OpenRaiser/Intern-Atlas huggingface dataset:
Experimental Design for Multi-Channel Imaging via Task-Driven Feature Selection
Venue: Conference ICLR 2024
Year: 2024

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel
Towards Cheaper Inference in Deep Networks with Lower Bit-Width Accumulators
Venue: Conference ICLR 2024
Year: 2024

The majority of the research on the quantization of Deep Neural Networks (DNNs) is focused on reducing the precision of tensors visible by high-level frameworks (e.g., weights, activations, and gradients). However, current hardware still relies on high-accuracy core operations. Most significant is the operation of accumulating products. This high-precision accumulation operation is gradually becoming the main computational bottleneck. This is because, so far, the usage of low-precision accumulators led to a significant degradation in performance. In this work, we present a simple method to train and fine-tune high-end DNNs, to allow, for the first time, utilization of cheaper, $12$-bits accumulators, with no significant degradation in accuracy. Lastly, we show that as we decrease the accumulation precision further, using fine-grained gradient approximations can improve the DNN accuracy.
On the Markov Property of Neural Algorithmic Reasoning: Analyses and Methods
Venue: Conference ICLR 2024
Year: 2024

Neural algorithmic reasoning is an emerging research direction that endows neural networks with the ability to mimic algorithmic executions step-by-step. A common paradigm in existing designs involves the use of historical embeddings in predicting the results of future execution steps. Our observation in this work is that such historical dependence intrinsically contradicts the Markov nature of algorithmic reasoning tasks. Based on this motivation, we present our ForgetNet, which does not use historical embeddings and thus is consistent with the Markov nature of the tasks. To address challenges in training ForgetNet at early stages, we further introduce G-ForgetNet, which uses a gating mechanism to allow for the selective integration of historical embeddings. Such an enhanced capability provides valuable computational pathways during the model's early training phase. Our extensive experiments, based on the CLRS-30 algorithmic reasoning benchmark, demonstrate that both ForgetNet and G-ForgetNet achieve better generalization capability than existing methods. Furthermore, we investigate the behavior of the gating mechanism, highlighting its degree of alignment with our intuitions and its effectiveness for robust performance.
When can transformers reason with abstract symbols?
Venue: Conference ICLR 2024
Year: 2024

We investigate the capabilities of transformer models on relational reasoning tasks. In these tasks, models are trained on a set of strings encoding abstract relations, and are then tested out-of-distribution on data that contains symbols that did not appear in the training dataset. We prove that for any relational reasoning task in a large family of tasks, transformers learn the abstract relations and generalize to the test set when trained by gradient descent on sufficiently large quantities of training data. This is in contrast to classical fully-connected networks, which we prove fail to learn to reason. Our results inspire modifications of the transformer architecture that add only two trainable parameters per head, and that we empirically demonstrate improve data efficiency for learning to reason.
Jumanji: a Diverse Suite of Scalable Reinforcement Learning Environments in JAX
Venue: Conference ICLR 2024
Year: 2024

Open-source reinforcement learning (RL) environments have played a crucial role in driving progress in the development of AI algorithms. In modern RL research, there is a need for simulated environments that are performant, scalable, and modular to enable their utilization in a wider range of potential real-world applications. Therefore, we present Jumanji, a suite of diverse RL environments specifically designed to be fast, flexible, and scalable. Jumanji provides a suite of environments focusing on combinatorial problems frequently encountered in industry, as well as challenging general decision-making tasks. By leveraging the efficiency of JAX and hardware accelerators like GPUs and TPUs, Jumanji enables rapid iteration of research ideas and large-scale experimentation, ultimately empowering more capable agents. Unlike existing RL environment suites, Jumanji is highly customizable, allowing users to tailor the initial state distribution and problem complexity to their needs. Furthermore, we provide actor-critic baselines for each environment, accompanied by preliminary findings on scaling and generalization scenarios. Jumanji aims to set a new standard for speed, adaptability, and scalability of RL environments.
SE(3)-Stochastic Flow Matching for Protein Backbone Generation
Venue: Conference ICLR 2024
Year: 2024

The computational design of novel protein structures has the potential to impact numerous scientific disciplines greatly. Toward this goal, we introduce FoldFlow, a series of novel generative models of increasing modeling power based on the flow-matching paradigm over $3\mathrm{D}$ rigid motions -- i.e. the group $\text{SE}(3)$ -- enabling accurate modeling of protein backbones. We first introduce FoldFlow-Base, a simulation-free approach to learning deterministic continuous-time dynamics and matching invariant target distributions on $\text{SE}(3)$. We next accelerate training by incorporating Riemannian optimal transport to create FoldFlow-OT, leading to the construction of both more simple and stable flows. Finally, we design FoldFlow-SFM, coupling both Riemannian OT and simulation-free training to learn stochastic continuous-time dynamics over $\text{SE}(3)$. Our family of FoldFlow, generative models offers several key advantages over previous approaches to the generative modeling of proteins: they are more stable and faster to train than diffusion-based approaches, and our models enjoy the ability to map any invariant source distribution to any invariant target distribution over $\text{SE}(3)$. Empirically, we validate FoldFlow, on protein backbone generation of up to $300$ amino acids leading to high-quality designable, diverse, and novel samples.
On Double Descent in Reinforcement Learning with LSTD and Random Features
Venue: Conference ICLR 2024
Year: 2024

Temporal Difference (TD) algorithms are widely used in Deep Reinforcement Learning (RL). Their performance is heavily influenced by the size of the neural network. While in supervised learning, the regime of over-parameterization and its benefits are well understood, the situation in RL is much less clear. In this paper, we present a theoretical analysis of the influence of network size and $l_2$-regularization on performance. We identify the ratio between the number of parameters and the number of visited states as a crucial factor and define over-parameterization as the regime when it is larger than one. Furthermore, we observe a double descent phenomenon, i.e., a sudden drop in performance around the parameter/state ratio of one. Leveraging random features and the lazy training regime, we study the regularized Least-Square Temporal Difference (LSTD) algorithm in an asymptotic regime, as both the number of parameters and states go to infinity, maintaining a constant ratio. We derive deterministic limits of both the empirical and the true Mean-Squared Bellman Error (MSBE) that feature correction terms responsible for the double descent. Correction terms vanish when the $l_2$-regularization is increased or the number of unvisited states goes to zero. Numerical experiments with synthetic and small real-world environments closely match the theoretical predictions.
Learning Disentangled Audio Representations through Controlled Synthesis
Venue: Conference ICLR 2024
Year: 2024

This paper tackles the scarcity of benchmarking data in disentangled auditory representation learning. We introduce SynTone, a synthetic dataset with explicit ground truth explanatory factors for evaluating disentanglement techniques. Benchmarking state-of-the-art methods on SynTone highlights its utility for method evaluation. Our results underscore strengths and limitations in audio disentanglement, motivating future research.
Enhancing Neural Training via a Correlated Dynamics Model
Venue: Conference ICLR 2024
Year: 2024

As neural networks grow in scale, their training becomes both computationally demanding and rich in dynamics. Amidst the flourishing interest in these training dynamics, we present a novel observation: Parameters during training exhibit intrinsic correlations over time. Capitalizing on this, we introduce Correlation Mode Decomposition (CMD). This algorithm clusters the parameter space into groups, termed modes, that display synchronized behavior across epochs. This enables CMD to efficiently represent the training dynamics of complex networks, like ResNets and Transformers, using only a few modes. Moreover, test set generalization is enhanced. We introduce an efficient CMD variant, designed to run concurrently with training. Our experiments indicate that CMD surpasses the state-of-the-art method for compactly modeled dynamics on image classification. Our modeling can improve training efficiency and lower communication overhead, as shown by our preliminary experiments in the context of federated learning.
Learning to design protein-protein interactions with enhanced generalization
Venue: Conference ICLR 2024
Year: 2024

Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often struggle to generalize beyond training data in practical scenarios. The contributions of this work are three-fold. First, we construct PPIRef, the largest and non-redundant dataset of 3D protein-protein interactions, enabling effective large-scale learning. Second, we leverage the PPIRef dataset to pre-train PPIformer, a new SE(3)-equivariant model generalizing across diverse protein-binder variants. We fine-tune PPIformer to predict effects of mutations on protein-protein interactions via a thermodynamically motivated adjustment of the pre-training loss function. Finally, we demonstrate the enhanced generalization of our new PPIformer approach by outperforming other state-of-the-art methods on new, non-leaking splits of standard labeled PPI mutational data and independent case studies optimizing a human antibody against SARS-CoV-2 and increasing the thrombolytic activity of staphylokinase.
Information Bottleneck Analysis of Deep Neural Networks via Lossy Compression
Venue: Conference ICLR 2024
Year: 2024

The Information Bottleneck (IB) principle offers an information-theoretic framework for analyzing the training process of deep neural networks (DNNs). Its essence lies in tracking the dynamics of two mutual information (MI) values: between the hidden layer output and the DNN input/target. According to the hypothesis put forth by Shwartz-Ziv & Tishby (2017), the training process consists of two distinct phases: fitting and compression. The latter phase is believed to account for the good generalization performance exhibited by DNNs. Due to the challenging nature of estimating MI between high-dimensional random vectors, this hypothesis was only partially verified for NNs of tiny sizes or specific types, such as quantized NNs. In this paper, we introduce a framework for conducting IB analysis of general NNs. Our approach leverages the stochastic NN method proposed by Goldfeld et al. (2019) and incorporates a compression step to overcome the obstacles associated with high dimensionality. In other words, we estimate the MI between the compressed representations of high-dimensional random vectors. The proposed method is supported by both theoretical and practical justifications. Notably, we demonstrate the accuracy of our estimator through synthetic experiments featuring predefined MI values and comparison with MINE (Belghazi et al., 2018). Finally, we perform IB analysis on a close-to-real-scale convolutional DNN, which reveals new features of the MI dynamics.
fairret: a Framework for Differentiable Fairness Regularization Terms
Venue: Conference ICLR 2024
Year: 2024

Current fairness toolkits in machine learning only admit a limited range of fairness definitions and have seen little integration with automatic differentiation libraries, despite the central role these libraries play in modern machine learning pipelines. We introduce a framework of fairness regularization terms (fairrets) which quantify bias as modular, flexible objectives that are easily integrated in automatic differentiation pipelines. By employing a general definition of fairness in terms of linear-fractional statistics, a wide class of fairrets can be computed efficiently. Experiments show the behavior of their gradients and their utility in enforcing fairness with minimal loss of predictive power compared to baselines. Our contribution includes a PyTorch implementation of the fairret framework.
Large Language Models as Tool Makers
Venue: Conference ICLR 2024
Year: 2024

Recent research has highlighted the potential of large language models (LLMs) to improve their problem-solving capabilities with the aid of suitable external tools. In our work, we further advance this concept by introducing a closed-loop framework, referred to as LLMs A s Tool Makers (LATM), where LLMs create their own reusable tools for problem-solving. Our approach consists of two phases: 1) tool making: an LLM acts as the tool maker that crafts tools for a set of tasks. 2) tool using: another LLM acts as the tool user, which applies the tool built by the tool maker for problem-solving. On the problem-solving server side, tool-making enables continual tool generation and caching as new requests emerge. This framework enables subsequent requests to access cached tools via their corresponding APIs, enhancing the efficiency of task resolution. Recognizing that tool-making requires more sophisticated capabilities, we assign this task to a powerful, albeit resource-intensive, model. Conversely, the simpler tool-using phase is delegated to a lightweight model. This strategic division of labor allows the once-off cost of tool-making to be spread over multiple instances of tool-using, significantly reducing average costs while maintaining strong performance. Furthermore, our method offers a functional cache through the caching and reuse of tools, which stores the functionality of a class of requests instead of the natural language responses from LLMs, thus extending the applicability of the conventional cache mechanism. We evaluate our approach across various complex reasoning tasks, including Big-Bench tasks. With GPT-4 as the tool maker and GPT-3.5 as the tool user, LATM demonstrates performance equivalent to using GPT-4 for both roles, but with a significantly reduced inference cost.
From Bricks to Bridges: Product of Invariances to Enhance Latent Space Communication
Venue: Conference ICLR 2024
Year: 2024

It has been observed that representations learned by distinct neural networks conceal structural similarities when the models are trained under similar inductive biases. From a geometric perspective, identifying the classes of transformations and the related invariances that connect these representations is fundamental to unlocking applications, such as merging, stitching, and reusing different neural modules. However, estimating task-specific transformations a priori can be challenging and expensive due to several factors (e.g., weights initialization, training hyperparameters, or data modality). To this end, we introduce a versatile method to directly incorporate a set of invariances into the representations, constructing a product space of invariant components on top of the latent representations without requiring prior knowledge about the optimal invariance to infuse. We validate our solution on classification and reconstruction tasks, observing consistent latent similarity and downstream performance improvements in a zero-shot stitching setting. The experimental analysis comprises three modalities (vision, text, and graphs), twelve pretrained foundational models, nine benchmarks, and several architectures trained from scratch.
Retrieval is Accurate Generation
Venue: Conference ICLR 2024
Year: 2024

Standard language models generate text by selecting tokens from a fixed, finite, and standalone vocabulary. We introduce a novel method that selects context-aware phrases from a collection of supporting documents. One of the most significant challenges for this paradigm shift is determining the training oracles, because a string of text can be segmented in various ways and each segment can be retrieved from numerous possible documents. To address this, we propose to initialize the training oracles using linguistic heuristics and, more importantly, bootstrap the oracles through iterative self-reinforcement. Extensive experiments show that our model not only outperforms standard language models on a variety of knowledge-intensive tasks but also demonstrates improved generation quality in open-ended text generation. For instance, compared to the standard language model counterpart, our model raises the accuracy from 23.47% to 36.27% on OpenbookQA, and improves the MAUVE score from 42.61% to 81.58% in open-ended text generation. Remarkably, our model also achieves the best performance and the lowest latency among several retrieval-augmented baselines. In conclusion, we assert that retrieval is more accurate generation and hope that our work will encourage further research on this new paradigm shift.
TEMPO: Prompt-based Generative Pre-trained Transformer for Time Series Forecasting
Venue: Conference ICLR 2024
Year: 2024

The past decade has witnessed significant advances in time series modeling with deep learning. While achieving state-of-the-art results, the best-performing architectures vary highly across applications and domains. Meanwhile, for natural language processing, the Generative Pre-trained Transformer (GPT) has demonstrated impressive performance via training one general-purpose model across various textual datasets. It is intriguing to explore whether GPT-type architectures can be effective for time series, capturing the intrinsic dynamic attributes and leading to significant accuracy improvements. In this paper, we propose a novel framework, TEMPO, that can effectively learn time series representations. We focus on utilizing two essential inductive biases of the time series task for pre-trained models: (i) decomposition of the complex interaction between trend, seasonal and residual components; and (ii) introducing the design of prompts to facilitate distribution adaptation in different types of time series. TEMPO expands the capability for dynamically modeling real-world temporal phenomena from data within diverse domains. Our experiments demonstrate the superior performance of TEMPO over state-of-the-art methods on zero shot setting for a number of time series benchmark datasets. This performance gain is observed not only in scenarios involving previously unseen datasets but also in scenarios with multi-modal inputs. This compelling finding highlights TEMPO's potential to constitute a foundational model-building framework.
IRAD: Implicit Representation-driven Image Resampling against Adversarial Attacks
Venue: Conference ICLR 2024
Year: 2024

We introduce a novel approach to counter adversarial attacks, namely, image resampling. Image resampling transforms a discrete image into a new one, simulating the process of scene recapturing or rerendering as specified by a geometrical transformation. The underlying rationale behind our idea is that image resampling can alleviate the influence of adversarial perturbations while preserving essential semantic information, thereby conferring an inherent advantage in defending against adversarial attacks. To validate this concept, we present a comprehensive study on leveraging image resampling to defend against adversarial attacks. We have developed basic resampling methods that employ interpolation strategies and coordinate shifting magnitudes. Our analysis reveals that these basic methods can partially mitigate adversarial attacks. However, they come with apparent limitations: the accuracy of clean images noticeably decreases, while the improvement in accuracy on adversarial examples is not substantial. We propose implicit representation-driven image resampling (IRAD) to overcome these limitations. First, we construct an implicit continuous representation that enables us to represent any input image within a continuous coordinate space. Second, we introduce SampleNet, which automatically generates pixel-wise shifts for resampling in response to different inputs. Furthermore, we can extend our approach to the state-of-the-art diffusion-based method, accelerating it with fewer time steps while preserving its defense capability. Extensive experiments demonstrate that our method significantly enhances the adversarial robustness of diverse deep models against various attacks while maintaining high accuracy on clean images.
Physics-Regulated Deep Reinforcement Learning: Invariant Embeddings
Venue: Conference ICLR 2024
Year: 2024

This paper proposes the Phy-DRL: a physics-regulated deep reinforcement learning (DRL) framework for safety-critical autonomous systems. The Phy-DRL has three distinguished invariant-embedding designs: i) residual action policy (i.e., integrating data-driven-DRL action policy and physics-model-based action policy), ii) automatically constructed safety-embedded reward, and iii) physics-model-guided neural network (NN) editing, including link editing and activation editing. Theoretically, the Phy-DRL exhibits 1) a mathematically provable safety guarantee and 2) strict compliance of critic and actor networks with physics knowledge about the action-value function and action policy. Finally, we evaluate the Phy-DRL on a cart-pole system and a quadruped robot. The experiments validate our theoretical results and demonstrate that Phy-DRL features guaranteed safety compared to purely data-driven DRL and solely model-based design while offering remarkably fewer learning parameters and fast training towards safety guarantee.