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Contemporary graph learning algorithms are not well-defined for large molecules since they do not consider the hierarchical interactions among the atoms, which are essential to determine the molecular properties of macromolecules. In this work, we propose Multiresolution Graph Transformers (MGT), the first graph transformer architecture that can learn to represent large molecules at multiple scales. MGT can learn to produce representations for the atoms and group them into meaningful functional groups or repeating units. We also introduce Wavelet Positional Encoding (WavePE), a new positional encoding method that can guarantee localization in both spectral and spatial domains. Our proposed model achieves competitive results on two macromolecule datasets consisting of polymers and peptides, and one drug-like molecule dataset. Importantly, our model outperforms other state-of-the-art methods and achieves chemical accuracy in estimating molecular properties (e.g., GAP, HOMO and LUMO) calculated by Density Functional Theory (DFT) in the polymers dataset. Furthermore, the visualizations, including clustering results on macromolecules and low-dimensional spaces of their representations, demonstrate the capability of our methodology in learning to represent long-range and hierarchical structures. Our PyTorch implementation is publicly available at //github.com/HySonLab/Multires-Graph-Transformer

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In the field of unsupervised feature selection, sparse principal component analysis (SPCA) methods have attracted more and more attention recently. Compared to spectral-based methods, SPCA methods don't rely on the construction of a similarity matrix and show better feature selection ability on real-world data. The original SPCA formulates a nonconvex optimization problem. Existing convex SPCA methods reformulate SPCA as a convex model by regarding the reconstruction matrix as an optimization variable. However, they are lack of constraints equivalent to the orthogonality restriction in SPCA, leading to larger solution space. In this paper, it's proved that the optimal solution to a convex SPCA model falls onto the Positive Semidefinite (PSD) cone. A standard convex SPCA-based model with PSD constraint for unsupervised feature selection is proposed. Further, a two-step fast optimization algorithm via PSD projection is presented to solve the proposed model. Two other existing convex SPCA-based models are also proven to have their solutions optimized on the PSD cone in this paper. Therefore, the PSD versions of these two models are proposed to accelerate their convergence as well. We also provide a regularization parameter setting strategy for our proposed method. Experiments on synthetic and real-world datasets demonstrate the effectiveness and efficiency of the proposed methods.

Due to the large-scale availability of data, machine learning (ML) algorithms are being deployed in distributed topologies, where different nodes collaborate to train ML models over their individual data by exchanging model-related information (e.g., gradients) with a central server. However, distributed learning schemes are notably vulnerable to two threats. First, Byzantine nodes can single-handedly corrupt the learning by sending incorrect information to the server, e.g., erroneous gradients. The standard approach to mitigate such behavior is to use a non-linear robust aggregation method at the server. Second, the server can violate the privacy of the nodes. Recent attacks have shown that exchanging (unencrypted) gradients enables a curious server to recover the totality of the nodes' data. The use of homomorphic encryption (HE), a gold standard security primitive, has extensively been studied as a privacy-preserving solution to distributed learning in non-Byzantine scenarios. However, due to HE's large computational demand especially for high-dimensional ML models, there has not yet been any attempt to design purely homomorphic operators for non-linear robust aggregators. In this work, we present SABLE, the first completely homomorphic and Byzantine robust distributed learning algorithm. SABLE essentially relies on a novel plaintext encoding method that enables us to implement the robust aggregator over batching-friendly BGV. Moreover, this encoding scheme also accelerates state-of-the-art homomorphic sorting with larger security margins and smaller ciphertext size. We perform extensive experiments on image classification tasks and show that our algorithm achieves practical execution times while matching the ML performance of its non-private counterpart.

Text augmentation is a technique for constructing synthetic data from an under-resourced corpus to improve predictive performance. Synthetic data generation is common in numerous domains. However, recently text augmentation has emerged in natural language processing (NLP) to improve downstream tasks. One of the current state-of-the-art text augmentation techniques is easy data augmentation (EDA), which augments the training data by injecting and replacing synonyms and randomly permuting sentences. One major obstacle with EDA is the need for versatile and complete synonym dictionaries, which cannot be easily found in low-resource languages. To improve the utility of EDA, we propose two extensions, easy distributional data augmentation (EDDA) and type specific similar word replacement (TSSR), which uses semantic word context information and part-of-speech tags for word replacement and augmentation. In an extensive empirical evaluation, we show the utility of the proposed methods, measured by F1 score, on two representative datasets in Swedish as an example of a low-resource language. With the proposed methods, we show that augmented data improve classification performances in low-resource settings.

Overlapped arithmetic codes, featured by overlapped intervals, are a variant of arithmetic codes that can be used to implement Slepian-Wolf coding. To analyze overlapped arithmetic codes, we have proposed two theoretical tools: Coset Cardinality Spectrum (CCS) and Hamming Distance Spectrum (HDS). The former describes how source space is partitioned into cosets (equally or unequally), and the latter describes how codewords are structured within each coset (densely or sparsely). However, until now, these two tools are almost parallel to each other, and it seems that there is no intersection between them. The main contribution of this paper is bridging HDS with CCS through a rigorous mathematical proof. Specifically, HDS can be quickly and accurately calculated with CCS in some cases. All theoretical analyses are perfectly verified by simulation results.

The inductive biases of graph representation learning algorithms are often encoded in the background geometry of their embedding space. In this paper, we show that general directed graphs can be effectively represented by an embedding model that combines three components: a pseudo-Riemannian metric structure, a non-trivial global topology, and a unique likelihood function that explicitly incorporates a preferred direction in embedding space. We demonstrate the representational capabilities of this method by applying it to the task of link prediction on a series of synthetic and real directed graphs from natural language applications and biology. In particular, we show that low-dimensional cylindrical Minkowski and anti-de Sitter spacetimes can produce equal or better graph representations than curved Riemannian manifolds of higher dimensions.

Behaviors of the synthetic characters in current military simulations are limited since they are generally generated by rule-based and reactive computational models with minimal intelligence. Such computational models cannot adapt to reflect the experience of the characters, resulting in brittle intelligence for even the most effective behavior models devised via costly and labor-intensive processes. Observation-based behavior model adaptation that leverages machine learning and the experience of synthetic entities in combination with appropriate prior knowledge can address the issues in the existing computational behavior models to create a better training experience in military training simulations. In this paper, we introduce a framework that aims to create autonomous synthetic characters that can perform coherent sequences of believable behavior while being aware of human trainees and their needs within a training simulation. This framework brings together three mutually complementary components. The first component is a Unity-based simulation environment - Rapid Integration and Development Environment (RIDE) - supporting One World Terrain (OWT) models and capable of running and supporting machine learning experiments. The second is Shiva, a novel multi-agent reinforcement and imitation learning framework that can interface with a variety of simulation environments, and that can additionally utilize a variety of learning algorithms. The final component is the Sigma Cognitive Architecture that will augment the behavior models with symbolic and probabilistic reasoning capabilities. We have successfully created proof-of-concept behavior models leveraging this framework on realistic terrain as an essential step towards bringing machine learning into military simulations.

Knowledge graph completion aims to predict missing relations between entities in a knowledge graph. While many different methods have been proposed, there is a lack of a unifying framework that would lead to state-of-the-art results. Here we develop PathCon, a knowledge graph completion method that harnesses four novel insights to outperform existing methods. PathCon predicts relations between a pair of entities by: (1) Considering the Relational Context of each entity by capturing the relation types adjacent to the entity and modeled through a novel edge-based message passing scheme; (2) Considering the Relational Paths capturing all paths between the two entities; And, (3) adaptively integrating the Relational Context and Relational Path through a learnable attention mechanism. Importantly, (4) in contrast to conventional node-based representations, PathCon represents context and path only using the relation types, which makes it applicable in an inductive setting. Experimental results on knowledge graph benchmarks as well as our newly proposed dataset show that PathCon outperforms state-of-the-art knowledge graph completion methods by a large margin. Finally, PathCon is able to provide interpretable explanations by identifying relations that provide the context and paths that are important for a given predicted relation.

Embedding entities and relations into a continuous multi-dimensional vector space have become the dominant method for knowledge graph embedding in representation learning. However, most existing models ignore to represent hierarchical knowledge, such as the similarities and dissimilarities of entities in one domain. We proposed to learn a Domain Representations over existing knowledge graph embedding models, such that entities that have similar attributes are organized into the same domain. Such hierarchical knowledge of domains can give further evidence in link prediction. Experimental results show that domain embeddings give a significant improvement over the most recent state-of-art baseline knowledge graph embedding models.

Dynamic programming (DP) solves a variety of structured combinatorial problems by iteratively breaking them down into smaller subproblems. In spite of their versatility, DP algorithms are usually non-differentiable, which hampers their use as a layer in neural networks trained by backpropagation. To address this issue, we propose to smooth the max operator in the dynamic programming recursion, using a strongly convex regularizer. This allows to relax both the optimal value and solution of the original combinatorial problem, and turns a broad class of DP algorithms into differentiable operators. Theoretically, we provide a new probabilistic perspective on backpropagating through these DP operators, and relate them to inference in graphical models. We derive two particular instantiations of our framework, a smoothed Viterbi algorithm for sequence prediction and a smoothed DTW algorithm for time-series alignment. We showcase these instantiations on two structured prediction tasks and on structured and sparse attention for neural machine translation.

While existing machine learning models have achieved great success for sentiment classification, they typically do not explicitly capture sentiment-oriented word interaction, which can lead to poor results for fine-grained analysis at the snippet level (a phrase or sentence). Factorization Machine provides a possible approach to learning element-wise interaction for recommender systems, but they are not directly applicable to our task due to the inability to model contexts and word sequences. In this work, we develop two Position-aware Factorization Machines which consider word interaction, context and position information. Such information is jointly encoded in a set of sentiment-oriented word interaction vectors. Compared to traditional word embeddings, SWI vectors explicitly capture sentiment-oriented word interaction and simplify the parameter learning. Experimental results show that while they have comparable performance with state-of-the-art methods for document-level classification, they benefit the snippet/sentence-level sentiment analysis.

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