of popular activation functions, by analyzing the signal propagation in the artificial neural network. We corroborate our results with numerical simulations of both random matrices and ResNets applied to the CIFAR-10 classification problem. Moreover, we study the consequence of this universal behavior for the initial and late phases of the learning processes. We conclude by drawing attention to the simple fact, that initialization acts as a confounding factor between the choice of activation function and the rate of learning. We propose that in ResNets this can be resolved based on our results, by ensuring the same level of dynamical isometry at initialization.

Stanisław Jastrzębski, Zachary Kenton, Nicolas Ballas et al.

Stochastic Gradient Descent (SGD) based training of neural networks with a large learning rate or a small batch-size typically ends in well-generalizing, flat regions of the weight space, as indicated by small eigenvalues of the Hessian of the training loss. However, the curvature along the SGD trajectory is poorly understood. An empirical investigation shows that initially SGD visits increasingly sharp regions, reaching a maximum sharpness determined by both the learning rate and the batch-size of SGD. When studying the SGD dynamics in relation to the sharpest directions in this initial phase, we find that the SGD step is large compared to the curvature and commonly fails to minimize the loss along the sharpest directions. Furthermore, using a reduced learning rate along these directions can improve training speed while leading to both sharper and better generalizing solutions compared to vanilla SGD. In summary, our analysis of the dynamics of SGD in the subspace of the sharpest directions shows that they influence the regions that SGD steers to (where larger learning rate or smaller batch size result in wider regions visited), the overall training speed, and the generalization ability of the final model.

Szymon Knop, Jacek Tabor, Przemysław Spurek et al.

We propose a new generative model, Cramer-Wold Autoencoder (CWAE). Following WAE, we directly encourage normality of the latent space. Our paper uses also the recent idea from Sliced WAE (SWAE) model, which uses one-dimensional projections as a method of verifying closeness of two distributions. The crucial new ingredient is the introduction of a new (Cramer-Wold) metric in the space of densities, which replaces the Wasserstein metric used in SWAE. We show that the Cramer-Wold metric between Gaussian mixtures is given by a simple analytic formula, which results in the removal of sampling necessary to estimate the cost function in WAE and SWAE models. As a consequence, while drastically simplifying the optimization procedure, CWAE produces samples of a matching perceptual quality to other SOTA models.

Stanisław Jastrzębski, Dzmitry Bahdanau, Seyedarian Hosseini et al.

Commonsense knowledge bases such as ConceptNet represent knowledge in the form of relational triples. Inspired by the recent work by Li et al., we analyse if knowledge base completion models can be used to mine commonsense knowledge from raw text. We propose novelty of predicted triples with respect to the training set as an important factor in interpreting results. We critically analyse the difficulty of mining novel commonsense knowledge, and show that a simple baseline method outperforms the previous state of the art on predicting more novel.

Stanisław Jastrzębski, Zachary Kenton, Devansh Arpit et al.

We investigate the dynamical and convergent properties of stochastic gradient descent (SGD) applied to Deep Neural Networks (DNNs). Characterizing the relation between learning rate, batch size and the properties of the final minima, such as width or generalization, remains an open question. In order to tackle this problem we investigate the previously proposed approximation of SGD by a stochastic differential equation (SDE). We theoretically argue that three factors - learning rate, batch size and gradient covariance - influence the minima found by SGD. In particular we find that the ratio of learning rate to batch size is a key determinant of SGD dynamics and of the width of the final minima, and that higher values of the ratio lead to wider minima and often better generalization. We confirm these findings experimentally. Further, we include experiments which show that learning rate schedules can be replaced with batch size schedules and that the ratio of learning rate to batch size is an important factor influencing the memorization process.

Stanisław Jastrzębski, Devansh Arpit, Nicolas Ballas et al.

Residual networks (Resnets) have become a prominent architecture in deep learning. However, a comprehensive understanding of Resnets is still a topic of ongoing research. A recent view argues that Resnets perform iterative refinement of features. We attempt to further expose properties of this aspect. To this end, we study Resnets both analytically and empirically. We formalize the notion of iterative refinement in Resnets by showing that residual connections naturally encourage features of residual blocks to move along the negative gradient of loss as we go from one block to the next. In addition, our empirical analysis suggests that Resnets are able to perform both representation learning and iterative refinement. In general, a Resnet block tends to concentrate representation learning behavior in the first few layers while higher layers perform iterative refinement of features. Finally we observe that sharing residual layers naively leads to representation explosion and counterintuitively, overfitting, and we show that simple existing strategies can help alleviating this problem.

Devansh Arpit, Stanisław Jastrzębski, Nicolas Ballas et al.

We examine the role of memorization in deep learning, drawing connections to capacity, generalization, and adversarial robustness. While deep networks are capable of memorizing noise data, our results suggest that they tend to prioritize learning simple patterns first. In our experiments, we expose qualitative differences in gradient-based optimization of deep neural networks (DNNs) on noise vs. real data. We also demonstrate that for appropriately tuned explicit regularization (e.g., dropout) we can degrade DNN training performance on noise datasets without compromising generalization on real data. Our analysis suggests that the notions of effective capacity which are dataset independent are unlikely to explain the generalization performance of deep networks when trained with gradient based methods because training data itself plays an important role in determining the degree of memorization.

Dzmitry Bahdanau, Tom Bosc, Stanisław Jastrzębski et al.

Words in natural language follow a Zipfian distribution whereby some words are frequent but most are rare. Learning representations for words in the "long tail" of this distribution requires enormous amounts of data. Representations of rare words trained directly on end tasks are usually poor, requiring us to pre-train embeddings on external data, or treat all rare words as out-of-vocabulary words with a unique representation. We provide a method for predicting embeddings of rare words on the fly from small amounts of auxiliary data with a network trained end-to-end for the downstream task. We show that this improves results against baselines where embeddings are trained on the end task for reading comprehension, recognizing textual entailment and language modeling.

Stanisław Jastrzębski, Damian Leśniak, Wojciech Marian Czarnecki

This paper shows how one can directly apply natural language processing (NLP) methods to classification problems in cheminformatics. Connection between these seemingly separate fields is shown by considering standard textual representation of compound, SMILES. The problem of activity prediction against a target protein is considered, which is a crucial part of computer aided drug design process. Conducted experiments show that this way one can not only outrank state of the art results of hand crafted representations but also gets direct structural insights into the way decisions are made.