NeurIPS 2023 Papers

Antibodies have become an important class of therapeutic agents to treat human diseases. To accelerate therapeutic antibody discovery, computational methods, especially machine learning, have attracted considerable interest for predicting specific interactions between antibody candidates and target antigens such as viruses and bacteria. However, the publicly available datasets in existing works have notable limitations, such as small sizes and the lack of non-binding samples and exact amino acid sequences. To overcome these limitations, we have developed AVIDa-hIL6, a large-scale dataset for predicting antigen-antibody interactions in the variable domain of heavy chain of heavy chain antibodies (VHHs), produced from an alpaca immunized with the human interleukin-6 (IL-6) protein, as antigens. By leveraging the simple structure of VHHs, which facilitates identification of full-length amino acid sequences by DNA sequencing technology, AVIDa-hIL6 contains 573,891 antigen-VHH pairs with amino acid sequences. All the antigen-VHH pairs have reliable labels for binding or non-binding, as generated by a novel labeling method. Furthermore, via introduction of artificial mutations, AVIDa-hIL6 contains 30 different mutants in addition to wild-type IL-6 protein. This characteristic provides opportunities to develop machine learning models for predicting changes in antibody binding by antigen mutations. We report experimental benchmark results on AVIDa-hIL6 by using machine learning models. The results indicate that the existing models have potential, but further research is needed to generalize them to predict effective antibodies against unknown mutants. The dataset is available at https://avida-hil6.cognanous.com.

Vision Transformer (ViT) faces obstacles in wide application due to its huge computational cost. Almost all existing studies on compressing ViT adopt the manner of splitting an image with a single granularity, with very few exploration of splitting an image with multi-granularity. As we know, important information often randomly concentrate in few regions of an image, necessitating multi-granularity attention allocation to an image. Enlightened by this, we introduce the multi-granularity strategy to compress ViT, which is simple but effective. We propose a two-stage multi-granularity framework, MG-ViT, to balance ViT’s performance and computational cost. In single-granularity inference stage, an input image is split into a small number of patches for simple inference. If necessary, multi-granularity inference stage will be instigated, where the important patches are further subsplit into multi-finer-grained patches for subsequent inference. Moreover, prior studies on compression only for classification, while we extend the multi-granularity strategy to hierarchical ViT for downstream tasks such as detection and segmentation. Extensive experiments Prove the effectiveness of the multi-granularity strategy. For instance, on ImageNet, without any loss of performance, MG-ViT reduces 47\% FLOPs of LV-ViT-S and 56\% FLOPs of DeiT-S.

Sparse linear models are one of several core tools for interpretable machine learning, a field of emerging importance as predictive models permeate decision-making in many domains. Unfortunately, sparse linear models are far less flexible as functions of their input features than black-box models like deep neural networks. With this capability gap in mind, we study a not-uncommon situation where the input features dichotomize into two groups: explanatory features, which are candidates for inclusion as variables in an interpretable model, and contextual features, which select from the candidate variables and determine their effects. This dichotomy leads us to the contextual lasso, a new statistical estimator that fits a sparse linear model to the explanatory features such that the sparsity pattern and coefficients vary as a function of the contextual features. The fitting process learns this function nonparametrically via a deep neural network. To attain sparse coefficients, we train the network with a novel lasso regularizer in the form of a projection layer that maps the network's output onto the space of $\ell_1$-constrained linear models. An extensive suite of experiments on real and synthetic data suggests that the learned models, which remain highly transparent, can be sparser than the regular lasso without sacrificing the predictive power of a standard deep neural network.

We propose an automated algorithm to stress-test a trained visual model by generating language-guided counterfactual test images (LANCE). Our method leverages recent progress in large language modeling and text-based image editing to augment an IID test set with a suite of diverse, realistic, and challenging test images without altering model weights. We benchmark the performance of a diverse set of pre-trained models on our generated data and observe significant and consistent performance drops. We further analyze model sensitivity across different types of edits, and demonstrate its applicability at surfacing previously unknown class-level model biases in ImageNet. Code is available at https://github.com/virajprabhu/lance.

Despite the recent advancements in offline reinforcement learning via supervised learning (RvS) and the success of the decision transformer (DT) architecture in various domains, DTs have fallen short in several challenging benchmarks. The root cause of this underperformance lies in their inability to seamlessly connect segments of suboptimal trajectories. To overcome this limitation, we present a novel approach to enhance RvS methods by integrating intermediate targets. We introduce the Waypoint Transformer (WT), using an architecture that builds upon the DT framework and conditioned on automatically-generated waypoints. The results show a significant increase in the final return compared to existing RvS methods, with performance on par or greater than existing state-of-the-art temporal difference learning-based methods. Additionally, the performance and stability improvements are largest in the most challenging environments and data configurations, including AntMaze Large Play/Diverse and Kitchen Mixed/Partial.

Offline reinforcement learning (RL) has received considerable attention in recent years due to its attractive capability of learning policies from offline datasets without environmental interactions. Despite some success in the single-agent setting, offline multi-agent RL (MARL) remains to be a challenge. The large joint state-action space and the coupled multi-agent behaviors pose extra complexities for offline policy optimization. Most existing offline MARL studies simply apply offline data-related regularizations on individual agents, without fully considering the multi-agent system at the global level. In this work, we present OMIGA, a new offline multi-agent RL algorithm with implicit global-to-local value regularization. OMIGA provides a principled framework to convert global-level value regularization into equivalent implicit local value regularizations and simultaneously enables in-sample learning, thus elegantly bridging multi-agent value decomposition and policy learning with offline regularizations. Based on comprehensive experiments on the offline multi-agent MuJoCo and StarCraft II micro-management tasks, we show that OMIGA achieves superior performance over the state-of-the-art offline MARL methods in almost all tasks.

Despite the remarkable achievements of neural radiance fields (NeRF) in representing 3D scenes and generating novel view images, the aliasing issue, rendering 'jaggies' or 'blurry' images at varying camera distances, remains unresolved in most existing approaches. The recently proposed mip-NeRF has effectively addressed this challenge by introducing integrated positional encodings (IPE). However, it relies on MLP architecture to represent the radiance fields, missing out on the fast training speed offered by the latest grid-based methods. In this work, we present mip-Grid, a novel approach that integrates anti-aliasing techniques into grid-based representations for radiance fields, mitigating the aliasing artifacts while enjoying fast training time. Notably, the proposed method uses a single-scale shared grid representation and a single-sampling approach, which only introduces minimal additions to the model parameters and computational costs. To handle scale ambiguity, mip-Grid generates multiple grids by applying simple convolution operations over the shared grid and uses the scale-aware coordinate to retrieve the appropriate features from the generated multiple grids. To test the effectiveness, we incorporated the proposed approach into the two recent representative grid-based methods, TensoRF and K-Planes. The experimental results demonstrated that mip-Grid greatly improved the rendering performance of both methods and showed comparable performance to mip-NeRF on multi-scale datasets while achieving significantly faster training time.

We present Pre-trained Machine Reader (PMR), a novel method for retrofitting pre-trained masked language models (MLMs) to pre-trained machine reading comprehension (MRC) models without acquiring labeled data. PMR can resolve the discrepancy between model pre-training and downstream fine-tuning of existing MLMs. To build the proposed PMR, we constructed a large volume of general-purpose and high-quality MRC-style training data by using Wikipedia hyperlinks and designed a Wiki Anchor Extraction task to guide the MRC-style pre-training. Apart from its simplicity, PMR effectively solves extraction tasks, such as Extractive Question Answering and Named Entity Recognition. PMR shows tremendous improvements over existing approaches, especially in low-resource scenarios. When applied to the sequence classification task in the MRC formulation, PMR enables the extraction of high-quality rationales to explain the classification process, thereby providing greater prediction explainability. PMR also has the potential to serve as a unified model for tackling various extraction and classification tasks in the MRC formulation.

Pruning schemes have been widely used in practice to reduce the complexity of trained models with a massive number of parameters. In fact, several practical studies have shown that if the pruned model is fine-tuned with some gradient-based updates it generalizes well to new samples. Although the above pipeline, which we refer to as pruning + fine-tuning, has been extremely successful in lowering the complexity of trained models, there is very little known about the theory behind this success. In this paper we address this issue by investigating the pruning + fine-tuning framework on the overparameterized matrix sensing problem with the ground truth denoted $U_\star \in \mathbb{R}^{d \times r}$ and the overparameterized model $U \in \mathbb{R}^{d \times k}$ with $k \gg r$. We study the approximate local minima of the mean square error, augmented with a smooth version of a group Lasso regularizer, $\sum_{i=1}^{k} \lVert Ue_i \rVert_2 $. In particular, we provably show that pruning all the columns below a certain explicit $\ell_2$-norm threshold results in a solution $U_{\text{prune}}$ which has the minimum number of columns $r$, yet close to the ground truth in training loss. Moreover, in the subsequent fine-tuning phase, gradient descent initialized at $U_{\text{prune}}$ converges at a linear rate to its limit. While our analysis provides insights into the role of regularization in pruning, we also show that running gradient descent in the absence of regularization results in models which {are not suitable for greedy pruning}, i.e., many columns could have their $\ell_2$ norm comparable to that of the maximum. Lastly, we show that our results also extend for the training and pruning of two-layer neural networks with quadratic activation functions. To the best of our knowledge, our results provide the first rigorous insights on why greedy pruning + fine-tuning leads to smaller models which also generalize well.

Despite the success of neural-based combinatorial optimization methods for end-to-end heuristic learning, out-of-distribution generalization remains a challenge. In this paper, we present a novel formulation of Combinatorial Optimization Problems (COPs) as Markov Decision Processes (MDPs) that effectively leverages common symmetries of COPs to improve out-of-distribution robustness. Starting from a direct MDP formulation of a constructive method, we introduce a generic way to reduce the state space, based on Bisimulation Quotienting (BQ) in MDPs. Then, for COPs with a recursive nature, we specialize the bisimulation and show how the reduced state exploits the symmetries of these problems and facilitates MDP solving. Our approach is principled and we prove that an optimal policy for the proposed BQ-MDP actually solves the associated COPs. We illustrate our approach on five classical problems: the Euclidean and Asymmetric Traveling Salesman, Capacitated Vehicle Routing, Orienteering and Knapsack Problems. Furthermore, for each problem, we introduce a simple attention-based policy network for the BQ-MDPs, which we train by imitation of (near) optimal solutions of small instances from a single distribution. We obtain new state-of-the-art results for the five COPs on both synthetic and realistic benchmarks. Notably, in contrast to most existing neural approaches, our learned policies show excellent generalization performance to much larger instances than seen during training, without any additional search procedure. Our code is available at: [link](https://github.com/naver/bq-nco).

What can be learned about causality and experimentation from passive data? This question is salient given recent successes of passively-trained language models in interactive domains such as tool use. Passive learning is inherently limited. However, we show that purely passive learning can in fact allow an agent to learn generalizable strategies for determining and using causal structures, as long as the agent can intervene at test time. We formally illustrate that learning a strategy of first experimenting, then seeking goals, can allow generalization from passive learning in principle. We then show empirically that agents trained via imitation on expert data can indeed generalize at test time to infer and use causal links which are never present in the training data; these agents can also generalize experimentation strategies to novel variable sets never observed in training. We then show that strategies for causal intervention and exploitation can be generalized from passive data even in a more complex environment with high-dimensional observations, with the support of natural language explanations. Explanations can even allow passive learners to generalize out-of-distribution from perfectly-confounded training data. Finally, we show that language models, trained only on passive next-word prediction, can generalize causal intervention strategies from a few-shot prompt containing explanations and reasoning. These results highlight the surprising power of passive learning of active causal strategies, and have implications for understanding the behaviors and capabilities of language models.

Differentially private mechanisms restrict the membership inference capabilities of powerful (optimal) adversaries against machine learning models. Such adversaries are rarely encountered in practice. In this work, we examine a more realistic threat model relaxation, where (sub-optimal) adversaries lack access to the exact model training database, but may possess related or partial data. We then formally characterise and experimentally validate adversarial membership inference capabilities in this setting in terms of hypothesis testing errors. Our work helps users to interpret the privacy properties of sensitive data processing systems under realistic threat model relaxations and choose appropriate noise levels for their use-case.

Automated reasoning with unstructured natural text is a key requirement for many potential applications of NLP and for developing robust AI systems. Recently, Language Models (LMs) have demonstrated complex reasoning capacities even without any finetuning. However, existing evaluation for automated reasoning assumes access to a consistent and coherent set of information over which models reason. When reasoning in the real-world, the available information is frequently inconsistent or contradictory, and therefore models need to be equipped with a strategy to resolve such conflicts when they arise. One widely-applicable way of resolving conflicts is to impose preferences over information sources (e.g., based on source credibility or information recency) and adopt the source with higher preference. In this paper, we formulate the problem of reasoning with contradictory information guided by preferences over sources as the classical problem of defeasible reasoning, and develop a dataset called BoardgameQA for measuring the reasoning capacity of LMs in this setting. BoardgameQA also incorporates reasoning with implicit background knowledge, to better reflect reasoning problems in downstream applications. We benchmark various LMs on BoardgameQA and the results reveal a significant gap in the reasoning capacity of state-of-the-art LMs on this problem, showing that reasoning with conflicting information does not surface out-of-the-box in LMs. While performance can be improved with finetuning, it nevertheless remains poor.

Existing contrastive learning methods rely on pairwise sample contrast $z_x^\top z_{x'}$ to learn data representations, but the learned features often lack clear interpretability from a human perspective. Theoretically, it lacks feature identifiability and different initialization may lead to totally different features. In this paper, we study a new method named tri-factor contrastive learning (triCL) that involves a 3-factor contrast in the form of $z_x^\top S z_{x'}$, where $S=\text{diag}(s_1,\dots,s_k)$ is a learnable diagonal matrix that automatically captures the importance of each feature. We show that by this simple extension, triCL can not only obtain identifiable features that eliminate randomness but also obtain more interpretable features that are ordered according to the importance matrix $S$. We show that features with high importance have nice interpretability by capturing common classwise features, and obtain superior performance when evaluated for image retrieval using a few features. The proposed triCL objective is general and can be applied to different contrastive learning methods like SimCLR and CLIP. We believe that it is a better alternative to existing 2-factor contrastive learning by improving its identifiability and interpretability with minimal overhead. Code is available at https://github.com/PKU-ML/Tri-factor-Contrastive-Learning.

With the popularity of automatic code generation tools, such as Copilot, the study of the potential hazards of these tools is gaining importance. In this work, we explore the social bias problem in pre-trained code generation models. We propose a new paradigm to construct code prompts and successfully uncover social biases in code generation models. To quantify the severity of social biases in generated code, we develop a dataset along with three metrics to evaluate the overall social bias and fine-grained unfairness across different demographics. Experimental results on three pre-trained code generation models (Codex, InCoder, and CodeGen) with varying sizes, reveal severe social biases. Moreover, we conduct analysis to provide useful insights for further choice of code generation models with low social bias.

We introduce VisoGender, a novel dataset for benchmarking gender bias in vision-language models. We focus on occupation-related biases within a hegemonic system of binary gender, inspired by Winograd and Winogender schemas, where each image is associated with a caption containing a pronoun relationship of subjects and objects in the scene. VisoGender is balanced by gender representation in professional roles, supporting bias evaluation in two ways: i) resolution bias, where we evaluate the difference between pronoun resolution accuracies for image subjects with gender presentations perceived as masculine versus feminine by human annotators and ii) retrieval bias, where we compare ratios of professionals perceived to have masculine and feminine gender presentations retrieved for a gender-neutral search query. We benchmark several state-of-the-art vision-language models and find that they demonstrate bias in resolving binary gender in complex scenes. While the direction and magnitude of gender bias depends on the task and the model being evaluated, captioning models are generally less biased than Vision-Language Encoders.

Recent discoveries have revealed that deep neural networks might behave in a biased manner in many real-world scenarios. For instance, deep networks trained on a large-scale face recognition dataset CelebA tend to predict blonde hair for females and black hair for males. Such biases not only jeopardize the robustness of models but also perpetuate and amplify social biases, which is especially concerning for automated decision-making processes in healthcare, recruitment, etc., as they could exacerbate unfair economic and social inequalities among different groups. Existing debiasing methods suffer from high costs in bias labeling or model re-training, while also exhibiting a deficiency in terms of elucidating the origins of biases within the model. To this respect, we propose a fast model debiasing method (FMD) which offers an efficient approach to identify, evaluate and remove biases inherent in trained models. The FMD identifies biased attributes through an explicit counterfactual concept and quantifies the influence of data samples with influence functions. Moreover, we design a machine unlearning-based strategy to efficiently and effectively remove the bias in a trained model with a small counterfactual dataset. Experiments on the Colored MNIST, CelebA, and Adult Income datasets demonstrate that our method achieves superior or competing classification accuracies compared with state-of-the-art retraining-based methods while attaining significantly fewer biases and requiring much less debiasing cost. Notably, our method requires only a small external dataset and updating a minimal amount of model parameters, without the requirement of access to training data that may be too large or unavailable in practice.

The performance of deep learning models heavily relies on the quality of the training data. Inadequacies in the training data, such as corrupt input or noisy labels, can lead to the failure of model generalization. Recent studies propose repairing the model by identifying the training samples that contribute to the failure and removing their influence from the model. However, it is important to note that the identified data may contain both beneficial and detrimental information. Simply erasing the information of the identified data from the model can have a negative impact on its performance, especially when accurate data is mistakenly identified as detrimental and removed. To overcome this challenge, we propose a novel approach that leverages the knowledge obtained from a retained clean set. Our method first identifies harmful data by utilizing the clean set, then separates the beneficial and detrimental information within the identified data. Finally, we utilize the extracted beneficial information to enhance the model's performance. Through empirical evaluations, we demonstrate that our method outperforms baseline approaches in both identifying harmful data and rectifying model failures. Particularly in scenarios where identification is challenging and a significant amount of benign data is involved, our method improves performance while the baselines deteriorate due to the erroneous removal of beneficial information.

Modern recommender systems perform large-scale retrieval by embedding queries and item candidates in the same unified space, followed by approximate nearest neighbor search to select top candidates given a query embedding. In this paper, we propose a novel generative retrieval approach, where the retrieval model autoregressively decodes the identifiers of the target candidates. To that end, we create semantically meaningful tuple of codewords to serve as a Semantic ID for each item. Given Semantic IDs for items in a user session, a Transformer-based sequence-to-sequence model is trained to predict the Semantic ID of the next item that the user will interact with. We show that recommender systems trained with the proposed paradigm significantly outperform the current SOTA models on various datasets. In addition, we show that incorporating Semantic IDs into the sequence-to-sequence model enhances its ability to generalize, as evidenced by the improved retrieval performance observed for items with no prior interaction history.