nils-herrmann/clean_scirepeval huggingface dataset:
Perceiver IO: A General Architecture for Structured Inputs & Outputs
Authors: Andrew Jaegle, Sebastian Borgeaud, Jean-Baptiste Alayrac, Carl Doersch, Catalin Ionescu, David Ding, Skanda Koppula, Daniel Zoran, Andrew Brock, Evan Shelhamer, Olivier J Henaff, Matthew Botvinick, Andrew Zisserman, Oriol Vinyals, Joao Carreira

A central goal of machine learning is the development of systems that can solve many problems in as many data domains as possible. Current architectures, however, cannot be applied beyond a small set of stereotyped settings, as they bake in domain & task assumptions or scale poorly to large inputs or outputs. In this work, we propose Perceiver IO, a general-purpose architecture that handles data from arbitrary settings while scaling linearly with the size of inputs and outputs. Our model augments the Perceiver with a flexible querying mechanism that enables outputs of various sizes and semantics, doing away with the need for task-specific architecture engineering. The same architecture achieves strong results on tasks spanning natural language and visual understanding, multi-task and multi-modal reasoning, and StarCraft II. As highlights, Perceiver IO outperforms a Transformer-based BERT baseline on the GLUE language benchmark despite removing input tokenization and achieves state-of-the-art performance on Sintel optical flow estimation with no explicit mechanisms for multiscale correspondence.
Individualised Dose-Response Estimation using Generative Adversarial Nets
Authors: Ioana Bica, James Jordon, Mihaela van der Schaar

The problem of estimating treatment responses from observational data is by now a well-studied one. Less well studied, though, is the problem of treatment response estimation when the treatments are accompanied by a continuous dosage parameter. In this paper, we tackle this lesser studied problem by building on a modification of the generative adversarial networks (GANs) framework that has already demonstrated effectiveness in the former problem. Our model, DRGAN, is flexible, capable of handling multiple treatments each accompanied by a dosage parameter. The key idea is to use a significantly modified GAN model to generate entire dose-response curves for each sample in the training data which will then allow us to use standard supervised methods to learn an inference model capable of estimating these curves for a new sample. Our model consists of 3 blocks: (1) a generator, (2) a discriminator, (3) an inference block. In order to address the challenge presented by the introduction of dosages, we propose novel architectures for both our generator and discriminator. We model the generator as a multi-task deep neural network. In order to address the increased complexity of the treatment space (because of the addition of dosages), we develop a hierarchical discriminator consisting of several networks: (a) a treatment discriminator, (b) a dosage discriminator for each treatment. In the experiments section, we introduce a new semi-synthetic data simulation for use in the dose-response setting and demonstrate improvements over the existing benchmark models.
BANANA: a Benchmark for the Assessment of Neural Architectures for Nucleic Acids
Authors: Luca Salvatore Lorello, Andrea Galassi, Paolo Torroni

Machine learning has always played an important role in bioinformatics and recent applications of deep learning have allowed solving a new spectrum of biologically relevant tasks.
However, there is still a  gap between the  ``mainstream'' AI and the bioinformatics communities. This is partially due to the format of bioinformatics data, which are typically difficult to process and adapt to machine learning tasks without deep domain knowledge.
Moreover, the lack of standardized evaluation methods makes it difficult to rigorously compare different models and assess their true performance.
To help to bridge this gap, and inspired by work such as SuperGLUE and TAPE, we present BANANA, a benchmark consisting of six supervised classification tasks designed to assess language model performance in the DNA and RNA domains. The tasks are defined over three genomics and one transcriptomics languages (human DNA, bacterial 16S gene, nematoda ITS2 gene, human mRNA) and measure a model's ability to perform whole-sequence classification in a variety of setups.
Each task was built from readily available data and is presented in a ready-to-use format, with defined labels, splits, and evaluation metrics.
We use BANANA to test state-of-the-art NLP architectures, such as Transformer-based models, observing that, in general, self-supervised pretraining without external corpora is beneficial in every task.
FUNCTIONAL VARIATIONAL BAYESIAN NEURAL NETWORKS
Authors: Shengyang Sun, Guodong Zhang, Jiaxin Shi, Roger Grosse

Variational Bayesian neural networks (BNN) perform variational inference over weights, but it is difficult to specify meaningful priors and approximating posteriors in a high-dimensional weight space. We introduce functional variational Bayesian neural networks (fBNNs), which maximize an Evidence Lower BOund (ELBO) defined directly on stochastic processes, i.e. distributions over functions. We prove that the KL divergence between stochastic processes is equal to the supremum of marginal KL divergences over all finite sets of inputs. Based on this, we introduce a practical training objective which approximates the functional ELBO using finite measurement sets and the spectral Stein gradient estimator. With fBNNs, we can specify priors which entail rich structure, including Gaussian processes and implicit stochastic processes. Empirically, we find that fBNNs extrapolate well using various structured priors, provide reliable uncertainty estimates, and can scale to large datasets.
Feature Attribution As Feature Selection
Authors: Satoshi Hara, Koichi Ikeno, Tasuku Soma, Takanori Maehara

Feature attribution methods identify "relevant" features as an explanation of a complex machine learning model. Several feature attribution methods have been proposed; however, only a few studies have attempted to define the "relevance" of each feature mathematically. In this study, we formalize the feature attribution problem as a feature selection problem. In our proposed formalization, there arise two possible definitions of relevance. We name the feature attribution problems based on these two relevances as Exclusive Feature Selection (EFS) and Inclusive Feature Selection (IFS). We show that several existing feature attribution methods can be interpreted as approximation algorithms for EFS and IFS. Moreover, through exhaustive experiments, we show that IFS is better suited as the formalization for the feature attribution problem than EFS.
Cross-Modal Retrieval Augmentation for Multi-Modal Classification
Authors: Shir Gur, Natalia Neverova, Chris Stauffer, Ser-Nam Lim, Douwe Kiela, Austin Reiter

Recent advances in using retrieval components over external knowledge sources have shown impressive results for a variety of downstream tasks in natural language processing. Here, we explore the use of unstructured external knowledge sources of images and their corresponding captions for improving visual question answering (VQA). First, we train a novel alignment model for embedding images and captions in the same space, which achieves state-of-the-art image-caption retrieval performance w.r.t. similar methods.
Second, we show that retrieval-augmented multi-modal transformers using the trained alignment model
significantly improve results on VQA over strong baselines.
We further conduct extensive experiments to establish the promise of this approach, and examine novel applications for inference time such as hot-swapping indices.
Status-Quo Policy Gradient in Multi-agent Reinforcement Learning
Authors: Pinkesh Badjatiya, Mausoom Sarkar, Abhishek Sinha, Nikaash Puri, Jayakumar Subramanian, Siddharth Singh, Balaji Krishnamurthy

Individual rationality, which involves maximizing expected individual return, does not always lead to optimal individual or group outcomes in multi-agent problems. For instance, in social dilemma situations, Reinforcement Learning (RL) agents trained to maximize individual rewards converge to mutual defection that is individually and socially sub-optimal. In contrast, humans evolve individual and socially optimal strategies in such social dilemmas. Inspired by ideas from human psychology that attribute this behavior in humans to the status-quo bias, we present a status-quo loss (SQLoss) and the corresponding policy gradient algorithm that incorporates this bias in an RL agent. We demonstrate that agents trained with SQLoss evolve individually as well as socially optimal behavior in several social dilemma matrix games. To apply SQLoss to games where cooperation and defection are determined by a sequence of non-trivial actions, we present GameDistill, an algorithm that reduces a multi-step game with visual input to a matrix game. We empirically show how agents trained with SQLoss on a GameDistill reduced version of the Coin Game evolve optimal policies.
MQTransformer: Multi-Horizon Forecasts with Context Dependent and Feedback-Aware Attention
Authors: Carson Eisenach, Yagna Patel, Dhruv Madeka

Recent advances in neural forecasting have produced major improvements in accuracy for probabilistic demand prediction. In this work, we propose novel improvements to the current state of the art by incorporating changes inspired by recent advances in Transformer architectures for Natural Language Processing. We develop a novel decoder-encoder attention for context-alignment, improving forecasting accuracy by allowing the network to study its own history based on the context for which it is producing a forecast. We also present a novel positional encoding that allows the neural network to learn context-dependent seasonality functions as well as arbitrary holiday distances. Finally we show that the current state of the art MQ-Forecaster (Wen et al., 2017) models display excess variability by failing to leverage previous errors in the forecast to improve accuracy. We propose a novel decoder-self attention scheme for forecasting that produces significant improvements in the excess variation of the forecast.
Fast MNAS: Uncertainty-aware Neural Architecture Search with Lifelong Learning
Authors: Jihao Liu, Yangting Sun, Ming Zhang, Boxiao Liu, Yu Liu

Sampling-based neural architecture search (NAS) always guarantees better convergence yet suffers from huge computational resources compared with gradient-based approaches, due to the rollout bottleneck -- exhaustive training for each sampled generation on proxy tasks. This work provides a general pipeline to accelerate the convergence of the rollout process as well as the RL learning process in sampling-based NAS. It is motivated by the interesting observation that both the architecture and the parameter knowledge can be transferred between different experiments and even different tasks. We first introduce an uncertainty-aware critic (value function) in PPO to utilize the architecture knowledge in previous experiments, which stabilizes the training process and reduces the searching time by 4 times. Further, a life-long knowledge pool together with a block similarity function is proposed to utilize the lifelong parameter knowledge and reduces the searching time by 2 times. It is the first to introduce block-level weight sharing in RL-based NAS. The block similarity function guarantees a 100% hitting ratio with strict fairness.  Besides, we show a simply designed off-policy correction factor that enables 'replay buffer' in RL optimization and further reduces half of the searching time. Experiments on the MNAS search space show the proposed FNAS accelerates standard RL-based NAS process by $\sim$10x (e.g. $\sim$256 2x2 TPUv2*days / 20,000 GPU*hour $\rightarrow$ 2,000 GPU*hour for MNAS), and guarantees better performance on various vision tasks.
Directional Analysis of Stochastic Gradient Descent via von Mises-Fisher Distributions in Deep Learning
Authors: Cheolhyoung Lee, Kyunghyun Cho, Wanmo Kang

Although stochastic gradient descent (SGD) is a driving force behind the recent success of deep learning, our understanding of its dynamics in a high-dimensional parameter space is limited. In recent years, some researchers have used the stochasticity of minibatch gradients, or the signal-to-noise ratio, to better characterize the learning dynamics of SGD. Inspired from these work, we here analyze SGD from a geometrical perspective by inspecting the stochasticity of the norms and directions of minibatch gradients. We propose a model of the directional concentration for minibatch gradients through von Mises-Fisher (VMF) distribution, and show that the directional uniformity of minibatch gradients increases over the course of SGD. We empirically verify our result using deep convolutional networks and observe a higher correlation between the gradient stochasticity and the proposed directional uniformity than that against the gradient norm stochasticity, suggesting that the directional statistics of minibatch gradients is a major factor behind SGD.
Dopamine: A Research Framework for Deep Reinforcement Learning
Authors: Pablo Samuel Castro, Subhodeep Moitra, Carles Gelada, Saurabh Kumar, Marc G. Bellemare

Deep reinforcement learning (deep RL) research has grown significantly in recent years. A number of software offerings now exist that provide stable, comprehensive implementations for benchmarking. At the same time, recent deep RL research
has become more diverse in its goals. In this paper we introduce Dopamine, a new research framework for deep RL that aims to support some of that diversity. Dopamine is open-source, TensorFlow-based, and provides compact yet reliable
implementations of some state-of-the-art deep RL agents. We complement this offering with a taxonomy of the different research objectives in deep RL research. While by no means exhaustive, our analysis highlights the heterogeneity of research
in the field, and the value of frameworks such as ours.
How Neural Networks Extrapolate: From Feedforward to Graph Neural Networks
Authors: Keyulu Xu, Mozhi Zhang, Jingling Li, Simon Shaolei Du, Ken-Ichi Kawarabayashi, Stefanie Jegelka

We study how neural networks trained by gradient descent  extrapolate, i.e., what they learn outside the support of the training distribution. Previous works report mixed empirical results when extrapolating with neural networks: while feedforward neural networks, a.k.a. multilayer perceptrons (MLPs), do not extrapolate well in certain simple tasks, Graph Neural Networks (GNNs) -- structured networks with MLP modules -- have shown some success in more complex tasks.  Working towards a theoretical explanation, we identify conditions under which MLPs and GNNs extrapolate well. First, we quantify the observation that ReLU MLPs quickly converge to linear functions along any direction from the origin, which implies that ReLU MLPs do not extrapolate most nonlinear functions. But, they can provably learn a linear target function when the training distribution is sufficiently diverse. Second, in connection to analyzing the successes and limitations of GNNs, these results suggest a hypothesis for which we provide theoretical and empirical evidence: the success of GNNs in extrapolating algorithmic tasks to new data (e.g., larger graphs or edge weights) relies on encoding task-specific non-linearities in the architecture or features. Our theoretical analysis builds on a connection of over-parameterized networks to the neural tangent kernel.  Empirically, our theory holds across different training settings.
Model-Invariant State Abstractions for Model-Based Reinforcement Learning
Authors: Manan Tomar, Amy Zhang, Roberto Calandra, Matthew E. Taylor, Joelle Pineau

Accuracy and generalization of dynamics models is key to the success of model-based reinforcement learning (MBRL). As the complexity of tasks increases, learning accurate dynamics models becomes increasingly sample inefficient. However, many complex tasks also exhibit sparsity in dynamics, i.e., actions have only a local effect on the system dynamics. In this paper, we exploit this property with a causal invariance perspective in the single-task setting, introducing a new type of state abstraction called \textit{model-invariance}. Unlike previous forms of state abstractions, a model-invariance state abstraction  leverages causal sparsity over state variables. This allows for compositional generalization to unseen states, something that non-factored forms of state abstractions cannot do. We prove that an optimal policy can be learned over this model-invariance state abstraction and show improved generalization in a simple toy domain. Next, we propose a practical method to approximately learn a model-invariant representation for complex domains and validate our approach by showing improved modelling performance over standard maximum likelihood approaches on challenging tasks, such as the MuJoCo-based Humanoid. Finally, within the MBRL setting we show strong performance gains with respect to sample efficiency across a host of continuous control tasks.
Learning Latent Semantic Representation from Pre-defined Generative Model
Authors: Jin-Young Kim, Sung-Bae Cho

Learning representations of data is an important issue in machine learning. Though GAN has led to significant improvements in the data representations, it still has several problems such as unstable training, hidden manifold of data, and huge computational overhead. GAN tends to produce the data simply without any information about the manifold of the data, which hinders from controlling desired features to generate. Moreover, most of GAN’s have a large size of manifold, resulting in poor scalability. In this paper, we propose a novel GAN to control the latent semantic representation, called LSC-GAN, which allows us to produce desired data to generate and learns a representation of the data efficiently. Unlike the conventional GAN models with hidden distribution of latent space, we define the distributions explicitly in advance that are trained to generate the data based on the corresponding features by inputting the latent variables that follow the distribution. As the larger scale of latent space caused by deploying various distributions in one latent space makes training unstable while maintaining the dimension of latent space, we need to separate the process of defining the distributions explicitly and operation of generation. We prove that a VAE is proper for the former and modify a loss function of VAE to map the data into the pre-defined latent space so as to locate the reconstructed data as close to the input data according to its characteristics. Moreover, we add the KL divergence to the loss function of LSC-GAN to include this process. The decoder of VAE, which generates the data with the corresponding features from the pre-defined latent space, is used as the generator of the LSC-GAN. Several experiments on the CelebA dataset are conducted to verify the usefulness of the proposed method to generate desired data stably and efficiently, achieving a high compression ratio that can hold about 24 pixels of information in each dimension of latent space. Besides, our model learns the reverse of features such as not laughing (rather frowning) only with data of ordinary and smiling facial expression.
Learning Grid Cells as Vector Representation of Self-Position Coupled with Matrix Representation of Self-Motion
Authors: Ruiqi Gao, Jianwen Xie, Song-Chun Zhu, Ying Nian Wu

This paper proposes a representational model for grid cells. In this model, the 2D self-position of the agent is represented by a high-dimensional vector, and the 2D self-motion or displacement of the agent is represented by a matrix that transforms the vector. Each component of the vector is a unit or a cell. The model consists of the following three sub-models. (1) Vector-matrix multiplication. The movement from the current position to the next position is modeled by matrix-vector multi- plication, i.e., the vector of the next position is obtained by multiplying the matrix of the motion to the vector of the current position. (2) Magnified local isometry. The angle between two nearby vectors equals the Euclidean distance between the two corresponding positions multiplied by a magnifying factor. (3) Global adjacency kernel. The inner product between two vectors measures the adjacency between the two corresponding positions, which is defined by a kernel function of the Euclidean distance between the two positions. Our representational model has explicit algebra and geometry. It can learn hexagon patterns of grid cells, and it is capable of error correction, path integral and path planning.
One After Another: Learning Incremental Skills for a Changing World
Authors: Nur Muhammad Mahi Shafiullah, Lerrel Pinto

Reward-free, unsupervised discovery of skills is an attractive alternative to the bottleneck of hand-designing rewards in environments where task supervision is scarce or expensive. However, current skill pre-training methods, like many RL techniques, make a fundamental assumption -- stationary environments during training. Traditional methods learn all their skills simultaneously, which makes it difficult for them to both quickly adapt to changes in the environment, and to not forget earlier skills after such adaptation. On the other hand, in an evolving or expanding environment, skill learning must be able to adapt fast to new environment situations while not forgetting previously learned skills. These two conditions make it difficult for classic skill discovery to do well in an evolving environment. In this work, we propose a new framework for skill discovery, where skills are learned one after another in an incremental fashion. This framework allows newly learned skills to adapt to new environment or agent dynamics, while the fixed old skills ensure the agent doesn't forget a learned skill. We demonstrate experimentally that in both evolving and static environments, incremental skills significantly outperform current state-of-the-art skill discovery methods on both skill quality and the ability to solve downstream tasks. Videos for learned skills and code are made public on https://notmahi.github.io/disk
How Faithful is your Synthetic Data? Sample-level Metrics for Evaluating and Auditing Generative Models
Authors: Ahmed Alaa, Boris van Breugel, Evgeny Saveliev, Mihaela van der Schaar

Devising domain- and model-agnostic evaluation metrics for generative models is an important and as yet unresolved problem. Most existing metrics, which were tailored solely to the image synthesis setup, exhibit a limited capacity for diagnosing the modes of failure of generative models across broader application domains. In this paper, we introduce a 3-dimensional evaluation metric, ($\alpha$-Precision, $\beta$-Recall, Authenticity), that characterizes the fidelity, diversity and generalization performance of  any generative model in a domain-agnostic fashion. Our metric unifies statistical divergence measures with precision-recall analysis, enabling sample-level and distribution-level diagnoses of model fidelity and diversity. We introduce generalization as an additional dimension for model performance that quantifies the extent to which a model copies training data---a crucial performance indicator when modeling sensitive data with requirements on privacy. The three metric components correspond to (interpretable) probabilistic quantities, and are estimated via sample-level binary classification. The sample-level nature of our metric inspires a novel use case which we call model auditing, wherein we judge the quality of individual samples generated by a (black-box) model, discarding low-quality samples and hence improving the overall model performance in a post-hoc manner.