nils-herrmann/clean_scirepeval huggingface dataset:
All SMILES Variational Autoencoder

Variational autoencoders (VAEs) defined over SMILES string and graph-based representations of molecules promise to improve the optimization of molecular properties, thereby revolutionizing the pharmaceuticals and materials industries. However, these VAEs are hindered by the non-unique nature of SMILES strings and the computational cost of graph convolutions. To efficiently pass messages along all paths through the molecular graph, we encode multiple SMILES strings of a single molecule using a set of stacked recurrent neural networks, pooling hidden representations of each atom between SMILES representations, and use attentional pooling to build a final fixed-length latent representation. By then decoding to a disjoint set of SMILES strings of the molecule, our All SMILES VAE learns an almost bijective mapping between molecules and latent representations near the high-probability-mass subspace of the prior. Our SMILES-derived but molecule-based latent representations significantly surpass the state-of-the-art in a variety of fully- and semi-supervised property regression and molecular property optimization tasks.
Reinforcement Learning for Mean Field Game

Stochastic games provide a framework for interactions among multiple agents and enable a myriad of applications. In these games, agents decide on actions simultaneously. After taking an action, the state of every agent updates to the next state, and each agent receives a reward. However, finding an equilibrium (if exists) in this game is often difficult when the number of agents becomes large. This paper focuses on finding a mean-field equilibrium (MFE) in an action-coupled stochastic game setting in an episodic framework. It is assumed that an agent can approximate the impact of the other agents’ by the empirical distribution of the mean of the actions. All agents know the action distribution and employ lower-myopic best response dynamics to choose the optimal oblivious strategy. This paper proposes a posterior sampling-based approach for reinforcement learning in the mean-field game, where each agent samples a transition probability from the previous transitions. We show that the policy and action distributions converge to the optimal oblivious strategy and the limiting distribution, respectively, which constitute an MFE.
Multi-modal Discriminative Model for Vision-and-Language Navigation

Vision-and-Language Navigation (VLN) is a natural language grounding task where agents have to interpret natural language instructions in the context of visual scenes in a dynamic environment to achieve prescribed navigation goals. Successful agents must have the ability to parse natural language of varying linguistic styles, ground them in potentially unfamiliar scenes, plan and react with ambiguous environmental feedback. Generalization ability is limited by the amount of human annotated data. In particular, paired vision-language sequence data is expensive to collect. We develop a discriminator that evaluates how well an instruction explains a given path in VLN task using multi-modal alignment. Our study reveals that only a small fraction of the high-quality augmented data from Fried et al., as scored by our discriminator, is useful for training VLN agents with similar performance. We also show that a VLN agent warm-started with pre-trained components from the discriminator outperforms the benchmark success rates of 35.5 by 10% relative measure.
Efficient Forward Architecture Search

We propose a neural architecture search (NAS) algorithm, Petridish, to iteratively add shortcut connections to existing network layers. The added shortcut connections effectively perform gradient boosting on the augmented layers. The proposed algorithm is motivated by the feature selection algorithm forward stage-wise linear regression, since we consider NAS as a generalization of feature selection for regression, where NAS selects shortcuts among layers instead of selecting features. In order to reduce the number of trials of possible connection combinations, we train jointly all possible connections at each stage of growth while leveraging feature selection techniques to choose a subset of them. We experimentally show this process to be an efficient forward architecture search algorithm that can find competitive models using few GPU days in both the search space of repeatable network modules (cell-search) and the space of general networks (macro-search). Petridish is particularly well-suited for warm-starting from existing models crucial for lifelong-learning scenarios.
DFS: A Dataset File System for Data Discovering Users

Many research questions can be answered quickly and efficiently using data already collected for previous research. This practice is called secondary data analysis, and has gained popularity due to lower costs and improved research efficiency. In this paper we propose DFS, a file system to standardize the metadata representation of datasets, and DDU, a scalable architecture based on DFS for semi-automated metadata generation and data recommendation on the cloud, and explores their implications on datasets stored in digital libraries.
Rewarding Smatch: Transition-Based AMR Parsing with Reinforcement Learning

Our work involves enriching the Stack-LSTM transition-based AMR parser (Ballesteros and Al-Onaizan, 2017) by augmenting training with Policy Learning and rewarding the Smatch score of sampled graphs. In addition, we also combined several AMR-to-text alignments with an attention mechanism and we supplemented the parser with pre-processed concept identification, named entities and contextualized embeddings. We achieve a highly competitive performance that is comparable to the best published results. We show an in-depth study ablating each of the new components of the parser.
MolecularRNN: Generating realistic molecular graphs with optimized properties

Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph recurrent generative model for molecular structures. Our model generates diverse realistic molecular graphs after likelihood pretraining on a big database of molecules. We perform an analysis of our pretrained models on large-scale generated datasets of 1 million samples. Further, the model is tuned with policy gradient algorithm, provided a critic that estimates the reward for the property of interest. We show a significant distribution shift to the desired range for lipophilicity, drug-likeness, and melting point outperforming state-of-the-art works. With the use of rejection sampling based on valency constraints, our model yields 100% validity. Moreover, we show that invalid molecules provide a rich signal to the model through the use of structure penalty in our reinforcement learning pipeline.
Supervised Online Hashing via Similarity Distribution Learning

Online hashing has attracted extensive research attention when facing streaming data. Most online hashing methods, learning binary codes based on pairwise similarities of training instances, fail to capture the semantic relationship, and suffer from a poor generalization in large-scale applications due to large variations. In this paper, we propose to model the similarity distributions between the input data and the hashing codes, upon which a novel supervised online hashing method, dubbed as Similarity Distribution based Online Hashing (SDOH), is proposed, to keep the intrinsic semantic relationship in the produced Hamming space. Specifically, we first transform the discrete similarity matrix into a probability matrix via a Gaussian-based normalization to address the extremely imbalanced distribution issue. And then, we introduce a scaling Student t-distribution to solve the challenging initialization problem, and efficiently bridge the gap between the known and unknown distributions. Lastly, we align the two distributions via minimizing the Kullback-Leibler divergence (KL-diverence) with stochastic gradient descent (SGD), by which an intuitive similarity constraint is imposed to update hashing model on the new streaming data with a powerful generalizing ability to the past data. Extensive experiments on three widely-used benchmarks validate the superiority of the proposed SDOH over the state-of-the-art methods in the online retrieval task.
Residual Networks as Nonlinear Systems: Stability Analysis using Linearization

We regard pre-trained residual networks (ResNets) as nonlinear systems and use linearization, a common method used in the qualitative analysis of nonlinear systems, to understand the behavior of the networks under small perturbations of the input images. We work with ResNet-56 and ResNet-110 trained on the CIFAR-10 data set. We linearize these networks at the level of residual units and network stages, and the singular value decomposition is used in the stability analysis of these components. It is found that most of the singular values of the linearizations of residual units are 1 and, in spite of the fact that the linearizations depend directly on the activation maps, the singular values differ only slightly for different input images. However, adjusting the scaling of the skip connection or the values of the weights in a residual unit has a significant impact on the singular value distributions. Inspection of how random and adversarial perturbations of input images propagate through the network reveals that there is a dramatic jump in the magnitude of adversarial perturbations towards the end of the final stage of the network that is not present in the case of random perturbations. We attempt to gain a better understanding of this phenomenon by projecting the perturbations onto singular vectors of the linearizations of the residual units.
Vehicle Detection in Deep Learning

Computer vision is developing rapidly with the support of deep learning techniques. This thesis proposes an advanced vehicle-detection model based on an improvement to classical convolutional neural networks. The advanced model was applied against a vehicle detection benchmark and was built to detect on-road objects. First, we propose a high-level architecture for our advanced model, which utilizes different state-of-the-art deep learning techniques. Then, we utilize the residual neural networks and region proposal network to achieve competitive performance according to the vehicle detection benchmark. Lastly, we describe the developing trend of vehicle detection techniques and the future direction of research.
Rethinking Table Parsing using Graph Neural Networks

Document structure analysis, such as zone segmentation and table parsing, is a complex problem in document processing and is an active area of research. The recent success of deep learning in solving various computer vision and machine learning problems has not been reflected in document structure analysis since conventional neural networks are not well suited to the input structure of the problem. In this paper, we propose an architecture based on graph networks as a better alternative to standard neural networks for table parsing. We argue that graph networks are a more natural choice for these problems, and explore two gradient-based graph neural networks. Our proposed architecture combines the benefits of convolutional neural networks for visual feature extraction and graph networks for dealing with the problem structure. We empirically demonstrate that our method outperforms the baseline by a significant margin. In addition, we identify the lack of large scale datasets as a major hindrance for deep learning research for structure analysis, and present a new large scale synthetic dataset for the problem of table parsing. Finally, we open-source our implementation of dataset generation and the training framework of our graph networks to promote reproducible research in this direction.
Deep ordinal classification based on cumulative link models

This paper proposes a deep convolutional neural network model for ordinal regression by considering a family of probabilistic ordinal link functions in the output layer. The link functions are those used for cumulative link models, which are traditional statistical linear models based on projecting each pattern into a 1-dimensional space. A set of ordered thresholds splits this space into the different classes of the problem. In our case, the projections are estimated by a non-linear deep neural network. To further improve the results, we combine these ordinal models with a loss function that takes into account the distance between the categories, based on the weighted Kappa index. Three different link functions are studied in the experimental study, and the results are contrasted with statistical analysis. The experiments run over two different ordinal classification problems, and the statistical tests confirm that these models improve the results of a nominal model and outperform other proposals considered in the literature.
Deep Representation Learning for Road Detection through Siamese Network

Robust road detection is a key challenge in safe autonomous driving. Recently, with the rapid development of 3D sensors, more and more researchers are trying to fuse information across different sensors to improve the performance of road detection. Although many successful works have been achieved in this field, methods for data fusion under deep learning framework is still an open problem. In this paper, we propose a Siamese deep neural network based on FCN-8s to detect road region. Our method uses data collected from a monocular color camera and a Velodyne-64 LiDAR sensor. We project the LiDAR point clouds onto the image plane to generate LiDAR images and feed them into one of the branches of the network. The RGB images are fed into another branch of our proposed network. The feature maps that these two branches extract in multiple scales are fused before each pooling layer, via padding additional fusion layers. Extensive experimental results on public dataset KITTI ROAD demonstrate the effectiveness of our proposed approach.
Extending Deep Model Predictive Control with Safety Augmented Value Estimation from Demonstrations

Reinforcement learning (RL) for robotics is challenging due to the difficulty in hand-engineering a dense cost function, which can lead to unintended behavior, and dynamical uncertainty, which makes it hard to enforce constraints during learning. We address these issues with a new model-based reinforcement learning algorithm, safety augmented value estimation from demonstrations (SAVED), which uses supervision that only identifies task completion and a modest set of suboptimal demonstrations to constrain exploration and learn efficiently while handling complex constraints. We derive iterative improvement guarantees for SAVED under known stochastic nonlinear systems. We then compare SAVED with 3 state-of-the-art model-based and model-free RL algorithms on 6 standard simulation benchmarks involving navigation and manipulation and 2 real-world tasks on the da Vinci surgical robot. Results suggest that SAVED outperforms prior methods in terms of success rate, constraint satisfaction, and sample efficiency, making it feasible to safely learn complex maneuvers directly on a real robot in less than an hour. For tasks on the robot, baselines succeed less than 5% of the time while SAVED has a success rate of over 75% in the first 50 training iterations.
Improving the resolution of Cryo-EM single particle analysis

We presented a new 3D refinement method for Cryo-EM single particle analysis which can improve the resolution of final electron density map in this paper. We proposed to enforce both sparsity and smoothness to improve the regularity of electron density map in the refinement process. To achieve this goal, we designed a novel type of real space penalty function and incorporated it into the refinement process. We bridged the backprojection step with local kernel regression, thus enabling us to embed the 3D model in reproducing kernel Hilbert space using specific kernels. We also proposed a first order method to solve the resulting optimization problem and implemented it efficiently with CUDA. We compared the performance of our new method with respect to the traditional method on real datasets using a set of widely used metrics for Cryo-EM model validation. We demonstrated that our method outperforms the traditional method in terms of those metrics. The implementation of our method can be found at this https URL.
TACNet: Transition-Aware Context Network for Spatio-Temporal Action Detection

Current state-of-the-art approaches for spatio-temporal action detection have achieved impressive results but remain unsatisfactory for temporal extent detection. The main reason comes from that, there are some ambiguous states similar to the real actions which may be treated as target actions even by a well trained network. In this paper, we define these ambiguous samples as “transitional states”, and propose a Transition-Aware Context Network (TACNet) to distinguish transitional states. The proposed TACNet includes two main components, i.e., temporal context detector and transition-aware classifier. The temporal context detector can extract long-term context information with constant time complexity by constructing a recurrent network. The transition-aware classifier can further distinguish transitional states by classifying action and transitional states simultaneously. Therefore, the proposed TACNet can substantially improve the performance of spatio-temporal action detection. We extensively evaluate the proposed TACNet on UCF101-24 and J-HMDB datasets. The experimental results demonstrate that TACNet obtains competitive performance on JHMDB and significantly outperforms the state-of-the-art methods on the untrimmed UCF101 24 in terms of both frame-mAP and video-mAP.
Cross-sectional Learning of Extremal Dependence Among Financial Assets

We propose a novel probabilistic model to facilitate the learning of multivariate tail dependence of multiple financial assets. Our method allows one to construct from known random vectors, e.g., standard normal, sophisticated joint heavy-tailed random vectors featuring not only distinct marginal tail heaviness, but also flexible tail dependence structure. The novelty lies in that pairwise tail dependence between any two dimensions is modeled separately from their correlation, and can vary respectively according to its own parameter rather than the correlation parameter, which is an essential advantage over many commonly used methods such as multivariate $t$ or elliptical distribution. It is also intuitive to interpret, easy to track, and simple to sample comparing to the copula approach. We show its flexible tail dependence structure through simulation. Coupled with a GARCH model to eliminate serial dependence of each individual asset return series, we use this novel method to model and forecast multivariate conditional distribution of stock returns, and obtain notable performance improvements in multi-dimensional coverage tests. Besides, our empirical finding about the asymmetry of tails of the idiosyncratic component as well as the market component is interesting and worth to be well studied in the future.
Content Word-based Sentence Decoding and Evaluating for Open-domain Neural Response Generation

Various encoder-decoder models have been applied to response generation in open-domain dialogs, but a majority of conventional models directly learn a mapping from lexical input to lexical output without explicitly modeling intermediate representations. Utilizing language hierarchy and modeling intermediate information have been shown to benefit many language understanding and generation tasks. Motivated by Broca's aphasia, we propose to use a content word sequence as an intermediate representation for open-domain response generation. Experimental results show that the proposed method improves content relatedness of produced responses, and our models can often choose correct grammar for generated content words. Meanwhile, instead of evaluating complete sentences, we propose to compute conventional metrics on content word sequences, which is a better indicator of content relevance.
Ordinal Bucketing for Game Trees using Dynamic Quantile Approximation

In this paper, we present a simple and cheap ordinal bucketing algorithm that approximately generates q-quantiles from an incremental data stream. The bucketing is done dynamically in the sense that the amount of buckets q increases with the number of seen samples. We show how this can be used in Ordinal Monte Carlo Tree Search (OMCTS) to yield better bounds on time and space complexity, especially in the presence of noisy rewards. Besides complexity analysis and quality tests of quantiles, we evaluate our method using OMCTS in the General Video Game Framework (GVGAI). Our results demonstrate its dominance over vanilla Monte Carlo Tree Search in the presence of noise, where OMCTS without bucketing has a very bad time and space complexity.
MultiQA: An Empirical Investigation of Generalization and Transfer in Reading Comprehension

A large number of reading comprehension (RC) datasets has been created recently, but little analysis has been done on whether they generalize to one another, and the extent to which existing datasets can be leveraged for improving performance on new ones. In this paper, we conduct such an investigation over ten RC datasets, training on one or more source RC datasets, and evaluating generalization, as well as transfer to a target RC dataset. We analyze the factors that contribute to generalization, and show that training on a source RC dataset and transferring to a target dataset substantially improves performance, even in the presence of powerful contextual representations from BERT (Devlin et al., 2019). We also find that training on multiple source RC datasets leads to robust generalization and transfer, and can reduce the cost of example collection for a new RC dataset. Following our analysis, we propose MultiQA, a BERT-based model, trained on multiple RC datasets, which leads to state-of-the-art performance on five RC datasets. We share our infrastructure for the benefit of the research community.
Combining Noise-to-Image and Image-to-Image GANs: Brain MR Image Augmentation for Tumor Detection

Convolutional Neural Networks (CNNs) achieve excellent computer-assisted diagnosis with sufficient annotated training data. However, most medical imaging datasets are small and fragmented. In this context, Generative Adversarial Networks (GANs) can synthesize realistic/diverse additional training images to fill the data lack in the real image distribution; researchers have improved classification by augmenting data with noise-to-image (e.g., random noise samples to diverse pathological images) or image-to-image GANs (e.g., a benign image to a malignant one). Yet, no research has reported results combining noise-to-image and image-to-image GANs for further performance boost. Therefore, to maximize the DA effect with the GAN combinations, we propose a two-step GAN-based DA that generates and refines brain Magnetic Resonance (MR) images with/without tumors separately: ( ${i}$ ) Progressive Growing of GANs (PGGANs), multi-stage noise-to-image GAN for high-resolution MR image generation, first generates realistic/diverse $256\times 256$ images; (ii) Multimodal UNsupervised Image-to-image Translation (MUNIT) that combines GANs/Variational AutoEncoders or SimGAN that uses a DA-focused GAN loss, further refines the texture/shape of the PGGAN-generated images similarly to the real ones. We thoroughly investigate CNN-based tumor classification results, also considering the influence of pre-training on ImageNet and discarding weird-looking GAN-generated images. The results show that, when combined with classic DA, our two-step GAN-based DA can significantly outperform the classic DA alone, in tumor detection (i.e., boosting sensitivity 93.67% to 97.48%) and also in other medical imaging tasks.