Coarse-graining is a molecular modeling technique in which an atomistic system is represented in a simplified fashion that retains the most significant system features that contribute to a target output, while removing the degrees of freedom that are less relevant. This reduction in model complexity allows coarse-grained molecular simulations to reach increased spatial and temporal scales compared to corresponding all-atom models. A core challenge in coarse-graining is to construct a force field that represents the interactions in the new representation in a way that preserves the atomistic-level properties. Many approaches to building coarse-grained force fields have limited transferability between different thermodynamic conditions as a result of averaging over internal fluctuations at a specific thermodynamic state point. Here, we use a graph-convolutional neural network architecture, the Hierarchically Interacting Particle Neural Network with Tensor Sensitivity (HIP-NN-TS), to develop a highly automated training pipeline for coarse grained force fields which allows for studying the transferability of coarse-grained models based on the force-matching approach. We show that this approach not only yields highly accurate force fields, but also that these force fields are more transferable through a variety of thermodynamic conditions. These results illustrate the potential of machine learning techniques such as graph neural networks to improve the construction of transferable coarse-grained force fields.

Representation Learning (RL) plays a pivotal role in the success of many problems including cyberattack detection. Most of the RL methods for cyberattack detection are based on the latent vector of Auto-Encoder (AE) models. An AE transforms raw data into a new latent representation that better exposes the underlying characteristics of the input data. Thus, it is very useful for identifying cyberattacks. However, due to the heterogeneity and sophistication of cyberattacks, the representation of AEs is often entangled/mixed resulting in the difficulty for downstream attack detection models. To tackle this problem, we propose a novel mod called Twin Auto-Encoder (TAE). TAE deterministically transforms the latent representation into a more distinguishable representation namely the \textit{separable representation} and the reconstructsuct the separable representation at the output. The output of TAE called the \textit{reconstruction representation} is input to downstream models to detect cyberattacks. We extensively evaluate the effectiveness of TAE using a wide range of bench-marking datasets. Experiment results show the superior accuracy of TAE over state-of-the-art RL models and well-known machine learning algorithms. Moreover, TAE also outperforms state-of-the-art models on some sophisticated and challenging attacks. We then investigate various characteristics of TAE to further demonstrate its superiority.

Non-autoregressive automatic speech recognition (NASR) models have gained attention due to their parallelism and fast inference. The encoder-based NASR, e.g. connectionist temporal classification (CTC), can be initialized from the speech foundation models (SFM) but does not account for any dependencies among intermediate tokens. The encoder-decoder-based NASR, like CTC alignment-based single-step non-autoregressive transformer (CASS-NAT), can mitigate the dependency problem but is not able to efficiently integrate SFM. Inspired by the success of recent work of speech-text joint pre-training with a shared transformer encoder, we propose a new encoder-based NASR, UniEnc-CASSNAT, to combine the advantages of CTC and CASS-NAT. UniEnc-CASSNAT consists of only an encoder as the major module, which can be the SFM. The encoder plays the role of both the CASS-NAT encoder and decoder by two forward passes. The first pass of the encoder accepts the speech signal as input, while the concatenation of the speech signal and the token-level acoustic embedding is used as the input for the second pass. Examined on the Librispeech 100h, MyST, and Aishell1 datasets, the proposed UniEnc-CASSNAT achieves state-of-the-art NASR results and is better or comparable to CASS-NAT with only an encoder and hence, fewer model parameters. Our codes are publicly available.

Generalization and sample efficiency have been long-standing issues concerning reinforcement learning, and thus the field of Offline Meta-Reinforcement Learning~(OMRL) has gained increasing attention due to its potential of solving a wide range of problems with static and limited offline data. Existing OMRL methods often assume sufficient training tasks and data coverage to apply contrastive learning to extract task representations. However, such assumptions are not applicable in several real-world applications and thus undermine the generalization ability of the representations. In this paper, we consider OMRL with two types of data limitations: limited training tasks and limited behavior diversity and propose a novel algorithm called GENTLE for learning generalizable task representations in the face of data limitations. GENTLE employs Task Auto-Encoder~(TAE), which is an encoder-decoder architecture to extract the characteristics of the tasks. Unlike existing methods, TAE is optimized solely by reconstruction of the state transition and reward, which captures the generative structure of the task models and produces generalizable representations when training tasks are limited. To alleviate the effect of limited behavior diversity, we consistently construct pseudo-transitions to align the data distribution used to train TAE with the data distribution encountered during testing. Empirically, GENTLE significantly outperforms existing OMRL methods on both in-distribution tasks and out-of-distribution tasks across both the given-context protocol and the one-shot protocol.

The central question in representation learning is what constitutes a good or meaningful representation. In this work we argue that if we consider data with inherent cluster structures, where clusters can be characterized through different means and covariances, those data structures should be represented in the embedding as well. While Autoencoders (AE) are widely used in practice for unsupervised representation learning, they do not fulfil the above condition on the embedding as they obtain a single representation of the data. To overcome this we propose a meta-algorithm that can be used to extend an arbitrary AE architecture to a tensorized version (TAE) that allows for learning cluster-specific embeddings while simultaneously learning the cluster assignment. For the linear setting we prove that TAE can recover the principle components of the different clusters in contrast to principle component of the entire data recovered by a standard AE. We validated this on planted models and for general, non-linear and convolutional AEs we empirically illustrate that tensorizing the AE is beneficial in clustering and de-noising tasks.

Recently introduced transformer-based article encoders (TAEs) designed to produce similar vector representations for mutually related scientific articles have demonstrated strong performance on benchmark datasets for scientific article recommendation. However, the existing benchmark datasets are predominantly focused on single domains and, in some cases, contain easy negatives in small candidate pools. Evaluating representations on such benchmarks might obscure the realistic performance of TAEs in setups with thousands of articles in candidate pools. In this work, we evaluate TAEs on large benchmarks with more challenging candidate pools. We compare the performance of TAEs with a lexical retrieval baseline model BM25 on the task of citation recommendation, where the model produces a list of recommendations for citing in a given input article. We find out that BM25 is still very competitive with the state-of-the-art neural retrievers, a finding which is surprising given the strong performance of TAEs on small benchmarks. As a remedy for the limitations of the existing benchmarks, we propose a new benchmark dataset for evaluating scientific article representations: Multi-Domain Citation Recommendation dataset (MDCR), which covers different scientific fields and contains challenging candidate pools.

As a widely used method in machine learning, principal component analysis (PCA) shows excellent properties for dimensionality reduction. It is a serious problem that PCA is sensitive to outliers, which has been improved by numerous Robust PCA (RPCA) versions. However, the existing state-of-the-art RPCA approaches cannot easily remove or tolerate outliers by a non-iterative manner. To tackle this issue, this paper proposes Angular Embedding (AE) to formulate a straightforward RPCA approach based on angular density, which is improved for large scale or high-dimensional data. Furthermore, a trimmed AE (TAE) is introduced to deal with data with large scale outliers. Extensive experiments on both synthetic and real-world datasets with vector-level or pixel-level outliers demonstrate that the proposed AE/TAE outperforms the state-of-the-art RPCA based methods.

We propose a new probabilistic method for unsupervised recovery of corrupted data. Given a large ensemble of degraded samples, our method recovers accurate posteriors of clean values, allowing the exploration of the manifold of possible reconstructed data and hence characterising the underlying uncertainty. In this setting, direct application of classical variational methods often gives rise to collapsed densities that do not adequately explore the solution space. Instead, we derive our novel reduced entropy condition approximate inference method that results in rich posteriors. We test our model in a data recovery task under the common setting of missing values and noise, demonstrating superior performance to existing variational methods for imputation and de-noising with different real data sets.

Scientists believe the world will see it's first working thermonuclear fusion reactor by the year 2025. That's a tall order in short form, especially when you consider that fusion has been "almost here" for nearly a century. Fusion reactors – not to be confused with common fission reactors – are the holiest of Grails when it comes to physics achievements. According to most experts, a successful fusion reactor would function as a near-unlimited source of energy. In other words, if there's a working demonstration of an actual fusion reactor by 2025, we could see an end to the global energy crisis within a few decades.

Current clinical practice guidelines for managing Coronary Artery Disease (CAD) account for general cardiovascular risk factors. However, they do not present a framework that considers personalized patient-specific characteristics. Using the electronic health records of 21,460 patients, we created data-driven models for personalized CAD management that significantly improve health outcomes relative to the standard of care. We develop binary classifiers to detect whether a patient will experience an adverse event due to CAD within a 10-year time frame. Combining the patients' medical history and clinical examination results, we achieve 81.5% AUC. For each treatment, we also create a series of regression models that are based on different supervised machine learning algorithms. We are able to estimate with average R squared = 0.801 the time from diagnosis to a potential adverse event (TAE) and gain accurate approximations of the counterfactual treatment effects. Leveraging combinations of these models, we present ML4CAD, a novel personalized prescriptive algorithm. Considering the recommendations of multiple predictive models at once, ML4CAD identifies for every patient the therapy with the best expected outcome using a voting mechanism. We evaluate its performance by measuring the prescription effectiveness and robustness under alternative ground truths. We show that our methodology improves the expected TAE upon the current baseline by 24.11%, increasing it from 4.56 to 5.66 years. The algorithm performs particularly well for the male (24.3% improvement) and Hispanic (58.41% improvement) subpopulations. Finally, we create an interactive interface, providing physicians with an intuitive, accurate, readily implementable, and effective tool.