Structure-based drug design (SBDD) is crucial for developing specific and effective therapeutics against protein targets but remains challenging due to complex protein-ligand interactions and vast chemical space. Although language models (LMs) have excelled in natural language processing, their application in SBDD is underexplored. To bridge this gap, we introduce a method, known as Frag2Seq, to apply LMs to SBDD by generating molecules in a fragment-based manner in which fragments correspond to functional modules. We transform 3D molecules into fragment-informed sequences using $SE(3)$-equivariant molecule and fragment local frames, extracting $SE(3)$-invariant sequences that preserve geometric information of 3D fragments. Furthermore, we incorporate protein pocket embeddings obtained from a pre-trained inverse folding model into the LMs via cross-attention to capture protein-ligand interaction, enabling effective target-aware molecule generation. Benefiting from employing LMs with fragment-based generation and effective protein context encoding, our model achieves the best performance on binding vina score and chemical properties such as QED and Lipinski, which shows our model’s efficacy in generating drug-like ligands with higher binding affinity against target proteins. Moreover, our method also exhibits higher sampling efficiency compared to atom-based autoregressive and diffusion baselines with at most $\times 300$ speedup. The code will be made publicly available at https://github.com/divelab/AIRS/tree/main/OpenMI/Frag2Seq.

Position bias has proven to be a prevalent issue of modern language models (LMs), where the models prioritize content based on its position within the given context. This bias often leads to unexpected model failures and hurts performance, robustness, and reliability across various applications. A simple mechanistic analysis attributes the position bias to two components employed in nearly all state-of-the-art LMs: causal attention and position embedding. Based on the analyses, we propose to **eliminate** position bias (e.g., different retrieved documents' orders in QA affect performance) with a **training-free zero-shot** approach. Our method changes the causal attention to bidirectional attention between documents and utilizes model attention values to decide the relative orders of documents instead of using the order provided in input prompts, therefore enabling Position-INvariant inferencE (PINE) at the document level. By eliminating position bias, models achieve better performance and reliability in downstream tasks, including LM-as-a-judge, retrieval-augmented QA, molecule generation, and math reasoning. Notably, PINE is especially useful when adapting LMs for evaluating reasoning pairs: it consistently provides $8$ to $10$ percentage points performance gains, making Llama-3-70B-Instruct perform even better than GPT-4-0125-preview and GPT-4o-2024-08-06 on the RewardBench reasoning set.

We consider learning underlying laws of dynamical systems governed by ordinary differential equations (ODE). A key challenge is how to discover intrinsic dynamics across multiple environments while circumventing environment-specific mechanisms. Unlike prior work, we tackle more complex environments where changes extend beyond function coefficients to entirely different function forms. For example, we demonstrate the discovery of ideal pendulum’s natural motion $\alpha^2 \sin{\theta_t}$ by observing pendulum dynamics in different environments, such as the damped environment $\alpha^2 \sin(\theta_t) - \rho \omega_t$ and powered environment $\alpha^2 \sin(\theta_t) + \rho \frac{\omega_t}{\left|\omega_t\right|}$. Here, we formulate this problem as an invariant function learning task and propose a new method, known as Disentanglement of Invariant Functions (DIF), that is grounded in causal analysis. We propose a causal graph and design an encoder-decoder hypernetwork that explicitly disentangles invariant functions from environment-specific dynamics. The discovery of invariant functions is guaranteed by our information-based principle that enforces the independence between extracted invariant functions and environments. Quantitative comparisons with meta-learning and invariant learning baselines on three ODE systems demonstrate the effectiveness and efficiency of our method. Furthermore, symbolic regression explanation results highlight the ability of our framework to uncover intrinsic laws.

We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries. Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. Here, we attempt to bridge this gap by proposing a novel method which converts molecular geometries into SE(3)-invariant 1D discrete sequences. Our method consists of canonical labeling and invariant spherical representation steps, which together maintain geometric and atomic fidelity in a format conducive to LMs. Our experiments show that, when coupled with our proposed method, various LMs excel in molecular geometry generation, especially in controlled generation tasks. Our code has been released as part of the AIRS library (https://github.com/divelab/AIRS/).

To fully leverage the capabilities of diffusion models, we are often interested in optimizing downstream reward functions during inference. While numerous algorithms for reward-guided generation have been recently proposed due to their significance, current approaches predominantly focus on single-shot generation, transitioning from fully noised to denoised states. We propose a novel framework for inference-time reward optimization with diffusion models. Our approach employs an iterative refinement process consisting of two steps in each iteration: noising and reward-guided denoising. This sequential refinement allows for the gradual correction of errors introduced during reward optimization. Finally, we provide a theoretical guarantee for our framework. Finally, we demonstrate its superior empirical performance in protein and DNA design.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require differentiable proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation.

Test-time adaptation (TTA) addresses distribution shifts for streaming test data in unsupervised settings. Currently, most TTA methods can only deal with minor shifts and rely heavily on heuristic and empirical studies. To advance TTA under domain shifts, we propose the novel problem setting of active test-time adaptation (ATTA) that integrates active learning within the fully TTA setting. We provide a learning theory analysis, demonstrating that incorporating limited labeled test instances enhances overall performances across test domains with a theoretical guarantee. We also present a sample entropy balancing for implementing ATTA while avoiding catastrophic forgetting (CF). We introduce a simple yet effective ATTA algorithm, known as SimATTA, using real-time sample selection techniques. Extensive experimental results confirm consistency with our theoretical analyses and show that the proposed ATTA method yields substantial performance improvements over TTA methods while maintaining efficiency and shares similar effectiveness to the more demanding active domain adaptation (ADA) methods. Our code is available at https://github.com/divelab/ATTA.

Large language models (LLMs) have gained considerable attention for their excellent natural language processing capabilities. Nonetheless, these LLMs present many challenges, particularly in the realm of trustworthiness. This paper introduces TrustLLM, a comprehensive study of trustworthiness in LLMs, including principles for different dimensions of trustworthiness, established benchmark, evaluation, and analysis of trustworthiness for mainstream LLMs, and discussion of open challenges and future directions. Specifically, we first propose a set of principles for trustworthy LLMs that span eight different dimensions. Based on these principles, we further establish a benchmark across six dimensions including truthfulness, safety, fairness, robustness, privacy, and machine ethics. We then present a study evaluating 16 mainstream LLMs in TrustLLM, consisting of over 30 datasets. Our findings firstly show that in general trustworthiness and capability (i.e., functional effectiveness) are positively related. Secondly, our observations reveal that proprietary LLMs generally outperform most open-source counterparts in terms of trustworthiness, raising concerns about the potential risks of widely accessible open-source LLMs. However, a few open-source LLMs come very close to proprietary ones, suggesting that open-source models can achieve high levels of trustworthiness without additional mechanisms like moderator, offering valuable insights for developers in this field. Thirdly, it is important to note that some LLMs may be overly calibrated towards exhibiting trustworthiness, to the extent that they compromise their utility by mistakenly treating benign prompts as harmful and consequently not responding. Besides these observations, we’ve uncovered key insights into the multifaceted trustworthiness in LLMs. We emphasize the importance of ensuring transparency not only in the models themselves but also in the technologies that underpin trustworthiness. We advocate that the establishment of an AI alliance between industry, academia, the open-source community to foster collaboration is imperative to advance the trustworthiness of LLMs.

Out-of-distribution (OOD) generalization deals with the prevalent learning scenario where test distribution shifts from training distribution. With rising application demands and inherent complexity, graph OOD problems call for specialized solutions. While data-centric methods exhibit performance enhancements on many generic machine learning tasks, there is a notable absence of data augmentation methods tailored for graph OOD generalization. In this work, we propose to achieve graph OOD generalization with the novel design of non-Euclidean-space linear extrapolation. The proposed augmentation strategy extrapolates structure spaces to generate OOD graph data. Our design tailors OOD samples for specific shifts without corrupting underlying causal mechanisms. Theoretical analysis and empirical results evidence the effectiveness of our method in solving target shifts, showing substantial and constant improvements across various graph OOD tasks.

We consider the problem of crystal materials generation using language models (LMs). A key step is to convert 3D crystal structures into 1D sequences to be processed by LMs. Prior studies used the crystallographic information framework (CIF) file stream, which fails to ensure SE(3) and periodic invariance and may not lead to unique sequence representations for a given crystal structure. Here, we propose a novel method, known as Mat2Seq, to tackle this challenge. Mat2Seq converts 3D crystal structures into 1D sequences and ensures that different mathematical descriptions of the same crystal are represented in a single unique sequence, thereby provably achieving SE(3) and periodic invariance. Experimental results show that, with language models, Mat2Seq achieves promising performance in crystal structure generation as compared with prior methods.

We tackle the problem of graph out-of-distribution (OOD) generalization. Existing graph OOD algorithms either rely on restricted assumptions or fail to exploit environment information in training data. In this work, we propose to simultaneously incorporate label and environment causal independence (LECI) to fully make use of label and environment information, thereby addressing the challenges faced by prior methods on identifying causal and invariant subgraphs. We further develop an adversarial training strategy to jointly optimize these two properties for casual subgraph discovery with theoretical guarantees. Extensive experiments and analysis show that LECI significantly outperforms prior methods on both synthetic and real-world datasets, establishing LECI as a practical and effective solution for graph OOD generalization.

Out-of-distribution (OOD) learning deals with scenarios in which training and test data follow different distributions. Although general OOD problems have been intensively studied in machine learning, graph OOD is only an emerging area of research. Currently, there lacks a systematic benchmark tailored to graph OOD method evaluation. In this work, we aim at developing an OOD benchmark, known as GOOD, for graphs specifically. We explicitly make distinctions between covariate and concept shifts and design data splits that accurately reflect different shifts. We consider both graph and node prediction tasks as there are key differences in designing shifts. Overall, GOOD contains 11 datasets with 17 domain selections. When combined with covariate, concept, and no shifts, we obtain 51 different splits. We provide performance results on 10 commonly used baseline methods with 10 random runs. This results in 510 dataset-model combinations in total. Our results show significant performance gaps between in-distribution and OOD settings. Our results also shed light on different performance trends between covariate and concept shifts by different methods. Our GOOD benchmark is a growing project and expects to expand in both quantity and variety of resources as the area develops. The GOOD benchmark can be accessed via https://github.com/divelab/GOOD/.

We present a study on the impact of packet loss on dynamic 3D point cloud streaming, encoded with MPEG Video-based Point Cloud Compression (V-PCC) standard. We show the distortion when different channels of V-PCC bitstream are lost, with the loss of occupancy and geometry data impacting the quality most significantly. Our results point to the need for better error concealment techniques. We end the paper by presenting preliminary thoughts and experimental results of two naive error concealment techniques in the point cloud domain, for attributes and geometry data, respectively, and highlight the limitations of each.