52 research outputs found

    Arabic-SOS: Segmentation, stemming, and orthography standardization for classical and pre-modern standard Arabic

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    This is an accepted manuscript of an article published by ACM in DATeCH2019: Proceedings of the 3rd International Conference on Digital Access to Textual Cultural Heritage in May 2019, available online: https://doi.org/10.1145/3322905.3322927 The accepted version of the publication may differ from the final published version.While morphological segmentation has always been a hot topic in Arabic, due to the morphological complexity of the language and the orthography, most effort has focused on Modern Standard Arabic. In this paper, we focus on pre-MSA texts. We use the Gradient Boosting algorithm to train a morphological segmenter with a corpus derived from Al-Manar, a late 19th/early 20th century magazine that focused on the Arabic and Islamic heritage. Since most of the cultural heritage Arabic available suffers from substandard orthography, we have trained a machine learner to standardize the text. Our segmentation accuracy reaches 98.47%, and the orthography standardization an F-macro of 0.98 and an F-micro of 0.99. We also produce stemming as a by-product of segmentation

    Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation?

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    Molecular conformation generation (MCG) is a fundamental and important problem in drug discovery. Many traditional methods have been developed to solve the MCG problem, such as systematic searching, model-building, random searching, distance geometry, molecular dynamics, Monte Carlo methods, etc. However, they have some limitations depending on the molecular structures. Recently, there are plenty of deep learning based MCG methods, which claim they largely outperform the traditional methods. However, to our surprise, we design a simple and cheap algorithm (parameter-free) based on the traditional methods and find it is comparable to or even outperforms deep learning based MCG methods in the widely used GEOM-QM9 and GEOM-Drugs benchmarks. In particular, our design algorithm is simply the clustering of the RDKIT-generated conformations. We hope our findings can help the community to revise the deep learning methods for MCG. The code of the proposed algorithm could be found at https://gist.github.com/ZhouGengmo/5b565f51adafcd911c0bc115b2ef027c

    Highly Accurate Quantum Chemical Property Prediction with Uni-Mol+

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    Recent developments in deep learning have made remarkable progress in speeding up the prediction of quantum chemical (QC) properties by removing the need for expensive electronic structure calculations like density functional theory. However, previous methods learned from 1D SMILES sequences or 2D molecular graphs failed to achieve high accuracy as QC properties primarily depend on the 3D equilibrium conformations optimized by electronic structure methods, far different from the sequence-type and graph-type data. In this paper, we propose a novel approach called Uni-Mol+ to tackle this challenge. Uni-Mol+ first generates a raw 3D molecule conformation from inexpensive methods such as RDKit. Then, the raw conformation is iteratively updated to its target DFT equilibrium conformation using neural networks, and the learned conformation will be used to predict the QC properties. To effectively learn this update process towards the equilibrium conformation, we introduce a two-track Transformer model backbone and train it with the QC property prediction task. We also design a novel approach to guide the model's training process. Our extensive benchmarking results demonstrate that the proposed Uni-Mol+ significantly improves the accuracy of QC property prediction in various datasets. We have made the code and model publicly available at \url{https://github.com/dptech-corp/Uni-Mol}

    Boosted ab initio Cryo-EM 3D Reconstruction with ACE-EM

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    The central problem in cryo-electron microscopy (cryo-EM) is to recover the 3D structure from noisy 2D projection images which requires estimating the missing projection angles (poses). Recent methods attempted to solve the 3D reconstruction problem with the autoencoder architecture, which suffers from the latent vector space sampling problem and frequently produces suboptimal pose inferences and inferior 3D reconstructions. Here we present an improved autoencoder architecture called ACE (Asymmetric Complementary autoEncoder), based on which we designed the ACE-EM method for cryo-EM 3D reconstructions. Compared to previous methods, ACE-EM reached higher pose space coverage within the same training time and boosted the reconstruction performance regardless of the choice of decoders. With this method, the Nyquist resolution (highest possible resolution) was reached for 3D reconstructions of both simulated and experimental cryo-EM datasets. Furthermore, ACE-EM is the only amortized inference method that reached the Nyquist resolution

    Light Multi-segment Activation for Model Compression

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    Model compression has become necessary when applying neural networks (NN) into many real application tasks that can accept slightly-reduced model accuracy with strict tolerance to model complexity. Recently, Knowledge Distillation, which distills the knowledge from well-trained and highly complex teacher model into a compact student model, has been widely used for model compression. However, under the strict requirement on the resource cost, it is quite challenging to achieve comparable performance with the teacher model, essentially due to the drastically-reduced expressiveness ability of the compact student model. Inspired by the nature of the expressiveness ability in Neural Networks, we propose to use multi-segment activation, which can significantly improve the expressiveness ability with very little cost, in the compact student model. Specifically, we propose a highly efficient multi-segment activation, called Light Multi-segment Activation (LMA), which can rapidly produce multiple linear regions with very few parameters by leveraging the statistical information. With using LMA, the compact student model is capable of achieving much better performance effectively and efficiently, than the ReLU-equipped one with same model scale. Furthermore, the proposed method is compatible with other model compression techniques, such as quantization, which means they can be used jointly for better compression performance. Experiments on state-of-the-art NN architectures over the real-world tasks demonstrate the effectiveness and extensibility of the LMA

    3D Molecular Generation via Virtual Dynamics

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    Structure-based drug design, i.e., finding molecules with high affinities to the target protein pocket, is one of the most critical tasks in drug discovery. Traditional solutions, like virtual screening, require exhaustively searching on a large molecular database, which are inefficient and cannot return novel molecules beyond the database. The pocket-based 3D molecular generation model, i.e., directly generating a molecule with a 3D structure and binding position in the pocket, is a new promising way to address this issue. Herein, we propose VD-Gen, a novel pocket-based 3D molecular generation pipeline. VD-Gen consists of several carefully designed stages to generate fine-grained 3D molecules with binding positions in the pocket cavity end-to-end. Rather than directly generating or sampling atoms with 3D positions in the pocket like in early attempts, in VD-Gen, we first randomly initialize many virtual particles in the pocket; then iteratively move these virtual particles, making the distribution of virtual particles approximate the distribution of molecular atoms. After virtual particles are stabilized in 3D space, we extract a 3D molecule from them. Finally, we further refine atoms in the extracted molecule by iterative movement again, to get a high-quality 3D molecule, and predict a confidence score for it. Extensive experiment results on pocket-based molecular generation demonstrate that VD-Gen can generate novel 3D molecules to fill the target pocket cavity with high binding affinities, significantly outperforming previous baselines

    Adversarial Meta Sampling for Multilingual Low-Resource Speech Recognition

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    Low-resource automatic speech recognition (ASR) is challenging, as the low-resource target language data cannot well train an ASR model. To solve this issue, meta-learning formulates ASR for each source language into many small ASR tasks and meta-learns a model initialization on all tasks from different source languages to access fast adaptation on unseen target languages. However, for different source languages, the quantity and difficulty vary greatly because of their different data scales and diverse phonological systems, which leads to task-quantity and task-difficulty imbalance issues and thus a failure of multilingual meta-learning ASR (MML-ASR). In this work, we solve this problem by developing a novel adversarial meta sampling (AMS) approach to improve MML-ASR. When sampling tasks in MML-ASR, AMS adaptively determines the task sampling probability for each source language. Specifically, for each source language, if the query loss is large, it means that its tasks are not well sampled to train ASR model in terms of its quantity and difficulty and thus should be sampled more frequently for extra learning. Inspired by this fact, we feed the historical task query loss of all source language domain into a network to learn a task sampling policy for adversarially increasing the current query loss of MML-ASR. Thus, the learnt task sampling policy can master the learning situation of each language and thus predicts good task sampling probability for each language for more effective learning. Finally, experiment results on two multilingual datasets show significant performance improvement when applying our AMS on MML-ASR, and also demonstrate the applicability of AMS to other low-resource speech tasks and transfer learning ASR approaches.Comment: accepted in AAAI202
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