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Decision tree learning is a widely used approach in machine learning, favoured in applications that require concise and interpretable models. Heuristic methods are traditionally used to quickly produce models with reasonably high accuracy. A commonly criticised point, however, is that the resulting trees may not necessarily be the best representation of the data in terms of accuracy and size. In recent years, this motivated the development of optimal classification tree algorithms that globally optimise the decision tree in contrast to heuristic methods that perform a sequence of locally optimal decisions. We follow this line of work and provide a novel algorithm for learning optimal classification trees based on dynamic programming and search. Our algorithm supports constraints on the depth of the tree and number of nodes. The success of our approach is attributed to a series of specialised techniques that exploit properties unique to classification trees. Whereas algorithms for optimal classification trees have traditionally been plagued by high runtimes and limited scalability, we show in a detailed experimental study that our approach uses only a fraction of the time required by the state-of-the-art and can handle datasets with tens of thousands of instances, providing several orders of magnitude improvements and notably contributing towards the practical realisation of optimal decision trees.

Molecular design and synthesis planning are two critical steps in the process of molecular discovery that we propose to formulate as a single shared task of conditional synthetic pathway generation. We report an amortized approach to generate synthetic pathways as a Markov decision process conditioned on a target molecular embedding. This approach allows us to conduct synthesis planning in a bottom-up manner and design synthesizable molecules by decoding from optimized conditional codes, demonstrating the potential to solve both problems of design and synthesis simultaneously. The approach leverages neural networks to probabilistically model the synthetic trees, one reaction step at a time, according to reactivity rules encoded in a discrete action space of reaction templates. We train these networks on hundreds of thousands of artificial pathways generated from a pool of purchasable compounds and a list of expert-curated templates. We validate our method with (a) the recovery of molecules using conditional generation, (b) the identification of synthesizable structural analogs, and (c) the optimization of molecular structures given oracle functions relevant to drug discovery.

A basic question in network community detection is how modular a given network is. This is usually addressed by evaluating the quality of partitions detected in the network. The Girvan-Newman (GN) modularity function is the standard way to make this assessment, but it has a number of drawbacks. Most importantly, it is not clearly interpretable, given that the measure can take relatively large values on partitions of random networks without communities. Here we propose a new measure based on the concept of robustness: modularity is the probability to find trivial partitions when the structure of the network is randomly perturbed. This concept can be implemented for any clustering algorithm capable of telling when a group structure is absent. Tests on artificial and real graphs reveal that robustness modularity can be used to assess and compare the strength of the community structure of different networks. We also introduce two other quality functions: modularity difference, a suitably normalized version of the GN modularity; information modularity, a measure of distance based on information compression. Both measures are strongly correlated with robustness modularity, and are promising options as well.

We show that it is provable in PA that there is an arithmetically definable sequence $\{\phi_{n}:n \in \omega\}$ of $\Pi^{0}_{2}$-sentences, such that - PRA+$\{\phi_{n}:n \in \omega\}$ is $\Pi^{0}_{2}$-sound and $\Pi^{0}_{1}$-complete - the length of $\phi_{n}$ is bounded above by a polynomial function of $n$ with positive leading coefficient - PRA+$\phi_{n+1}$ always proves 1-consistency of PRA+$\phi_{n}$. One has that the growth in logical strength is in some sense "as fast as possible", manifested in the fact that the total general recursive functions whose totality is asserted by the true $\Pi^{0}_{2}$-sentences in the sequence are cofinal growth-rate-wise in the set of all total general recursive functions. We then develop an argument which makes use of a sequence of sentences constructed by an application of the diagonal lemma, which are generalisations in a broad sense of Hugh Woodin's "Tower of Hanoi" construction as outlined in his essay "Tower of Hanoi" in Chapter 18 of the anthology "Truth in Mathematics". The argument establishes the result that it is provable in PA that $P \neq NP$. We indicate how to pull the argument all the way down into EFA.

Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine learning methods are ideal for the design of large amounts of potential new candidate molecules, which are naturally represented as graphs. Graph generation is being revolutionized by deep learning methods, and molecular generation is one of its most promising applications. In this paper, we introduce a sequential molecular graph generator based on a set of graph neural network modules, which we call MG^2N^2. At each step, a node or a group of nodes is added to the graph, along with its connections. The modular architecture simplifies the training procedure, also allowing an independent retraining of a single module. Sequentiality and modularity make the generation process interpretable. The use of graph neural networks maximizes the information in input at each generative step, which consists of the subgraph produced during the previous steps. Experiments of unconditional generation on the QM9 and Zinc datasets show that our model is capable of generalizing molecular patterns seen during the training phase, without overfitting. The results indicate that our method is competitive, and outperforms challenging baselines for unconditional generation.

Graph neural networks (GNNs) are typically applied to static graphs that are assumed to be known upfront. This static input structure is often informed purely by insight of the machine learning practitioner, and might not be optimal for the actual task the GNN is solving. In absence of reliable domain expertise, one might resort to inferring the latent graph structure, which is often difficult due to the vast search space of possible graphs. Here we introduce Pointer Graph Networks (PGNs) which augment sets or graphs with additional inferred edges for improved model expressivity. PGNs allow each node to dynamically point to another node, followed by message passing over these pointers. The sparsity of this adaptable graph structure makes learning tractable while still being sufficiently expressive to simulate complex algorithms. Critically, the pointing mechanism is directly supervised to model long-term sequences of operations on classical data structures, incorporating useful structural inductive biases from theoretical computer science. Qualitatively, we demonstrate that PGNs can learn parallelisable variants of pointer-based data structures, namely disjoint set unions and link/cut trees. PGNs generalise out-of-distribution to 5x larger test inputs on dynamic graph connectivity tasks, outperforming unrestricted GNNs and Deep Sets.

Molecular graph generation is a fundamental problem for drug discovery and has been attracting growing attention. The problem is challenging since it requires not only generating chemically valid molecular structures but also optimizing their chemical properties in the meantime. Inspired by the recent progress in deep generative models, in this paper we propose a flow-based autoregressive model for graph generation called GraphAF. GraphAF combines the advantages of both autoregressive and flow-based approaches and enjoys: (1) high model flexibility for data density estimation; (2) efficient parallel computation for training; (3) an iterative sampling process, which allows leveraging chemical domain knowledge for valency checking. Experimental results show that GraphAF is able to generate 68% chemically valid molecules even without chemical knowledge rules and 100% valid molecules with chemical rules. The training process of GraphAF is two times faster than the existing state-of-the-art approach GCPN. After fine-tuning the model for goal-directed property optimization with reinforcement learning, GraphAF achieves state-of-the-art performance on both chemical property optimization and constrained property optimization.

Meta-learning extracts the common knowledge acquired from learning different tasks and uses it for unseen tasks. It demonstrates a clear advantage on tasks that have insufficient training data, e.g., few-shot learning. In most meta-learning methods, tasks are implicitly related via the shared model or optimizer. In this paper, we show that a meta-learner that explicitly relates tasks on a graph describing the relations of their output dimensions (e.g., classes) can significantly improve the performance of few-shot learning. This type of graph is usually free or cheap to obtain but has rarely been explored in previous works. We study the prototype based few-shot classification, in which a prototype is generated for each class, such that the nearest neighbor search between the prototypes produces an accurate classification. We introduce "Gated Propagation Network (GPN)", which learns to propagate messages between prototypes of different classes on the graph, so that learning the prototype of each class benefits from the data of other related classes. In GPN, an attention mechanism is used for the aggregation of messages from neighboring classes, and a gate is deployed to choose between the aggregated messages and the message from the class itself. GPN is trained on a sequence of tasks from many-shot to few-shot generated by subgraph sampling. During training, it is able to reuse and update previously achieved prototypes from the memory in a life-long learning cycle. In experiments, we change the training-test discrepancy and test task generation settings for thorough evaluations. GPN outperforms recent meta-learning methods on two benchmark datasets in all studied cases.

Tracking vehicles in LIDAR point clouds is a challenging task due to the sparsity of the data and the dense search space. The lack of structure in point clouds impedes the use of convolution and correlation filters usually employed in 2D object tracking. In addition, structuring point clouds is cumbersome and implies losing fine-grained information. As a result, generating proposals in 3D space is expensive and inefficient. In this paper, we leverage the dense and structured Bird Eye View (BEV) representation of LIDAR point clouds to efficiently search for objects of interest. We use an efficient Region Proposal Network and generate a small number of object proposals in 3D. Successively, we refine our selection of 3D object candidates by exploiting the similarity capability of a 3D Siamese network. We regularize the latter 3D Siamese network for shape completion to enhance its discrimination capability. Our method attempts to solve both for an efficient search space in the BEV space and a meaningful selection using 3D LIDAR point cloud. We show that the Region Proposal in the BEV outperforms Bayesian methods such as Kalman and Particle Filters in providing proposal by a significant margin and that such candidates are suitable for the 3D Siamese network. By training our method end-to-end, we outperform the previous baseline in vehicle tracking by 12% / 18% in Success and Precision when using only 16 candidates.

Querying graph structured data is a fundamental operation that enables important applications including knowledge graph search, social network analysis, and cyber-network security. However, the growing size of real-world data graphs poses severe challenges for graph databases to meet the response-time requirements of the applications. Planning the computational steps of query processing - Query Planning - is central to address these challenges. In this paper, we study the problem of learning to speedup query planning in graph databases towards the goal of improving the computational-efficiency of query processing via training queries.We present a Learning to Plan (L2P) framework that is applicable to a large class of query reasoners that follow the Threshold Algorithm (TA) approach. First, we define a generic search space over candidate query plans, and identify target search trajectories (query plans) corresponding to the training queries by performing an expensive search. Subsequently, we learn greedy search control knowledge to imitate the search behavior of the target query plans. We provide a concrete instantiation of our L2P framework for STAR, a state-of-the-art graph query reasoner. Our experiments on benchmark knowledge graphs including DBpedia, YAGO, and Freebase show that using the query plans generated by the learned search control knowledge, we can significantly improve the speed of STAR with negligible loss in accuracy.