nils-herrmann/clean_scirepeval huggingface dataset:
Demystifying Graph Neural Network Via Graph Filter Assessment
Authors: Yewen Wang, Ziniu Hu, Yusong Ye, Yizhou Sun

Graph Neural Networks (GNNs) have received tremendous attention recently due to their power in handling graph data for different downstream tasks across different application domains. The key of GNN is its graph convolutional filters, and recently various kinds of filters are designed. However, there still lacks in-depth analysis on (1) Whether there exists a best filter that can perform best on all graph data; (2) Which graph properties will influence the optimal choice of graph filter; (3) How to design appropriate filter adaptive to the graph data. In this paper, we focus on addressing the above three questions. We first propose a novel assessment tool to evaluate the effectiveness of graph convolutional filters for a given graph. Using the assessment tool, we find out that there is no single filter as a `silver bullet' that perform the best on all possible graphs. In addition, different graph structure properties will influence the optimal graph convolutional filter's design choice. Based on these findings, we develop Adaptive Filter Graph Neural Network (AFGNN), a simple but powerful model that can adaptively learn task-specific filter. For a given graph, it leverages graph filter assessment as regularization and learns to combine from a set of base filters. Experiments on both synthetic and real-world benchmark datasets demonstrate that our proposed model can indeed learn an appropriate filter and perform well on graph tasks.
Molecular Graph Enhanced Transformer for Retrosynthesis Prediction
Authors: Kelong Mao, Peilin Zhao, Tingyang Xu, Yu Rong, Xi Xiao, Junzhou Huang

With massive possible synthetic routes in chemistry, retrosynthesis prediction is still a challenge for researchers. Recently, retrosynthesis prediction is formulated as a Machine Translation (MT) task. Namely, since each molecule can be represented as a Simpliﬁed Molecular-Input Line-Entry System (SMILES) string, the process of synthesis is analogized to a process of language translation from reactants to products. However, the MT models that applied on SMILES data usually ignore the information of natural atomic connections and the topology of molecules. In this paper, we propose a Graph Enhanced Transformer (GET) framework, which adopts both the sequential and graphical information of molecules. Four different GET designs are proposed, which fuse the SMILES representations with atom embedding learned from our improved Graph Neural Network (GNN). Empirical results show that our model signiﬁcantly outperforms the Transformer model in test accuracy.
Molecule Optimization by Explainable Evolution
Authors: Binghong Chen, Tianzhe Wang, Chengtao Li, Hanjun Dai, Le Song

Optimizing molecules for desired properties is a fundamental yet challenging task in chemistry, material science, and drug discovery. This paper develops a novel algorithm for optimizing molecular properties via an Expectation-Maximization (EM) like explainable evolutionary process. The algorithm is designed to mimic human experts in the process of searching for desirable molecules and alternate between two stages: the first stage on explainable local search which identifies rationales, i.e., critical subgraph patterns accounting for desired molecular properties, and the second stage on molecule completion which explores the larger space of molecules containing good rationales. We test our approach against various baselines on a real-world multi-property optimization task where each method is given the same number of queries to the property oracle. We show that our evolution-by-explanation algorithm is 79% better than the best baseline in terms of a generic metric combining aspects such as success rate, novelty, and diversity. Human expert evaluation on optimized molecules shows that 60% of top molecules obtained from our methods are deemed successful.
LatTe Flows: Latent Temporal Flows for Multivariate Sequence Analysis 
Authors: Magda Amiridi, Gregory Darnell, Sean Jewell

We introduce Latent Temporal Flows (\emph{LatTe-Flows}), a method for probabilistic multivariate time-series analysis tailored for high dimensional systems whose temporal dynamics are driven by variations in a lower-dimensional discriminative subspace. We perform indirect learning from hidden traits of observed sequences by assuming that the random vector representing the data is generated from an unobserved low-dimensional latent vector. \emph{LatTe-Flows} jointly learns auto-encoder mappings to a latent space and learns the temporal distribution of lower-dimensional embeddings of input sequences. Since encoder networks retain only the essential information to generate a latent manifold, the temporal distribution transitions can be more efficiently uncovered by time conditioned Normalizing Flows. The learned latent effects can then be directly transferred into the observed space through the decoder network. We demonstrate that the proposed method significantly outperforms the state-of-the-art on multi-step forecasting benchmarks, while enjoying reduced computational complexity on several real-world datasets. We apply {\emph{LatTe-Flows}} to a challenging sensor-signal forecasting task, using multivariate time-series measurements collected by wearable devices, an increasingly relevant health application.
A preconditioned accelerated stochastic gradient descent algorithm
Authors: Alexandru Onose, Seyed Iman Mossavat, Henk-Jan H. Smilde

We propose a preconditioned accelerated stochastic gradient method suitable for large scale optimization. We derive sufficient convergence conditions for the minimization of convex functions using a generic class of diagonal preconditioners and provide a formal convergence proof based on a framework originally used for on-line learning. Inspired by recent popular adaptive per-feature algorithms, we propose a specific preconditioner based on the second moment of the gradient. The sufficient convergence conditions motivate a critical adaptation of the per-feature updates in order to ensure convergence. We show empirical results for the minimization of convex and non-convex cost functions, in the context of neural network training. The method compares favorably with respect to current, first order, stochastic optimization methods.
Information Bottleneck: Exact Analysis of (Quantized) Neural Networks
Authors: Stephan Sloth Lorenzen, Christian Igel, Mads Nielsen

The information bottleneck (IB) principle has been suggested as a way to analyze deep neural networks. The learning dynamics are studied by inspecting the mutual information (MI) between the hidden layers and the input and output. Notably, separate fitting and compression phases  during training have been reported. This led to some controversy including claims that the observations are not reproducible and strongly dependent on the type of activation function used as well as on the way the MI is estimated. Our study confirms that  different ways of binning  when computing the MI lead to qualitatively different results, either supporting or refusing IB conjectures.
To resolve the controversy, we study the IB principle in settings where MI is non-trivial and can be computed exactly. We monitor the dynamics of quantized neural networks, that is, we discretize the whole deep learning system so that no approximation is required when computing the MI. This allows us to quantify the information flow without measurement errors. 
In this setting, we observed a fitting phase for all layers and a compression phase for the output layer in all experiments; the compression in the hidden layers was dependent on the type of activation function. Our study shows that the initial IB results were not artifacts of binning when computing the MI. However, the critical claim that the compression phase may not be observed for some networks also holds true.
Towards Finding Longer Proofs
Authors: Zsolt Zombori, Adrián Csiszárik, Henryk Michalewski, Cezary Kaliszyk, Josef Urban

We present a reinforcement learning (RL) based guidance system for automated theorem proving geared towards Finding Longer Proofs (FLoP). FLoP is a step towards learning to reason by analogy, reducing the dependence on large scale search in automated theorem provers. We use several simple, structured datasets with very long proofs to show that FLoP can successfully generalise a single training proof to a large class of related problems, implementing a simple form of analogical reasoning. On these benchmarks, FLoP is competitive with strong theorem provers despite using very limited search.
Do We Need Anisotropic Graph Neural Networks?
Authors: Shyam A. Tailor, Felix Opolka, Pietro Lio, Nicholas Donald Lane

Common wisdom in the graph neural network (GNN) community dictates that anisotropic models---in which messages sent between nodes are a function of both the source and target node---are required to achieve state-of-the-art performance. Benchmarks to date have demonstrated that these models perform better than comparable isotropic models---where messages are a function of the source node only. In this work we provide empirical evidence challenging this narrative: we propose an isotropic GNN, which we call Efficient Graph Convolution (EGC), that consistently outperforms comparable anisotropic models, including the popular GAT or PNA architectures by using spatially-varying adaptive filters. In addition to raising important questions for the GNN community, our work has significant real-world implications for efficiency. EGC achieves higher model accuracy, with lower memory consumption and latency, along with characteristics suited to accelerator implementation, while being a drop-in replacement for existing architectures. As an isotropic model, it requires memory proportional to the number of vertices in the graph ($\mathcal{O}(V)$); in contrast, anisotropic models require memory proportional to the number of edges ($\mathcal{O}(E)$). We demonstrate that EGC outperforms existing approaches across 6 large and diverse benchmark datasets, and conclude by discussing questions that our work raise for the community going forward. Code and pretrained models for our experiments are provided at https://github.com/shyam196/egc.
PI-GNN: Towards Robust Semi-Supervised Node Classification against Noisy Labels
Authors: Xuefeng Du, Tian Bian, Yu Rong, Bo Han, Tongliang Liu, Tingyang Xu, Wenbing Huang, Junzhou Huang

Semi-supervised node classification on graphs is a fundamental problem in graph mining that uses a small set of labeled nodes and many unlabeled nodes for training, so that its performance is quite sensitive to the quality of the node labels. However, it is expensive to maintain the label quality for real-world graph datasets, which presents huge challenges for the learning algorithm to keep a good generalization ability. In this paper, we propose a novel robust learning objective dubbed pairwise interactions (PI) for the model, such as Graph Neural Network (GNN) to combat against noisy labels. Unlike classic robust training approaches that operate on the pointwise interactions between node and class label pairs, PI explicitly forces the embeddings for node pairs that hold a positive PI label to be close to each other, which can be applied to both labeled and unlabeled nodes. We design several instantiations for the PI labels based on the graph structure as well as node class labels, and further propose a new uncertainty-aware training technique to mitigate the negative effect of the sub-optimal PI labels. Extensive experiments on different datasets and GNN architectures demonstrate the effectiveness of PI, which also brings a promising improvement over the state-of-the-art methods.
The Geometry of Memoryless Stochastic Policy Optimization in Infinite-Horizon POMDPs
Authors: Johannes Müller, Guido Montufar

We consider the problem of finding the best memoryless stochastic policy for an infinite-horizon partially observable Markov decision process (POMDP) with finite state and action spaces with respect to either the discounted or mean reward criterion. We show that the (discounted) state-action frequencies and the expected cumulative reward are rational functions of the policy, whereby the degree is determined by the degree of partial observability. We then describe the optimization problem as a linear optimization problem in the space of feasible state-action frequencies subject to polynomial constraints that we characterize explicitly. This allows us to address the combinatorial and geometric complexity of the optimization problem using recent tools from polynomial optimization. In particular, we demonstrate how the partial observability constraints can lead to multiple smooth and non-smooth local optimizers and we estimate the number of critical points.
Energy-Inspired Molecular Conformation Optimization
Authors: Jiaqi Guan, Wesley Wei Qian, qiang liu, Wei-Ying Ma, Jianzhu Ma, Jian Peng

This paper studies an important problem in computational chemistry: predicting a molecule's spatial atom arrangements, or a molecular conformation. We propose a neural energy minimization formulation that casts the prediction problem into an unrolled optimization process, where a neural network is parametrized to learn the gradient fields of an implicit conformational energy landscape. Assuming different forms of the underlying potential energy function, we can not only reinterpret and unify many of the existing models but also derive new variants of SE(3)-equivariant neural networks in a principled manner. In our experiments, these new variants show superior performance in molecular conformation optimization comparing to existing SE(3)-equivariant neural networks. Moreover, our energy-inspired formulation is also suitable for molecular conformation generation, where we can generate more diverse and accurate conformers comparing to existing baselines.
A Critique of Self-Expressive Deep Subspace Clustering
Authors: Benjamin David Haeffele, Chong You, Rene Vidal

Subspace clustering is an unsupervised clustering technique designed to cluster data that is supported on a union of linear subspaces, with each subspace defining a cluster with dimension lower than the ambient space. Many existing formulations for this problem are based on exploiting the self-expressive property of linear subspaces, where any point within a subspace can be represented as linear combination of other points within the subspace. To extend this approach to data supported on a union of non-linear manifolds, numerous studies have proposed learning an embedding of the original data using  a neural network which is regularized by a self-expressive loss function on the data in the embedded space to encourage a union of linear subspaces prior on the data in the embedded space. Here we show that there are a number of potential flaws with this approach which have not been adequately addressed in prior work. In particular, we show the model formulation is often ill-posed in that it can lead to a degenerate embedding of the data, which need not correspond to a union of subspaces at all and is poorly suited for clustering. We validate our theoretical results experimentally and also repeat prior experiments reported in the literature, where we conclude that a significant portion of the previously claimed performance benefits can be attributed to an ad-hoc post processing step rather than the deep subspace clustering model.
GeDi: Generative Discriminator Guided Sequence Generation
Authors: Ben Krause, Akhilesh Deepak Gotmare, Bryan McCann, Nitish Shirish Keskar, Shafiq Joty, richard socher, Nazneen Rajani

While large-scale language models (LMs) are able to imitate the distribution of natural language well enough to generate realistic text, it is difficult to control which regions of the distribution they generate. This is especially problematic because datasets used for training large LMs usually contain significant toxicity, hate, bias, and negativity. We propose GeDi as an efficient method for using smaller LMs as generative discriminators to guide generation from large LMs to make them safer and more controllable. GeDi guides generation at each step by computing classification probabilities for all possible next tokens via Bayes rule by normalizing over two class-conditional distributions; one conditioned on the desired attribute, or control code, and another conditioned on the undesired attribute, or anti control code. We find that GeDi gives controllability on par with or better than the state of the art method in a variety of settings, while also achieving generation speeds more than $30$ times faster. Additionally, training GeDi on only three topics allows us to controllably generate new topics zero-shot from just a keyword. Lastly, we show that GeDi can make GPT-2 and GPT-3 significantly less toxic without sacrificing on linguistic fluency, making it by far the most practical existing method for detoxifying large language models while maintaining a fast generation speed.
Measuring Compositionality in Representation Learning
Authors: Jacob Andreas

Many machine learning algorithms represent input data with vector embeddings or discrete codes. When inputs exhibit compositional structure (e.g. objects built from parts or procedures from subroutines), it is natural to ask whether this compositional structure is reflected in the the inputs’ learned representations. While the assessment of compositionality in languages has received significant attention in linguistics and adjacent fields, the machine learning literature lacks general-purpose tools for producing graded measurements of compositional structure in more general (e.g. vector-valued) representation spaces. We describe a procedure for evaluating compositionality by measuring how well the true representation-producing model can be approximated by a model that explicitly composes a collection of inferred representational primitives. We use the procedure to provide formal and empirical characterizations of compositional structure in a variety of settings, exploring the relationship between compositionality and learning dynamics, human judgments, representational similarity, and generalization.
Representation-Agnostic Shape Fields
Authors: Xiaoyang Huang, Jiancheng Yang, Yanjun Wang, Ziyu Chen, Linguo Li, Teng Li, Bingbing Ni, Wenjun Zhang

3D shape analysis has been widely explored in the era of deep learning. Numerous models have been developed for various 3D data representation formats, e.g., MeshCNN for meshes, PointNet for point clouds and VoxNet for voxels. In this study, we present Representation-Agnostic Shape Fields (RASF), a generalizable and computation-efficient shape embedding module for 3D deep learning. RASF is implemented with a learnable 3D grid with multiple channels to store local geometry. Based on RASF, shape embeddings for various 3D shape representations (point clouds, meshes and voxels) are retrieved by coordinate indexing. While there are multiple ways to optimize the learnable parameters of RASF, we provide two effective schemes among all in this paper for RASF pre-training: shape reconstruction and normal estimation. Once trained, RASF becomes a plug-and-play performance booster with negligible cost. Extensive experiments on diverse 3D representation formats, networks and applications, validate the universal effectiveness of the proposed RASF. Code and pre-trained models are publicly available\footnote{\url{https://github.com/seanywang0408/RASF}}.
Learning Two-Step Hybrid Policy for Graph-Based Interpretable Reinforcement Learning
Authors: Tongzhou Mu, Kaixiang Lin, Feiyang Niu, Govind Thattai

We present a two-step hybrid reinforcement learning (RL) policy that is designed to generate interpretable and robust hierarchical policies
on the RL problem with graph-based input. Unlike prior deep reinforcement learning policies parameterized by an end-to-end black-box graph neural network, our approach disentangles the decision-making process into two steps. The first step is a simplified classification problem that maps the graph input to an action group where all actions share a similar semantic meaning. The second step implements a sophisticated rule-miner that conduct explicit one-hop reasoning over the graph and identifies decisive edges in the graph input without the necessity of heavy domain knowledge. This two-step hybrid policy presents human-friendly interpretations and achieves better performance in terms of generalization and robustness. Extensive experimental studies on four levels of complex text-based games have demonstrated the superiority of the proposed method compared to the state-of-the-art.
Kronecker-factored Curvature Approximations for Recurrent Neural Networks
Authors: James Martens, Jimmy Ba, Matt Johnson

Kronecker-factor Approximate Curvature (Martens & Grosse, 2015) (K-FAC) is a 2nd-order optimization method which has been shown to give state-of-the-art performance on large-scale neural network optimization tasks (Ba et al., 2017).  It is based on an approximation to the Fisher information matrix (FIM) that makes assumptions about the particular structure of the network and the way it is parameterized. The original K-FAC method was applicable only to fully-connected networks, although it has been recently extended by Grosse & Martens (2016) to handle convolutional networks as well. In this work we extend the method to handle RNNs by introducing a novel approximation to the FIM for RNNs. This approximation works by modelling the covariance structure between the gradient contributions at different time-steps using a chain-structured linear Gaussian graphical model, summing the various cross-covariances, and computing the inverse in closed form. We demonstrate in experiments that our method significantly outperforms general purpose state-of-the-art optimizers like SGD with momentum and Adam on several challenging RNN training tasks.
How unlabeled data improve generalization in self-training? A one-hidden-layer theoretical analysis
Authors: Shuai Zhang, Meng Wang, Sijia Liu, Pin-Yu Chen, Jinjun Xiong

Self-training, a semi-supervised learning algorithm, leverages a large amount of unlabeled data to improve learning when the labeled data are limited. Despite empirical successes, its theoretical characterization remains elusive. To the best of our knowledge, this work establishes the first theoretical analysis for the known iterative self-training paradigm and formally proves the benefits of unlabeled data in both training convergence and generalization ability. To make our theoretical analysis feasible, we focus on the case of one-hidden-layer neural networks. However, theoretical understanding of iterative self-training is non-trivial even for a shallow neural network. One of the key challenges is that existing neural network landscape analysis built upon supervised learning no longer holds in the (semi-supervised) self-training paradigm. We address this challenge and prove that iterative self-training converges linearly with both convergence rate and generalization accuracy improved in the order of $1/\sqrt{M}$, where $M$ is the number of unlabeled samples. Extensive experiments from shallow neural networks to deep neural networks are also provided to justify the correctness of our established theoretical insights on self-training.