GenAI4ELab/papercli-papers huggingface dataset:
A Newborn Embodied Turing Test for Comparing Object Segmentation Across Animals and Machines
Authors: Manju Garimella; Denizhan Pak; Justin Newell Wood; Samantha Marie Waters Wood
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: Newborn brains rapidly learn to solve challenging object recognition tasks, including segmenting objects from backgrounds and recognizing objects across novel backgrounds and viewpoints. Conversely, modern machine-learning (ML) algorithms are "data hungry," requiring more training data than brains to reach similar performance levels. How do we close this learning gap between brains and machines? Here we introduce a new benchmark—a Newborn Embodied Turing Test (NETT) for object segmentation—in which newborn animals and machines are raised in the same environments and tested with the same tasks, permitting direct comparison of their learning abilities. First, we raised newborn chicks in controlled environments containing a single object rotating on a single background, then tested their ability to recognize that object across new backgrounds and viewpoints. Second, we performed “digital twin” experiments in which we reared and tested artificial chicks in virtual environments that mimicked the rearing and testing conditions of the biological chicks. We inserted a variety of ML “brains” into the artificial chicks and measured whether those algorithms learned common object recognition behavior as biological chicks. All biological chicks solved this one-shot object segmentation task, successfully learning background-invariant object representations that generalized across new backgrounds and viewpoints. In contrast, none of the artificial chicks solved this object segmentation task, instead learning background-dependent representations that failed to generalize across new backgrounds and viewpoints. This digital twin design exposes core limitations in current ML algorithms in achieving brain-like object perception. Our NETT is publicly available for comparing ML algorithms with newborn chicks. Ultimately, we anticipate that NETT benchmarks will allow researchers to build embodied AI systems that learn as efficiently and robustly as newborn brains.
Robust Model-Based Optimization for Challenging Fitness Landscapes
Authors: Saba Ghaffari; Ehsan Saleh; Alex Schwing; Yu-Xiong Wang; Martin D. Burke; Saurabh Sinha
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of “separation” in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.
Solving High Frequency and Multi-Scale PDEs with Gaussian Processes
Authors: Shikai Fang; Madison Cooley; Da Long; Shibo Li; Mike Kirby; Shandian Zhe
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: Machine learning based solvers have garnered much attention in physical simulation and scientific computing, with a prominent example, physics-informed neural networks (PINNs). However, PINNs often struggle to solve high-frequency and multi-scale PDEs, which can be due to spectral bias during neural network training. To address this problem, we resort to the Gaussian process (GP) framework. To flexibly capture the dominant frequencies, we model the power spectrum of the PDE solution with a student $t$ mixture or Gaussian mixture. We apply the inverse Fourier transform to obtain the covariance function (by  Wiener-Khinchin theorem). The covariance derived from the Gaussian mixture spectrum corresponds to the known spectral mixture kernel. Next,  we estimate the mixture weights in the log domain, which we show is equivalent to placing a Jeffreys prior. It automatically induces sparsity, prunes excessive frequencies, and adjusts the remaining toward the ground truth. Third, to enable efficient and scalable computation on massive collocation points, which are critical to capture high frequencies, we place the collocation points on a grid, and multiply our covariance function at each input dimension. We use the GP conditional mean to predict the solution and its derivatives so as to fit the boundary condition and the equation itself. 
As a result, we can derive a Kronecker product structure in the covariance matrix. We use Kronecker product properties and multilinear algebra to promote computational efficiency and scalability, without low-rank approximations. We show the advantage of our method in systematic experiments. The code is released at {https://github.com/xuangu-fang/Gaussian-Process-Slover-for-High-Freq-PDE}.
OpenWebMath: An Open Dataset of High-Quality Mathematical Web Text
Authors: Keiran Paster; Marco Dos Santos; Zhangir Azerbayev; Jimmy Ba
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: There is growing evidence that pretraining on high quality, carefully thought-out tokens such as code or mathematics plays an important role in improving the reasoning abilities of large language models. For example, Minerva, a PaLM model finetuned on billions of tokens of mathematical documents from arXiv and the web, reported dramatically improved performance on problems that require quantitative reasoning. However, because all known open source web datasets employ preprocessing that does not faithfully preserve mathematical notation, the benefits of large scale training on quantitive web documents are unavailable to the research community. We introduce OpenWebMath, an open dataset inspired by these works containing 14.7B tokens of mathematical webpages from Common Crawl. We describe in detail our method for extracting text and LaTeX content and removing boilerplate from HTML documents, as well as our methods for quality filtering and deduplication. Additionally, we run small-scale experiments by training 1.4B language models on OpenWebMath, showing that models trained on 14.7B tokens of our dataset surpass the performance of models trained on over 20x the amount of general language data. We hope that our dataset, open-sourced and released on the Hugging Face Hub, will help spur advances in the reasoning abilities of large language models.
Replay across Experiments: A Natural Extension of Off-Policy RL
Authors: Dhruva Tirumala; Thomas Lampe; Jose Enrique Chen; Tuomas Haarnoja; Sandy Huang; Guy Lever; Ben Moran; Tim Hertweck; Leonard Hasenclever; Martin Riedmiller; Nicolas Heess; Markus Wulfmeier
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: Replaying data is a principal mechanism underlying the stability and data efficiency of off-policy reinforcement learning (RL).
We present an effective yet simple framework to extend the use of replays across multiple experiments, minimally adapting the RL workflow for sizeable improvements in controller performance and research iteration times.
At its core, Replay across Experiments (RaE) involves reusing experience from previous experiments to improve exploration and bootstrap learning while reducing required changes to a minimum in comparison to prior work. 
We empirically show benefits across a number of RL algorithms and challenging control domains spanning both locomotion and manipulation, including hard exploration tasks from egocentric vision. 
Through comprehensive ablations, we demonstrate  robustness to the quality and amount of data available and various hyperparameter choices. Finally, we discuss how our approach can be applied more broadly across research life cycles and can increase resilience by reloading data across random seeds or hyperparameter variations.
Understanding Transferable Representation Learning and Zero-shot Transfer in CLIP
Authors: Zixiang Chen; Yihe Deng; Yuanzhi Li; Quanquan Gu
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: Multi-modal learning has become increasingly popular due to its ability to leverage information from different data sources (e.g., text and images) to improve the model performance. Recently, CLIP has emerged as an effective approach that employs vision-language contrastive pretraining to learn joint image and text representations and exhibits remarkable performance in zero-shot learning and text-guided natural image generation. Despite the substantial practical success of CLIP, its theoretical understanding remains elusive. In this paper, we formally study transferrable representation learning underlying CLIP and demonstrate how features from different modalities get aligned. We also analyze its zero-shot transfer performance on the downstream tasks. In addition, we conduct empirical evaluations on real data to back
up our theory. Inspired by our analysis, we propose a new CLIP-type approach, which achieves better performance than CLIP and other state-of-the-art methods on benchmark datasets.
Conditional Variational Diffusion Models
Authors: Gabriel Della Maggiora; Luis Alberto Croquevielle; Nikita Deshpande; Harry Horsley; Thomas Heinis; Artur Yakimovich
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: Inverse problems aim to determine parameters from observations, a crucial task in engineering and science. Lately, generative models, especially diffusion models, have gained popularity in this area for their ability to produce realistic solutions and their good mathematical properties. Despite their success, an important drawback of diffusion models is their sensitivity to the choice of variance schedule, which controls the dynamics of the diffusion process. Fine-tuning this schedule for specific applications is crucial but time-consuming and does not guarantee an optimal result. We propose a novel approach for learning the schedule as part of the training process. Our method supports probabilistic conditioning on data, provides high-quality solutions, and is flexible, proving able to adapt to different applications with minimum overhead. This approach is tested in two unrelated inverse problems: super-resolution microscopy and quantitative phase imaging, yielding comparable or superior results to previous methods and fine-tuned diffusion models. We conclude that fine-tuning the schedule by experimentation should be avoided because it can be learned during training in a stable way that yields better results. The code is available on https://github.com/casus/cvdm
Better Neural PDE Solvers Through Data-Free Mesh Movers
Authors: Peiyan Hu; Yue Wang; Zhi-Ming Ma
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: Recently, neural networks have been extensively employed to solve partial differential equations (PDEs) in physical system modeling. While major studies focus on learning system evolution on predefined static mesh discretizations, some methods utilize reinforcement learning or supervised learning techniques to create adaptive and dynamic meshes, due to the dynamic nature of these systems. However, these approaches face two primary challenges: (1) the need for expensive optimal mesh data, and (2) the change of the solution space's degree of freedom and topology during mesh refinement. To address these challenges, this paper proposes a neural PDE solver with a neural mesh adapter. To begin with, we introduce a novel data-free neural mesh adaptor, called Data-free Mesh Mover (DMM), with two main innovations. Firstly, it is an operator that maps the solution to adaptive meshes and is trained using the Monge-Ampère equation without optimal mesh data. Secondly, it dynamically changes the mesh by moving existing nodes rather than adding or deleting nodes and edges. Theoretical analysis shows that meshes generated by DMM have the lowest interpolation error bound. Based on DMM, to efficiently and accurately model dynamic systems, we develop a moving mesh based neural PDE solver (MM-PDE) that embeds the moving mesh with a two-branch architecture and a learnable interpolation framework to preserve information within the data. Empirical experiments demonstrate that our method generates suitable meshes and considerably enhances accuracy when modeling widely considered PDE systems. The code can be found at: https://github.com/Peiyannn/MM-PDE.git.
From Latent Graph to Latent Topology Inference: Differentiable Cell Complex Module
Authors: Claudio Battiloro; Indro Spinelli; Lev Telyatnikov; Michael M. Bronstein; Simone Scardapane; Paolo Di Lorenzo
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: Latent Graph Inference (LGI) relaxed the reliance of Graph Neural Networks (GNNs) on a given graph topology by dynamically learning it. However, most of LGI methods assume to have a (noisy, incomplete, improvable, ...) input graph to rewire and can solely learn regular graph topologies. In the wake of the success of  Topological Deep Learning (TDL), we study Latent Topology Inference (LTI) for learning higher-order cell complexes (with sparse and not regular topology) describing multi-way interactions between data points. To this aim, we introduce the Differentiable Cell Complex Module (DCM), a novel learnable function that computes cell probabilities in the complex to improve the downstream task. We show how to integrate DCM with cell complex message-passing networks layers and train it in an end-to-end fashion, thanks to a two-step inference procedure that avoids an exhaustive search across all possible cells in the input, thus maintaining scalability. Our model is tested on several homophilic and heterophilic graph datasets and it is shown to outperform other state-of-the-art techniques, offering significant improvements especially in cases where an input graph is not provided.
Subtractive Mixture Models via Squaring: Representation and Learning
Authors: Lorenzo Loconte; Aleksanteri Mikulus Sladek; Stefan Mengel; Martin Trapp; Arno Solin; Nicolas Gillis; Antonio Vergari
Venue: ICLR 2024 (ICLR 2024 spotlight)

Abstract: Mixture models are traditionally represented and learned by adding several distributions as components. Allowing mixtures to subtract probability mass or density can drastically reduce the number of components needed to model complex distributions. However, learning such subtractive mixtures while ensuring they still encode a non-negative function is challenging. We investigate how to learn and perform inference on deep subtractive mixtures by squaring them. We do this in the framework of probabilistic circuits, which enable us to represent tensorized mixtures and generalize several other subtractive models. We theoretically prove that the class of squared circuits allowing subtractions can be exponentially more expressive than traditional additive mixtures; and, we empirically show this increased expressiveness on a series of real-world distribution estimation tasks.
On the Provable Advantage of Unsupervised Pretraining
Authors: Jiawei Ge; Shange Tang; Jianqing Fan; Chi Jin
Venue: ICLR 2024 (ICLR 2024 spotlight)

Abstract: Unsupervised pretraining, which learns a useful representation using a large amount of unlabeled data to facilitate the learning of downstream tasks, is a critical component of modern large-scale machine learning systems. Despite its tremendous empirical success, the rigorous theoretical understanding of why unsupervised pretraining generally helps remains rather limited---most existing results are restricted to particular methods or approaches for unsupervised pretraining with specialized structural assumptions. This paper studies a generic framework,
where the unsupervised representation learning task is specified by an abstract class of latent variable models $\Phi$ and the downstream task is specified by a class of prediction functions $\Psi$. We consider a natural approach of using Maximum Likelihood Estimation (MLE) for unsupervised pretraining and Empirical Risk Minimization (ERM) for learning downstream tasks. We prove that, under a mild ``informative'' condition, our algorithm achieves an excess risk of $\\tilde{\\mathcal{O}}(\sqrt{\mathcal{C}\_\Phi/m} + \sqrt{\mathcal{C}\_\Psi/n})$ for downstream tasks, where $\mathcal{C}\_\Phi, \mathcal{C}\_\Psi$ are complexity measures of function classes $\Phi, \Psi$, and $m, n$ are the number of unlabeled and labeled data respectively. Comparing to the baseline of $\tilde{\mathcal{O}}(\sqrt{\mathcal{C}\_{\Phi \circ \Psi}/n})$ achieved by performing supervised learning using only the labeled data, our result rigorously shows the benefit of unsupervised pretraining when $m \gg n$ and $\mathcal{C}\_{\Phi\circ \Psi} > \mathcal{C}\_\Psi$. This paper further shows that our generic framework covers a wide range of approaches for unsupervised pretraining, including factor models, Gaussian mixture models, and contrastive learning.
BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks
Authors: Frederikke Isa Marin; Felix Teufel; Marc Horlacher; Dennis Madsen; Dennis Pultz; Ole Winther; Wouter Boomsma
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: The genome sequence contains the blueprint for governing cellular processes. 
  While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. 
  Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce **BEND**, a **BEN**chmark for **D**NA language models, featuring
  a collection of realistic and biologically meaningful downstream tasks defined on the human genome.
  We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features.
  BEND is available at https://github.com/frederikkemarin/BEND.
TorchRL: A data-driven decision-making library for PyTorch
Authors: Albert Bou; Matteo Bettini; Sebastian Dittert; Vikash Kumar; Shagun Sodhani; Xiaomeng Yang; Gianni De Fabritiis; Vincent Moens
Venue: ICLR 2024 (ICLR 2024 spotlight)

Abstract: PyTorch has ascended as a premier machine learning framework, yet it lacks a native and comprehensive library for decision and control tasks suitable for large development teams dealing with complex real-world data and environments. To address this issue, we propose TorchRL, a generalistic control library for PyTorch that provides well-integrated, yet standalone components. We introduce a new and flexible PyTorch primitive, the TensorDict, which facilitates streamlined algorithm development across the many branches of Reinforcement Learning (RL) and control. We provide a detailed description of the building blocks and an extensive overview of the library across domains and tasks. Finally, we experimentally demonstrate its reliability and flexibility, and show comparative benchmarks to demonstrate its computational efficiency. TorchRL fosters long-term support and is publicly available on GitHub for greater reproducibility and collaboration within the research community. The code is open-sourced on GitHub.
Towards Robust Offline Reinforcement Learning under Diverse Data Corruption
Authors: Rui Yang; Han Zhong; Jiawei Xu; Amy Zhang; Chongjie Zhang; Lei Han; Tong Zhang
Venue: ICLR 2024 (ICLR 2024 spotlight)

Abstract: Offline reinforcement learning (RL) presents a promising approach for learning reinforced policies from offline datasets without the need for costly or unsafe interactions with the environment. However, datasets collected by humans in real-world environments are often noisy and may even be maliciously corrupted, which can significantly degrade the performance of offline RL. In this work, we first investigate the performance of current offline RL algorithms under comprehensive data corruption, including states, actions, rewards, and dynamics. Our extensive experiments reveal that implicit Q-learning (IQL) demonstrates remarkable resilience to data corruption among various offline RL algorithms. Furthermore, we conduct both empirical and theoretical analyses to understand IQL's robust performance, identifying its supervised policy learning scheme as the key factor. Despite its relative robustness, IQL still suffers from heavy-tail targets of Q functions under dynamics corruption. To tackle this challenge, we draw inspiration from robust statistics to employ the Huber loss to handle the heavy-tailedness and utilize quantile estimators to balance penalization for corrupted data and learning stability. By incorporating these simple yet effective modifications into IQL, we propose a more robust offline RL approach named Robust IQL (RIQL). Extensive experiments demonstrate that RIQL exhibits highly robust performance when subjected to diverse data corruption scenarios.
Towards Robust Fidelity for Evaluating Explainability of Graph Neural Networks
Authors: Xu Zheng; Farhad Shirani; Tianchun Wang; Wei Cheng; Zhuomin Chen; Haifeng Chen; Hua Wei; Dongsheng Luo
Venue: ICLR 2024 (ICLR 2024 poster)

Abstract: Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their expansive application in sensitive domains requires a comprehensive understanding of their decision-making processes --- necessitating a framework for GNN explainability. An explanation function for GNNs takes a pre-trained GNN along with a graph as input, to produce a `sufficient statistic' subgraph with respect to the graph label. A main challenge in studying GNN explainability is to provide fidelity measures that evaluate the performance of these explanation functions. This paper studies this foundational challenge, spotlighting the inherent limitations of prevailing fidelity metrics, including $Fid_+$, $Fid_-$, and $Fid_\Delta$. Specifically, a formal, information-theoretic definition of explainability is introduced and it is shown that existing metrics often fail to align with this definition across various statistical scenarios. The reason is due to potential distribution shifts when subgraphs are removed in computing these fidelity measures. Subsequently, a robust class of fidelity measures are introduced, and it is shown analytically that they are resilient to distribution shift issues and are applicable in a wide range of scenarios. Extensive empirical analysis on both synthetic and real datasets are provided to illustrate that the proposed metrics are more coherent with gold standard metrics.