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Theory · Reinforcement Learning and Planning

Wenhan Cao, Wei Pan

Integral reinforcement learning (IntRL) demands the precise computation of the utility function's integral at its policy evaluation (PEV) stage. This is achieved through quadrature rules, which are weighted sums of utility functions evaluated from state samples obtained in discrete time. Our research reveals a critical yet underexplored phenomenon: the choice of the computational method -- in this case, the quadrature rule -- can significantly impact control performance. This impact is traced back to the fact that computational errors introduced in the PEV stage can affect the policy iteration's convergence behavior, which in turn affects the learned controller. To elucidate how computation impacts control, we draw a parallel between IntRL's policy iteration and Newton's method applied to the Hamilton-Jacobi-Bellman equation. In this light, computational error in PEV manifests as an extra error term in each iteration of Newton's method, with its upper bound proportional to the computational error. Further, we demonstrate that when the utility function resides in a reproducing kernel Hilbert space (RKHS), the optimal quadrature is achievable by employing Bayesian quadrature with the RKHS-inducing kernel function. We prove that the local convergence rates for IntRL using the trapezoidal rule and Bayesian quadrature with a Matérn kernel to be $O(N^{-2})$ and $O(N^{-b})$, where $N$ is the number of evenly-spaced samples and $b$ is the Matérn kernel's smoothness parameter. These theoretical findings are finally validated by two canonical control tasks.

Applications · Robotics

Heng Dong, Junyu Zhang, Chongjie Zhang

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.

Theory · Reinforcement Learning and Planning

DINGYUAN SHI, Yongxin Tong, Zimu Zhou, Ke Xu, Zheng Wang, Jieping Ye

Path planning underpins various applications such as transportation, logistics, and robotics.Conventionally, path planning is formulated with explicit optimization objectives such as distance or time.However, real-world data reveals that user intentions are hard-to-model, suggesting a need for data-driven path planning that implicitly incorporates the complex user intentions.In this paper, we propose GDP, a diffusion-based model for end-to-end data-driven path planning.It effectively learns path patterns via a novel diffusion process that incorporates constraints from road networks, and plans paths as conditional path generation given the origin and destination as prior evidence.GDP is the first solution that bypasses the traditional search-based frameworks, a long-standing performance bottleneck in path planning.We validate the efficacy of GDP on two real-world datasets.Our GDP beats strong baselines by 14.2% ~ 43.5% and achieves state-of-the-art performances.

Yeming Wen, Swarat Chaudhuri

Low-Rank Adaptation (LoRA) has recently gained attention for fine-tuning foundation models by incorporating trainable low-rank matrices, thereby reducing the number of trainable parameters. While \lora/ offers numerous advantages, its applicability for real-time serving to a diverse and global user base is constrained by its incapability to handle multiple task-specific adapters efficiently. This imposes a performance bottleneck in scenarios requiring personalized, task-specific adaptations for each incoming request.To address this, we introduce FLoRA (Fast LoRA), a framework in which each input example in a minibatch can be associated with its unique low-rank adaptation weights, allowing for efficient batching of heterogeneous requests. We empirically demonstrate that \flora/ retains the performance merits of \lora/, showcasing competitive results on the MultiPL-E code generation benchmark spanning over 8 languages and a multilingual speech recognition task across 6 languages.

Miscellaneous Aspects of Machine Learning · Representation Learning

Irene Cannistraci, Luca Moschella, Marco Fumero, Valentino Maiorca, Emanuele Rodolà

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.

Miscellaneous Aspects of Machine Learning · Causality

Ziqi Xu, Debo Cheng, Jiuyong Li, Jixue Liu, Lin Liu, Kui Yu

An essential and challenging problem in causal inference is causal effect estimation from observational data. The problem becomes more difficult with the presence of unobserved confounding variables. The front-door adjustment is an approach for dealing with unobserved confounding variables. However, the restriction for the standard front-door adjustment is difficult to satisfy in practice. In this paper, we relax some of the restrictions by proposing the concept of conditional front-door (CFD) adjustment and develop the theorem that guarantees the causal effect identifiability of CFD adjustment. By leveraging the ability of deep generative models, we propose CFDiVAE to learn the representation of the CFD adjustment variable directly from data with the identifiable Variational AutoEncoder and formally prove the model identifiability. Extensive experiments on synthetic datasets validate the effectiveness of CFDiVAE and its superiority over existing methods. The experiments also show that the performance of CFDiVAE is less sensitive to the causal strength of unobserved confounding variables. We further apply CFDiVAE to a real-world dataset to demonstrate its potential application.

Deep Learning

Jason Chun Lok Li, Steven Luo, Le Xu, Ngai Wong

Coordinate network or implicit neural representation (INR) is a fast-emerging method for encoding natural signals (such as images and videos) with the benefits of a compact neural representation. While numerous methods have been proposed to increase the encoding capabilities of an INR, an often overlooked aspect is the inference efficiency, usually measured in multiply-accumulate (MAC) count. This is particularly critical in use cases where inference bandwidth is greatly limited by hardware constraints. To this end, we propose the Activation-Sharing Multi-Resolution (ASMR) coordinate network that combines multi-resolution coordinate decomposition with hierarchical modulations. Specifically, an ASMR model enables the sharing of activations across grids of the data. This largely decouples its inference cost from its depth which is directly correlated to its reconstruction capability, and renders a near $O(1)$ inference complexity irrespective of the number of layers. Experiments show that ASMR can reduce the MAC of a vanilla SIREN model by up to 500$\times$ while achieving an even higher reconstruction quality than its SIREN baseline.

Deep Learning · Graph Neural Networks

Xiaoxin He, Xavier Bresson, Thomas Laurent, Adam Perold, Yann LeCun, Bryan Hooi

Representation learning on text-attributed graphs (TAGs) has become a critical research problem in recent years. A typical example of a TAG is a paper citation graph, where the text of each paper serves as node attributes. Initial graph neural network (GNN) pipelines handled these text attributes by transforming them into shallow or hand-crafted features, such as skip-gram or bag-of-words features. Recent efforts have focused on enhancing these pipelines with language models (LMs), which typically demand intricate designs and substantial computational resources. With the advent of powerful large language models (LLMs) such as GPT or Llama2, which demonstrate an ability to reason and to utilize general knowledge, there is a growing need for techniques which combine the textual modelling abilities of LLMs with the structural learning capabilities of GNNs. Hence, in this work, we focus on leveraging LLMs to capture textual information as features, which can be used to boost GNN performance on downstream tasks. A key innovation is our use of \emph{explanations as features}: we prompt an LLM to perform zero-shot classification, request textual explanations for its decision-making process, and design an \emph{LLM-to-LM interpreter} to translate these explanations into informative features for downstream GNNs. Our experiments demonstrate that our method achieves state-of-the-art results on well-established TAG datasets, including \texttt{Cora}, \texttt{PubMed}, \texttt{ogbn-arxiv}, as well as our newly introduced dataset, \texttt{tape-arxiv23}. Furthermore, our method significantly speeds up training, achieving a 2.88 times improvement over the closest baseline on \texttt{ogbn-arxiv}. Lastly, we believe the versatility of the proposed method extends beyond TAGs and holds the potential to enhance other tasks involving graph-text data~\footnote{Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/TAPE}}.

Linqi Zhou, Aaron Lou, Samar Khanna, Stefano Ermon

Diffusion models are powerful generative models that map noise to data using stochastic processes. However, for many applications such as image editing, the model input comes from a distribution that is not random noise. As such, diffusion models must rely on cumbersome methods like guidance or projected sampling to incorporate this information in the generative process. In our work, we propose Denoising Diffusion Bridge Models (DDBMs), a natural alternative to this paradigm based on *diffusion bridges*, a family of processes that interpolate between two paired distributions given as endpoints. Our method learns the score of the diffusion bridge from data and maps from one endpoint distribution to the other by solving a (stochastic) differential equation based on the learned score. Our method naturally unifies several classes of generative models, such as score-based diffusion models and OT-Flow-Matching, allowing us to adapt existing design and architectural choices to our more general problem. Empirically, we apply DDBMs to challenging image datasets in both pixel and latent space. On standard image translation problems, DDBMs achieve significant improvement over baseline methods, and, when we reduce the problem to image generation by setting the source distribution to random noise, DDBMs achieve comparable FID scores to state-of-the-art methods despite being built for a more general task.

Applications · Computer Vision

Samar Khanna, Patrick Liu, Linqi Zhou, Chenlin Meng, Robin Rombach, Marshall Burke, David Lobell, Stefano Ermon

Diffusion models have achieved state-of-the-art results on many modalities including images, speech, and video. However, existing models are not tailored to support remote sensing data, which is widely used in important applications including environmental monitoring and crop-yield prediction. Satellite images are significantly different from natural images -- they can be multi-spectral, irregularly sampled across time -- and existing diffusion models trained on images from the Web do not support them. Furthermore, remote sensing data is inherently spatio-temporal, requiring conditional generation tasks not supported by traditional methods based on captions or images. In this paper, we present DiffusionSat, to date the largest generative foundation model trained on a collection of publicly available large, high-resolution remote sensing datasets .As text-based captions are sparsely available for satellite images, we incorporate the associated metadata such as geolocation as conditioning information. Our method produces realistic samples and can be used to solve multiple generative tasks including temporal generation, multi-spectral superrresolution and in-painting. Our method outperforms previous state-of-the-art methods for satellite image generation and is the first large-scale _generative_ foundation model for satellite imagery.The project website can be found here: https://samar-khanna.github.io/DiffusionSat/

Social Aspects · Trustworthy Machine Learning

Maximilian Baader, Mark N Müller, Yuhao Mao, Martin Vechev

Convex relaxations are a key component of training and certifying provably safe neural networks. However, despite substantial progress, a wide and poorly understood accuracy gap to standard networks remains, raising the question of whether this is due to fundamental limitations of convex relaxations. Initial work investigating this question focused on the simple and widely used IBP relaxation. It revealed that some univariate, convex, continuous piecewise linear (CPWL) functions cannot be encoded by any ReLU network such that its IBP-analysis is precise.To explore whether this limitation is shared by more advanced convex relaxations, we conduct the first in-depth study on the expressive power of ReLU networks across all commonly used convex relaxations. We show that: (i) more advanced relaxations allow a larger class of univariate functions to be expressed as precisely analyzable ReLU networks, (ii) more precise relaxations can allow exponentially larger solution spaces of ReLU networks encoding the same functions, and (iii) even using the most precise single-neuron relaxations, it is impossible to construct precisely analyzable ReLU networks that express multivariate, convex, monotone CPWL functions.

Optimization · Large Scale, Parallel and Distributed

Yi-Rui Yang, Chang-Wei Shi, Wu-Jun Li

Byzantine-robust distributed learning (BRDL), in which computing devices are likely to behave abnormally due to accidental failures or malicious attacks, has recently become a hot research topic. However, even in the independent and identically distributed (i.i.d.) case, existing BRDL methods will suffer a significant drop on model accuracy due to the large variance of stochastic gradients. Increasing batch sizes is a simple yet effective way to reduce the variance. However, when the total number of gradient computation is fixed, a too-large batch size will lead to a too-small iteration number (update number), which may also degrade the model accuracy. In view of this challenge, we mainly study the effect of batch size when the total number of gradient computation is fixed in this work. In particular, we show that when the total number of gradient computation is fixed, the optimal batch size corresponding to the tightest theoretical upper bound in BRDL increases with the fraction of Byzantine workers. Therefore, compared to the case without attacks, a larger batch size is preferred when under Byzantine attacks. Motivated by the theoretical finding, we propose a novel method called Byzantine-robust stochastic gradient descent with normalized momentum (ByzSGDnm) in order to further increase model accuracy in BRDL. We theoretically prove the convergence of ByzSGDnm for general non-convex cases under Byzantine attacks. Empirical results show that when under Byzantine attacks, compared to the cases of small batch sizes, setting a relatively large batch size can significantly increase the model accuracy, which is consistent with our theoretical results. Moreover, ByzSGDnm can achieve higher model accuracy than existing BRDL methods when under deliberately crafted attacks. In addition, we empirically show that increasing batch sizes has the bonus of training acceleration.

Deep Learning · Generative Models and Autoencoders

Enshu Liu, Xuefei Ning, Huazhong Yang, Yu Wang

Recent years have witnessed the rapid progress and broad application of diffusion probabilistic models (DPMs). Sampling from DPMs can be viewed as solving an ordinary differential equation (ODE). Despite the promising performance, the generation of DPMs usually consumes much time due to the large number of function evaluations (NFE). Though recent works have accelerated the sampling to around 20 steps with high-order solvers, the sample quality with less than 10 NFE can still be improved. In this paper, we propose a unified sampling framework (USF) to study the optional strategies for solver. Under this framework, we further reveal that taking different solving strategies at different timesteps may help further decrease the truncation error, and a carefully designed \emph{solver schedule} has the potential to improve the sample quality by a large margin. Therefore, we propose a new sampling framework based on the exponential integral formulation that allows free choices of solver strategy at each step and design specific decisions for the framework. Moreover, we propose $S^3$, a predictor-based search method that automatically optimizes the solver schedule to get a better time-quality trade-off of sampling. We demonstrate that $S^3$ can find outstanding solver schedules which outperform the state-of-the-art sampling methods on CIFAR-10, CelebA, ImageNet-64, and LSUN-Bedroom datasets. Specifically, we achieve 2.69 FID with 9 NFE and 6.86 FID with 5 NFE on CIFAR-10 dataset, outperforming the SOTA method significantly. We further apply $S^3$ to Stable-Diffusion model and get an acceleration ratio of 2$\times$, showing the feasibility of sampling in very few steps without retraining of the neural network.

Yingtian Zou, Kenji Kawaguchi, Yingnan Liu, Jiashuo Liu, Mong-Li Lee, Wynne Hsu

Generalizing to out-of-distribution (OOD) data or unseen domain, termed OOD generalization, still lacks appropriate theoretical guarantees. Canonical OOD bounds focus on different distance measurements between source and target domains but fail to consider the optimization property of the learned model. As empirically shown in recent work, sharpness of learned minimum influences OOD generalization. To bridge this gap between optimization and OOD generalization, we study the effect of sharpness on how a model tolerates data change in domain shift which is usually captured by "robustness" in generalization. In this paper, we give a rigorous connection between sharpness and robustness, which gives better OOD guarantees for robust algorithms. It also provides a theoretical backing for "flat minima leads to better OOD generalization". Overall, we propose a sharpness-based OOD generalization bound by taking robustness into consideration, resulting in a tighter bound than non-robust guarantees. Our findings are supported by the experiments on a ridge regression model, as well as the experiments on deep learning classification tasks.

Wenxuan Zhou, Sheng Zhang, Yu Gu, Muhao Chen, Hoifung Poon

Large language models (LLMs) have demonstrated remarkable generalizability, such as understanding arbitrary entities and relations. Instruction tuning has proven effective for distilling LLMs into more cost-efficient models such as Alpaca and Vicuna. Yet such student models still trail the original LLMs by large margins in downstream applications. In this paper, we explore targeted distillation with mission-focused instruction tuning to train student models that can excel in a broad application class such as open information extraction. Using named entity recognition (NER) for case study, we show how ChatGPT can be distilled into much smaller UniversalNER models for open NER. For evaluation, we assemble the largest NER benchmark to date, comprising 43 datasets across 9 diverse domains such as biomedicine, programming, social media, law, finance. Without using any direct supervision, UniversalNER attains remarkable NER accuracy across tens of thousands of entity types, outperforming general instruction-tuned models such as Alpaca and Vicuna by over 30 absolute F1 points in average. With a tiny fraction of parameters, UniversalNER not only acquires ChatGPT's capability in recognizing arbitrary entity types, but also outperforms its NER accuracy by 7-9 absolute F1 points in average. Remarkably, UniversalNER even outperforms by a large margin state-of-the-art multi-task instruction-tuned systems such as InstructUIE, which uses supervised NER examples. We also conduct thorough ablation studies to assess the impact of various components in our distillation approach. We release the distillation recipe, data, and UniversalNER models to facilitate future research on targeted distillation.

Applications · Time Series

Xu Zheng, Tianchun Wang, Wei Cheng, Aitian Ma, Haifeng Chen, Mo Sha, Dongsheng Luo

Modern techniques like contrastive learning have been effectively used in many areas, including computer vision, natural language processing, and graph-structured data. Creating positive examples that assist the model in learning robust and discriminative representations is a crucial stage in contrastive learning approaches. Usually, preset human intuition directs the selection of relevant data augmentations. Due to patterns that are easily recognized by humans, this rule of thumb works well in the vision and language domains. However, it is impractical to visually inspect the temporal structures in time series. The diversity of time series augmentations at both the dataset and instance levels makes it difficult to choose meaningful augmentations on the fly. Thus, although prevalent, contrastive learning with data augmentation has been less studied in the time series domain. In this study, we address this gap by analyzing time series data augmentation using information theory and summarizing the most commonly adopted augmentations in a unified format. We then propose a parametric augmentation method, AutoTCL, which can be adaptively employed to support time series representation learning. The proposed approach is encoder-agnostic, allowing it to be seamlessly integrated with different backbone encoders. Experiments on univariate forecasting tasks demonstrate the highly competitive results of our method, with an average 6.5\% reduction in MSE and 4.7\% in MAE over the leading baselines. In classification tasks, AutoTCL achieves a $1.2\%$ increase in average accuracy.

Ibraheem Muhammad Moosa, Rui Zhang, Wenpeng Yin

Traditionally, Machine Translation (MT) Evaluation has been treated as a regression problem -- producing an absolute translation-quality score. This approach has two limitations: i) the scores lack interpretability, and human annotators struggle with giving consistent scores; ii) most scoring methods are based on (reference, translation) pairs, limiting their applicability in real-world scenarios where references are absent. In practice, we often care about whether a new MT system is better or worse than some competitors. In addition, reference-free MT evaluation is increasingly practical and necessary. Unfortunately, these two practical considerations have yet to be jointly explored. In this work, we formulate the reference-free MT evaluation into a pairwise ranking problem. Given the source sentence and a pair of translations, our system predicts which translation is better. In addition to proposing this new formulation, we further show that this new paradigm can demonstrate superior correlation with human judgments by merely using indirect supervision from natural language inference and weak supervision from our synthetic data. In the context of reference-free evaluation, MT-Ranker, trained without any human annotations, achieves state-of-the-art results on the WMT Shared Metrics Task benchmarks DARR20, MQM20, and MQM21. On a more challenging benchmark, ACES, which contains fine-grained evaluation criteria such as addition, omission, and mistranslation errors, MT-Ranker marks state-of-the-art against reference-free as well as reference-based baselines.

Optimization

Nuoya Xiong, Lijun Ding, Simon Du

This paper rigorously shows how over-parameterization dramatically changes the convergence behaviors of gradient descent (GD) for the matrix sensing problem, where the goal is to recover an unknown low-rank ground-truth matrix from near-isotropic linear measurements.First, we consider the symmetric setting with the symmetric parameterization where $M^* \in \mathbb{R}^{n \times n}$ is a positive semi-definite unknown matrix of rank $r \ll n$, and one uses a symmetric parameterization $XX^\top$ to learn $M^*$. Here $X \in \mathbb{R}^{n \times k}$ with $k > r$ is the factor matrix. We give a novel $\Omega\left(1/T^2\right)$ lower bound of randomly initialized GD for the over-parameterized case ($k >r$) where $T$ is the number of iterations. This is in stark contrast to the exact-parameterization scenario ($k=r$) where the convergence rate is $\exp\left(-\Omega\left(T\right)\right)$. Next, we study asymmetric setting where $M^* \in \mathbb{R}^{n_1 \times n_2}$ is the unknown matrix of rank $r \ll \min\{n_1,n_2\}$, and one uses an asymmetric parameterization $FG^\top$ to learn $M^*$ where $F \in \mathbb{R}^{n_1 \times k}$ and $G \in \mathbb{R}^{n_2 \times k}$. We give the first global exact convergence result of randomly initialized GD for the exact-parameterization case ($k=r$) with an $\exp\left(-\Omega\left(T\right)\right)$ rate. Furthermore, we give the first global exact convergence result for the over-parameterization case ($k>r$) with an $\exp\left(-\Omega\left(\alpha^2 T\right)\right)$ rate where $\alpha$ is the initialization scale. This linear convergence result in the over-parameterization case is especially significant because one can apply the asymmetric parameterization to the symmetric setting to speed up from $\Omega\left(1/T^2\right)$ to linear convergence. Therefore, we identify a surprising phenomenon: asymmetric parameterization can exponentially speed up convergence. Equally surprising is our analysis that highlights the importance of imbalance between $F$ and $G$. This is in sharp contrast to prior works which emphasize balance. We further give an example showing the dependency on $\alpha$ in the convergence rate is unavoidable in the worst case. On the other hand, we propose a novel method that only modifies one step of GD and obtains a convergence rate independent of $\alpha$, recovering the rate in the exact-parameterization case. We provide empirical studies to verify our theoretical findings.

Applications · Language, Speech and Dialog

Sreyan Ghosh, Ashish Seth, Sonal Kumar, Utkarsh Tyagi, Chandra Kiran Evuru, Ramaneswaran S, S Sakshi, Oriol Nieto, Ramani Duraiswami, Dinesh Manocha

A fundamental characteristic of audio is its compositional nature. Audio-language models (ALMs) trained using a contrastive approach (e.g., CLAP) that learns a shared representation between audio and language modalities have improved performance in many downstream applications, including zero-shot audio classification, audio retrieval, etc. However, the ability of these models to effectively perform compositional reasoning remains largely unexplored and necessitates additional research. In this paper, we propose CompA, a collection of two expert-annotated benchmarks with a majority of real-world audio samples, to evaluate compositional reasoning in ALMs. Our proposed CompA-order evaluates how well an ALM understands the order or occurrence of acoustic events in audio, and CompA-attribute evaluates attribute-binding of acoustic events. An instance from either benchmark consists of two audio-caption pairs, where both audios have the same acoustic events but with different compositions. An ALM is evaluated on how well it matches the right audio to the right caption. Using this benchmark, we first show that current ALMs perform only marginally better than random chance, thereby struggling with compositional reasoning. Next, we propose CompA-CLAP, where we fine-tune CLAP using a novel learning method to improve its compositional reasoning abilities. To train CompA-CLAP, we first propose improvements to contrastive training with composition-aware hard negatives, allowing for more focused training. Next, we propose a novel modular contrastive loss that helps the model learn fine-grained compositional understanding and overcomes the acute scarcity of openly available compositional audios. CompA-CLAP significantly improves over all our baseline models on the CompA benchmark, indicating its superior compositional reasoning capabilities.

Applications · Chemistry and Drug Discovery

Sihang Li, Zhiyuan Liu, Yanchen Luo, Xiang Wang, Xiangnan He, Kenji Kawaguchi, Tat-Seng Chua, Qi Tian

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder’s representation space and the LM’s input space. Moreover, to enhance 3DMoLM’s ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset – 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including moleculetext retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties. We will release our codes and datasets at https://github.com/lsh0520/3D-MoLM.