NeurIPS 2023 Papers

Conference on Neural Information Processing Systems

Decision breakdown

3,584papers

Counted from the official paper list; may differ slightly from the number the conference announced.

  • Oral
    772.1%
  • Spotlight
    40011.2%
  • Poster
    3,10786.7%

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DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing

Yangtian Zhang, Zuobai Zhang, Bozitao Zhong, Sanchit Misra, Jian Tang

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Proteins play a critical role in carrying out biological functions, and their 3D structures are essential in determining their functions. Accurately predicting the conformation of protein side-chains given their backbones is important for applications in protein structure prediction, design and protein-protein interactions. Traditional methods are computationally intensive and have limited accuracy, while existing machine learning methods treat the problem as a regression task and overlook the restrictions imposed by the constant covalent bond lengths and angles. In this work, we present DiffPack, a torsional diffusion model that learns the joint distribution of side-chain torsional angles, the only degrees of freedom in side-chain packing, by diffusing and denoising on the torsional space. To avoid issues arising from simultaneous perturbation of all four torsional angles, we propose autoregressively generating the four torsional angles from $\chi_1$ to $\chi_4$ and training diffusion models for each torsional angle. We evaluate the method on several benchmarks for protein side-chain packing and show that our method achieves improvements of 11.9% and 13.5% in angle accuracy on CASP13 and CASP14, respectively, with a significantly smaller model size ($60\times$ fewer parameters). Additionally, we show the effectiveness of our method in enhancing side-chain predictions in the AlphaFold2 model. Code is available at https://github.com/DeepGraphLearning/DiffPack.

Poster
Towards Revealing the Mystery behind Chain of Thought: A Theoretical Perspective

Guhao Feng, Bohang Zhang, Yuntian Gu, Haotian Ye, Di He, Liwei Wang

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Recent studies have discovered that Chain-of-Thought prompting (CoT) can dramatically improve the performance of Large Language Models (LLMs), particularly when dealing with complex tasks involving mathematics or reasoning. Despite the enormous empirical success, the underlying mechanisms behind CoT and how it unlocks the potential of LLMs remain elusive. In this paper, we take a first step towards theoretically answering these questions. Specifically, we examine the expressivity of LLMs with CoT in solving fundamental mathematical and decision-making problems. By using circuit complexity theory, we first give impossibility results showing that bounded-depth Transformers are unable to directly produce correct answers for basic arithmetic/equation tasks unless the model size grows super-polynomially with respect to the input length. In contrast, we then prove by construction that autoregressive Transformers of constant size suffice to solve both tasks by generating CoT derivations using a commonly used math language format. Moreover, we show LLMs with CoT can handle a general class of decision-making problems known as Dynamic Programming, thus justifying their power in tackling complex real-world tasks. Finally, an extensive set of experiments show that, while Transformers always fail to directly predict the answers, they can consistently learn to generate correct solutions step-by-step given sufficient CoT demonstrations.

Oral
Supply-Side Equilibria in Recommender Systems

Meena Jagadeesan, Nikhil Garg, Jacob Steinhardt

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Algorithmic recommender systems such as Spotify and Netflix affect not only consumer behavior but also *producer incentives*. Producers seek to create content that will be shown by the recommendation algorithm, which can impact both the diversity and quality of their content. In this work, we investigate the resulting supply-side equilibria in personalized content recommender systems. We model the decisions of producers as choosing *multi-dimensional* content vectors and users as having *heterogenous* preferences, which contrasts with classical low-dimensional models. Multi-dimensionality and heterogeneity creates the potential for *specialization*, where different producers create different types of content at equilibrium. Using a duality argument, we derive necessary and sufficient conditions for whether specialization occurs. Then, we characterize the distribution of content at equilibrium in concrete settings with two populations of users. Lastly, we show that specialization can enable producers to achieve *positive profit at equilibrium*, which means that specialization can reduce the competitiveness of the marketplace. At a conceptual level, our analysis of supply-side competition takes a step towards elucidating how personalized recommendations shape the marketplace of digital goods.

Poster
Deductive Verification of Chain-of-Thought Reasoning

Zhan Ling, Yunhao Fang, Xuanlin Li, Zhiao Huang, Mingu Lee, Roland Memisevic, Hao Su

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Large Language Models (LLMs) significantly benefit from Chain-of-thought (CoT) prompting in performing various reasoning tasks. While CoT allows models to produce more comprehensive reasoning processes, its emphasis on intermediate reasoning steps can inadvertently introduce hallucinations and accumulated errors, thereby limiting models’ ability to solve complex reasoning tasks. Inspired by how humans engage in careful and meticulous deductive logical reasoning processes to solve tasks, we seek to enable language models to perform explicit and rigorous deductive reasoning, and also ensure the trustworthiness of their reasoning process through self-verification. However, directly verifying the validity of an entire deductive reasoning process is challenging, even with advanced models like ChatGPT. In light of this, we propose to decompose a reasoning verification process into a series of step-by-step subprocesses, each only receiving their necessary context and premises. To facilitate this procedure, we propose Natural Program, a natural language-based deductive reasoning format. Our approach enables models to generate precise reasoning steps where subsequent steps are more rigorously grounded on prior steps. It also empowers language models to carry out reasoning self-verification in a step-by-step manner. By integrating this verification process into each deductive reasoning stage, we significantly enhance the rigor and trustfulness of generated reasoning steps. Along this process, we also improve the answer correctness on complex reasoning tasks.

Poster
Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model

Shiwei Liu, Tian Zhu, Milong Ren, Yu Chungong, Dongbo Bu, Haicang Zhang

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Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is important in protein engineering, including therapeutic discovery. However, the scarcity of annotated experimental data on binding energy poses a significant challenge for developing computational approaches, particularly deep learning-based methods. In this work, we propose SidechainDiff, a novel representation learning-based approach that leverages unlabelled experimental protein structures. SidechainDiff utilizes a Riemannian diffusion model to learn the generative process of side-chain conformations and can also give the structural context representations of mutations on the protein-protein interface. Leveraging the learned representations, we achieve state-of-the-art performance in predicting the mutational effects on protein-protein binding. Furthermore, SidechainDiff is the first diffusion-based generative model for side-chains, distinguishing it from prior efforts that have predominantly focused on the generation of protein backbone structures.

Poster