Molecular property prediction is of crucial importance in many disciplines such as drug discovery, molecular biology, or material and process design. The frequently employed quantitative structure-property/activity relationships (QSPRs/QSARs) characterize molecules by descriptors which are then mapped to the properties of interest via a linear or nonlinear model. In contrast, graph neural networks, a novel machine learning method, directly work on the molecular graph, i.e., a graph representation where atoms correspond to nodes and bonds correspond to edges. GNNs allow to learn properties in an end-to-end fashion, thereby avoiding the need for informative descriptors as in QSPRs/QSARs. GNNs have been shown to achieve state-of-the-art prediction performance on various property predictions tasks and represent an active field of research. We describe the fundamentals of GNNs and demonstrate the application of GNNs via two examples for molecular property prediction.

We study the problem of translating an image-based, step-by-step assembly manual created by human designers into machine-interpretable instructions. We formulate this problem as a sequential prediction task: at each step, our model reads the manual, locates the components to be added to the current shape, and infers their 3D poses. This task poses the challenge of establishing a 2D-3D correspondence between the manual image and the real 3D object, and 3D pose estimation for unseen 3D objects, since a new component to be added in a step can be an object built from previous steps. To address these two challenges, we present a novel learning-based framework, the Manual-to-Executable-Plan Network (MEPNet), which reconstructs the assembly steps from a sequence of manual images. The key idea is to integrate neural 2D keypoint detection modules and 2D-3D projection algorithms for high-precision prediction and strong generalization to unseen components. The MEPNet outperforms existing methods on three newly collected LEGO manual datasets and a Minecraft house dataset.

Developing semi-supervised task-oriented dialog (TOD) systems by leveraging unlabeled dialog data has attracted increasing interests. For semi-supervised learning of latent state TOD models, variational learning is often used, but suffers from the annoying high-variance of the gradients propagated through discrete latent variables and the drawback of indirectly optimizing the target log-likelihood. Recently, an alternative algorithm, called joint stochastic approximation (JSA), has emerged for learning discrete latent variable models with impressive performances. In this paper, we propose to apply JSA to semi-supervised learning of the latent state TOD models, which is referred to as JSA-TOD. To our knowledge, JSA-TOD represents the first work in developing JSA based semi-supervised learning of discrete latent variable conditional models for such long sequential generation problems like in TOD systems. Extensive experiments show that JSA-TOD significantly outperforms its variational learning counterpart. Remarkably, semi-supervised JSA-TOD using 20% labels performs close to the full-supervised baseline on MultiWOZ2.1.

Plasma is defined as the fourth state of matter and non-thermal plasma can be produced at atmospheric pressure under a high electrical field. The strong and broad-spectrum antimicrobial effect of plasma-activated liquids (PALs) is now well known. The proven applicability of machine learning (ML) in the medical field is encouraging for its application in the field of plasma medicine as well. Thus, ML applications on PALs could present a new perspective to better understand the influences of various parameters on their antimicrobial effects. In this paper, comparative supervised ML models are presented by using previously obtained data to qualitatively predict the in vitro antimicrobial activity of PALs. A literature search was performed and data is collected from 33 relevant articles. After the required preprocessing steps, two supervised ML methods, namely classification, and regression are applied to data to obtain microbial inactivation (MI) predictions. For classification, MI is labeled in four categories and for regression, MI is used as a continuous variable. Two different robust cross-validation strategies are conducted for classification and regression models to evaluate the proposed method; repeated stratified k-fold cross-validation and k-fold cross-validation, respectively. We also investigate the effect of different features on models. The results demonstrated that the hyperparameter-optimized Random Forest Classifier (oRFC) and Random Forest Regressor (oRFR) provided better results than other models for the classification and regression, respectively. Finally, the best test accuracy of 82.68% for oRFC and R2 of 0.75 for the oRFR are obtained. ML techniques could contribute to a better understanding of plasma parameters that have a dominant role in the desired antimicrobial effect. Furthermore, such findings may contribute to the definition of a plasma dose in the future.

Self-supervised, category-agnostic segmentation of real-world images is a challenging open problem in computer vision. Here, we show how to learn static grouping priors from motion self-supervision by building on the cognitive science concept of a Spelke Object: a set of physical stuff that moves together. We introduce the Excitatory-Inhibitory Segment Extraction Network (EISEN), which learns to extract pairwise affinity graphs for static scenes from motion-based training signals. EISEN then produces segments from affinities using a novel graph propagation and competition network. During training, objects that undergo correlated motion (such as robot arms and the objects they move) are decoupled by a bootstrapping process: EISEN explains away the motion of objects it has already learned to segment. We show that EISEN achieves a substantial improvement in the state of the art for self-supervised image segmentation on challenging synthetic and real-world robotics datasets.

Transfer-learning methods aim to improve performance in a data-scarce target domain using a model pretrained on a data-rich source domain. A cost-efficient strategy, linear probing, involves freezing the source model and training a new classification head for the target domain. This strategy is outperformed by a more costly but state-of-the-art method -- fine-tuning all parameters of the source model to the target domain -- possibly because fine-tuning allows the model to leverage useful information from intermediate layers which is otherwise discarded by the later pretrained layers. We explore the hypothesis that these intermediate layers might be directly exploited. We propose a method, Head-to-Toe probing (Head2Toe), that selects features from all layers of the source model to train a classification head for the target-domain. In evaluations on the VTAB-1k, Head2Toe matches performance obtained with fine-tuning on average while reducing training and storage cost hundred folds or more, but critically, for out-of-distribution transfer, Head2Toe outperforms fine-tuning.

Integrated Development Environments (IDEs) provide tool support to automate many source code editing tasks. Traditionally, IDEs use only the spatial context, i.e., the location where the developer is editing, to generate candidate edit recommendations. However, spatial context alone is often not sufficient to confidently predict the developer's next edit, and thus IDEs generate many suggestions at a location. Therefore, IDEs generally do not actively offer suggestions and instead, the developer is usually required to click on a specific icon or menu and then select from a large list of potential suggestions. As a consequence, developers often miss the opportunity to use the tool support because they are not aware it exists or forget to use it. To better understand common patterns in developer behavior and produce better edit recommendations, we can additionally use the temporal context, i.e., the edits that a developer was recently performing. To enable edit recommendations based on temporal context, we present Overwatch, a novel technique for learning edit sequence patterns from traces of developers' edits performed in an IDE. Our experiments show that Overwatch has 78% precision and that Overwatch not only completed edits when developers missed the opportunity to use the IDE tool support but also predicted new edits that have no tool support in the IDE.

In this paper we propose an adaptive approach for clustering and visualization of data by an orthogonalization process. Starting with the data points being represented by a Markov process using the diffusion map framework, the method adaptively increase the orthogonality of the clusters by applying a feedback mechanism inspired by the Gromov-Wasserstein distance. This mechanism iteratively increases the spectral gap and refines the orthogonality of the data to achieve a clustering with high specificity. By using the diffusion map framework and representing the relation between data points using transition probabilities, the method is robust with respect to both the underlying distance, noise in the data and random initialization. We prove that the method converges globally to a unique fixpoint for certain parameter values. We also propose a related approach where the transition probabilities in the Markov process are required to be doubly stochastic, in which case the method generates a minimizer to a nonconvex optimization problem. We apply the method on cryo-electron microscopy image data from biopharmaceutical manufacturing where we can confirm biologically relevant insights related to therapeutic efficacy. We consider an example with morphological variations of gene packaging and confirm that the method produces biologically meaningful clustering results consistent with human expert classification.

Model agnostic meta-learning algorithms aim to infer priors from several observed tasks that can then be used to adapt to a new task with few examples. Given the inherent diversity of tasks arising in existing benchmarks, recent methods use separate, learnable structure, such as hierarchies or graphs, for enabling task-specific adaptation of the prior. While these approaches have produced significantly better meta learners, our goal is to improve their performance when the heterogeneous task distribution contains challenging distribution shifts and semantic disparities. To this end, we introduce CAML (Contrastive Knowledge-Augmented Meta Learning), a novel approach for knowledge-enhanced few-shot learning that evolves a knowledge graph to effectively encode historical experience, and employs a contrastive distillation strategy to leverage the encoded knowledge for task-aware modulation of the base learner. Using standard benchmarks, we evaluate the performance of CAML in different few-shot learning scenarios. In addition to the standard few-shot task adaptation, we also consider the more challenging multi-domain task adaptation and few-shot dataset generalization settings in our empirical studies. Our results shows that CAML consistently outperforms best known approaches and achieves improved generalization.

Recent work has suggested that the generalisation performance of a DNN is related to the extent to which the Signal-to-Noise Ratio is optimised at each of the nodes. In contrast, Gradient Descent methods do not always lead to SNR-optimal weight configurations. One way to improve SNR performance is to suppress large weight updates and amplify small weight updates. Such balancing is already implicit in some common optimizers, but we propose an approach that makes this explicit. The method applies a non-linear function to gradients prior to making DNN parameter updates. We investigate the performance with such non-linear approaches. The result is an adaptation to existing optimizers that improves performance for many problem types.