Mechanism Design

To enhance the efficiency and practicality of federated bandit learning, recent advances have introduced incentives to motivate communication among clients, where a client participates only when the incentive offered by the server outweighs its participation cost. However, existing incentive mechanisms naively assume the clients are truthful: they all report their true cost and thus the higher cost one participating client claims, the more the server has to pay. Therefore, such mechanisms are vulnerable to strategic clients aiming to optimize their own utility by misreporting. To address this issue, we propose an incentive compatible (i.e., truthful) communication protocol, named Truth-FedBan, where the incentive for each participant is independent of its self-reported cost, and reporting the true cost is the only way to achieve the best utility. More importantly, Truth-FedBan still guarantees the sub-linear regret and communication cost without any overhead. In other words, the core conceptual contribution of this paper is, for the first time, demonstrating the possibility of simultaneously achieving incentive compatibility and nearly optimal regret in federated bandit learning. Extensive numerical studies further validate the effectiveness of our proposed solution.

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.

Privacy amplification exploits randomness in data selection to provide tighter differential privacy (DP) guarantees. This analysis is key to DP-SGD's success in machine learning (ML), but, is not readily applicable to the newer state-of-the-art (SOTA) algorithms. This is because these algorithms, known as DP-FTRL, use the matrix mechanism to add correlated noise instead of independent noise as in DP-SGD. In this paper, we propose "MMCC'' (matrix mechanism conditional composition), the first algorithm to analyze privacy amplification via sampling for any generic matrix mechanism. MMCC is nearly tight in that it approaches a lower bound as $\epsilon\to0$. To analyze correlated outputs in MMCC, we prove that they can be analyzed as if they were independent, by conditioning them on prior outputs. Our "conditional composition theorem'' has broad utility: we use it to show that the noise added to binary-tree-DP-FTRL can asymptotically match the noise added to DP-SGD with amplification. Our algorithm also has practical empirical utility. We show that amplification leads to significant improvement in the privacy/utility trade-offs for DP-FTRL style algorithms for standard benchmark tasks.

The training method of Spiking Neural Networks (SNNs) is an essential problem, and how to integrate local and global learning is a worthy research interest. However, the current integration methods do not consider the network conditions suitable for local and global learning, and thus fail to balance their advantages. In this paper, we propose an Excitation-Inhibition Mechanism-assisted Hybrid Learning(EIHL) algorithm that adjusts the network connectivity by using the excitation-inhibition mechanism and then switches between local and global learning according to the network connectivity. The experimental results on CIFAR10/100 and DVS-CIFAR10 demonstrate that the EIHL not only has better accuracy performance than other methods but also has excellent sparsity advantage. Especially, the Spiking VGG11 is trained by EIHL, STBP, and STDP on DVS_CIFAR10, respectively. The accuracy of the Spiking VGG11 model on EIHL is 62.45%, which is 4.35% higher than STBP and 11.40% higher than STDP, and the sparsity is 18.74%, which is 18.74% higher than the other two methods. Moreover, the excitation-inhibition mechanism used in our method also offers a new perspective on the field of SNN learning.

Interference is ubiquitous when conducting causal experiments over networks. Except for certain network structures, causal inference on the network in the presence of interference is difficult due to the entanglement between the treatment assignments and the interference levels. In this article, we conduct causal inference under interference on an observed, sparse, but connected network, and we propose a novel design of experiments based on an independent set. Compared to conventional designs, the independent-set design focuses on an independent subset of data and controls their interference exposures through the assignments to the rest (auxiliary set). We provide a lower bound on the size of the independent set from a greedy algorithm and justify the theoretical performance of estimators under the proposed design. Our approach is capable of estimating both spillover effects and treatment effects. We justify its superiority over conventional methods and illustrate the empirical performance through simulations.

Data attribution seeks to trace model outputs back to training data. With the recent development of diffusion models, data attribution has become a desired module to properly assign valuations for high-quality or copyrighted training samples, ensuring that data contributors are fairly compensated or credited. Several theoretically motivated methods have been proposed to implement data attribution, in an effort to improve the trade-off between computational scalability and effectiveness. In this work, we conduct extensive experiments and ablation studies on attributing diffusion models, specifically focusing on DDPMs trained on CIFAR-10 and CelebA, as well as a Stable Diffusion model LoRA-finetuned on ArtBench. Intriguingly, we report counter-intuitive observations that theoretically unjustified design choices for attribution empirically outperform previous baselines by a large margin, in terms of both linear datamodeling score and counterfactual evaluation. Our work presents a significantly more efficient approach for attributing diffusion models, while the unexpected findings suggest that at least in non-convex settings, constructions guided by theoretical assumptions may lead to inferior attribution performance. The code is available at https://github.com/sail-sg/D-TRAK.

As transformers are equivariant to the permutation of input tokens, encoding the positional information of tokens is necessary for many tasks. However, since existing positional encoding schemes have been initially designed for NLP tasks, their suitability for vision tasks, which typically exhibit different structural properties in their data, is questionable. We argue that existing positional encoding schemes are suboptimal for 3D vision tasks, as they do not respect their underlying 3D geometric structure. Based on this hypothesis, we propose a geometry-aware attention mechanism that encodes the geometric structure of tokens as relative transformation determined by the geometric relationship between queries and key-value pairs. By evaluating on multiple novel view synthesis (NVS) datasets in the sparse wide-baseline multi-view setting, we show that our attention, called Geometric Transform Attention (GTA), improves learning efficiency and performance of state-of-the-art transformer-based NVS models without any additional learned parameters and only minor computational overhead.

Multi-cellular robot design aims to create robots comprised of numerous cells that can be efficiently controlled to perform diverse tasks. Previous research has demonstrated the ability to generate robots for various tasks, but these approaches often optimize robots directly in the vast design space, resulting in robots with complicated morphologies that are hard to control. In response, this paper presents a novel coarse-to-fine method for designing multi-cellular robots. Initially, this strategy seeks optimal coarse-grained robots and progressively refines them. To mitigate the challenge of determining the precise refinement juncture during the coarse-to-fine transition, we introduce the Hyperbolic Embeddings for Robot Design (HERD) framework. HERD unifies robots of various granularity within a shared hyperbolic space and leverages a refined Cross-Entropy Method for optimization. This framework enables our method to autonomously identify areas of exploration in hyperbolic space and concentrate on regions demonstrating promise. Finally, the extensive empirical studies on various challenging tasks sourced from EvoGym show our approach's superior efficiency and generalization capability.

We investigate the mechanism design problem faced by a principal who hires \emph{multiple} agents to gather and report costly information. Then, the principal exploits the information to make an informed decision. We model this problem as a game, where the principal announces a mechanism consisting in action recommendations and a payment function, a.k.a. scoring rule. Then, each agent chooses an effort level and receives partial information about an underlying state of nature based on the effort. Finally, the agents report the information (possibly non-truthfully), the principal takes a decision based on this information, and the agents are paid according to the scoring rule. While previous work focuses on single-agent problems, we consider multi-agents settings. This poses the challenge of coordinating the agents' efforts and aggregating correlated information. Indeed, we show that optimal mechanisms must correlate agents' efforts, which introduces externalities among the agents, and hence complex incentive compatibility constraints and equilibrium selection problems. First, we design a polynomial-time algorithm to find an optimal incentive compatible mechanism. Then, we study an online problem, where the principal repeatedly interacts with a group of unknown agents. We design a no-regret algorithm that provides $\widetilde{\mathcal{O}}(T^{2/3})$ regret with respect to an optimal mechanism, matching the state-of-the-art bound for single-agent settings.

Integrated circuits or chips are key to enable computing in modern industry. Designing a chip relies on human experts to produce chip data through professional electronic design automation (EDA) software and complicated procedures. Nowadays, prompted by the wide variety of machine learning (ML) datasets, we have witnessed great advancement of ML algorithms in computer vision, natural language processing, and other fields. However, in chip design, high human workload and data sensitivity cause the lack of public datasets, which hinders the progress of ML development for EDA. To this end, we introduce an advanced large-scale dataset, CircuitNet 2.0, which targets promoting ML innovations in a realistic chip design environment. In order to approach the realistic chip design space, we collect more than 10,000 samples with a variety of chip designs (e.g., CPU, GPU, and AI Chip). All the designs are conducted through complete commercial design flows in a widely-used technology node, 14nm FinFET. We collect comprehensive data, including routability, timing, and power, from the design flow to support versatile ML tasks in EDA. Besides, we also introduce some realistic ML tasks with CircuitNet 2.0 to verify the potential for boosting innovations.

Recent studies have shown competitive performance in protein inverse folding, while most of them disregard the importance of predictive confidence, fail to cover the vast protein space, and do not incorporate common protein knowledge. Given the great success of pretrained models on diverse protein-related tasks and the fact that recovery is highly correlated with confidence, we wonder whether this knowledge can push the limits of protein design further. As a solution, we propose a knowledge-aware module that refines low-quality residues. We also introduce a memory-retrieval mechanism to save more than 50\% of the training time. We extensively evaluate our proposed method on the CATH, TS50, TS500, and PDB datasets and our results show that our KW-Design method outperforms the previous PiFold method by approximately 9\% on the CATH dataset. KW-Design is the first method that achieves 60+\% recovery on all these benchmarks. We also provide additional analysis to demonstrate the effectiveness of our proposed method. The code is publicly available via \href{https://github.com/A4Bio/ProteinInvBench}{GitHub}.

Time series forecasting is an important and forefront task whose techniques have been applied to electricity forecasting, trajectory prediction, labor planning, etc. However, most of time series forecasting techniques assume that the training data is clean without anomalies. This assumption is unrealistic since the collected time series data can be contaminated in practice. The forecasting model will be inferior if it is directly trained by time series with anomalies. Thus it is essential to develop methods to automatically learn a robust forecasting model from the contaminated data. In this paper, we first statistically define three types of anomalies, then theoretically and experimentally analyze the loss robustness and sample robustness when these anomalies exist. Based on our analyses, we propose a simple and efficient algorithm to learn a robust forecasting model. Extensive experiments show that our method is highly robust and outperforms all existing approaches. The code is available at https://github.com/haochenglouis/RobustTSF.

We study a strategic variant of the multi-armed bandit problem, which we coin the strategic click-bandit. This model is motivated by applications in online recommendation where the choice of recommended items depends on both the click-through rates and the post-click rewards. Like in classical bandits, rewards follow a fixed unknown distribution. However, we assume that the click-rate of each arm is chosen strategically by the arm (e.g., a host on Airbnb) in order to maximize the number of times it gets clicked. The algorithm designer does not know the post-click rewards nor the arms' actions (i.e., strategically chosen click-rates) in advance, and must learn both values over time. To solve this problem, we design an incentive-aware learning algorithm, UCB-S, which achieves two goals simultaneously: (a) incentivizing desirable arm behavior under uncertainty; (b) minimizing regret by learning unknown parameters. We approximately characterize all Nash equilibria of the arms under UCB-S and show a $\tilde{\mathcal{O}} (\sqrt{KT})$ regret bound uniformly in every equilibrium. We also show that incentive-unaware algorithms generally fail to achieve low regret in the strategic click-bandit. Finally, we support our theoretical results by simulations of strategic arm behavior which confirm the effectiveness and robustness of our proposed incentive design.

Although transformers demonstrate impressive capabilities in a variety of tasks, the fairness issue remains a significant concern when deploying these models. Existing works to address fairness issues in transformers require sensitive labels (such as age, gender, etc.), which can raise privacy concerns or violate legal regulations. An alternative way is through fairness without demographics. However, existing works that improve Rawlsian Max-Min fairness may impose overly restrictive constraints. Other methods that use auxiliary networks could be parameter inefficient. In this paper, we present a new approach to debiasing transformers by leveraging their inherent structure. By reconsidering the roles of important components (queries, keys, and values) in the attention mechanism, we introduce a simple yet effective debiasing strategy from two perspectives: 1) Grounded in theoretical analysis, we normalize and apply absolute value operations to queries and keys to minimize the bias in attention weight allocation; 2) We reduce the bias within values through local alignment via contrastive learning. Throughout the entire process, our approach does not require any sensitive labels. Furthermore, to enhance memory efficiency in the training phase, we propose a strategy that debias only the last encoder to improve fairness in pre-trained models. We conduct experiments in computer vision and natural language processing tasks and show that our method is comparable and even outperforms the state-of-the-art method with substantially lower energy consumption.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

As large language models (LLMs) are adopted as a fundamental component of language technologies, it is crucial to accurately characterize their performance. Because choices in prompt design can strongly influence model behavior, this design process is critical in effectively using any modern pre-trained generative language model. In this work, we focus on LLM sensitivity to a quintessential class of meaning-preserving design choices: prompt formatting. We find that several widely used open-source LLMs are extremely sensitive to subtle changes in prompt formatting in few-shot settings, with performance differences of up to 76 accuracy points when evaluated using LLaMA-2-13B. Sensitivity remains even when increasing model size, the number of few-shot examples, or performing instruction tuning. Our analysis suggests that work evaluating LLMs with prompting-based methods would benefit from reporting a range of performance across plausible prompt formats, instead of the currently-standard practice of reporting performance on a single format. We also show that format performance only weakly correlates between models, which puts into question the methodological validity of comparing models with an arbitrarily chosen, fixed prompt format. To facilitate systematic analysis we propose FormatSpread, an algorithm that rapidly evaluates a sampled set of plausible prompt formats for a given task, and reports the interval of expected performance without accessing model weights. Furthermore, we present a suite of analyses that characterize the nature of this sensitivity, including exploring the influence of particular atomic perturbations and the internal representation of particular formats.

Supervised learning datasets may contain multiple cues that explain the training set equally well, i.e., learning any of them would lead to the correct predictions on the training data. However, many of them can be spurious, i.e., lose their predictive power under a distribution shift and consequently fail to generalize to out-of-distribution (OOD) data. Recently developed "diversification" methods (Lee et al., 2023; Pagliardini et al., 2023) approach this problem by finding multiple diverse hypotheses that rely on different features. This paper aims to study this class of methods and identify the key components contributing to their OOD generalization abilities. We show that (1) diversification methods are highly sensitive to the distribution of the unlabeled data used for diversification and can underperform significantly when away from a method-specific sweet spot. (2) Diversification alone is insufficient for OOD generalization. The choice of the used learning algorithm, e.g., the model's architecture and pretraining, is crucial. In standard experiments (classification on Waterbirds and Office-Home datasets), using the second-best choice leads to an up to 20\% absolute drop in accuracy. (3) The optimal choice of learning algorithm depends on the unlabeled data and vice versa i.e. they are co-dependent. (4) Finally, we show that, in practice, the above pitfalls cannot be alleviated by increasing the number of diverse hypotheses, the major feature of diversification methods. These findings provide a clearer understanding of the critical design factors influencing the OOD generalization abilities of diversification methods. They can guide practitioners in how to use the existing methods best and guide researchers in developing new, better ones.

In federated learning (FL), incentivizing contributions of training resources (e.g., data, compute) from potentially competitive clients is crucial. Existing incentive mechanisms often distribute post-training monetary rewards, which suffer from practical challenges of timeliness and feasibility of the rewards. Rewarding the clients after the completion of training may incentivize them to abort the collaboration, and monetizing the contribution is challenging in practice. To address these problems, we propose an incentive-aware algorithm that offers differentiated training-time model rewards for each client at each FL iteration. We theoretically prove that such a $\textit{local}$ design ensures the $\textit{global}$ objective of client incentivization. Through theoretical analyses, we further identify the issue of error propagation in model rewards and thus propose a stochastic reference-model recovery strategy to ensure theoretically that all the clients eventually obtain the optimal model in the limit. We perform extensive experiments to demonstrate the superior incentivizing performance of our method compared to existing baselines.

Dropout is a widely utilized regularization technique in the training of neural networks, nevertheless, its underlying mechanism and impact on achieving good generalization abilities remain to be further understood. In this work, we start by undertaking a rigorous theoretical derivation of the stochastic modified equations, with the primary aim of providing an effective approximation for the discrete iterative process of dropout. Meanwhile, we experimentally verify SDE's ability to approximate dropout under a wider range of settings. Subsequently, we empirically delve into the intricate mechanisms by which dropout facilitates the identification of flatter minima. This exploration is conducted through intuitive approximations, exploiting the structural analogies inherent in the Hessian of loss landscape and the covariance of dropout. Our empirical findings substantiate the ubiquitous presence of the Hessian-variance alignment relation throughout the training process of dropout.

Advances like protein diffusion have marked revolutionary progress in $\textit{de novo}$ protein design, a central topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Only a few basic encoders, like IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we introduce the Vector Field Network (VFN), that enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential $\textit{universal encoder}$. In protein diffusion (frame modeling), VFN exhibits a impressive performance advantage over IPA, excelling in terms of both designability ($\textbf{67.04}$\% vs. 53.58\%) and diversity ($\textbf{66.54}$\% vs. 51.98\%). In inverse folding(frame and atom modeling), VFN outperforms the previous SoTA model, PiFold ($\textbf{54.7}$\% vs. 51.66\%), on sequence recovery rate; we also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA ($\textbf{62.67}$\% vs. 55.65\%), LM-Design, by a substantial margin. Code is available at https://github.com/aim-uofa/VFN