Numerical Methods for Distributed Stochastic Compositional Optimization Problems with Aggregative Structure

The paper studies the distributed stochastic compositional optimization problems over networks, where all the agents' inner-level function is the sum of each agent's private expectation function. Focusing on the aggregative structure of the inner-level function, we employ the hybrid variance reduction method to obtain the information on each agent's private expectation function, and apply the dynamic consensus mechanism to track the information on each agent's inner-level function. Then by combining with the standard distributed stochastic gradient descent method, we propose a distributed aggregative stochastic compositional gradient descent method. When the objective function is smooth, the proposed method achieves the optimal convergence rate $\mathcal{O}\left(K^{-1/2}\right)$. We further combine the proposed method with the communication compression and propose the communication compressed variant distributed aggregative stochastic compositional gradient descent method. The compressed variant of the proposed method maintains the optimal convergence rate $\mathcal{O}\left(K^{-1/2}\right)$. Simulated experiments on decentralized reinforcement learning verify the effectiveness of the proposed methods

Evaluating Self-Supervised Learning for Molecular Graph Embeddings

Graph Self-Supervised Learning (GSSL) provides a robust pathway for acquiring embeddings without expert labelling, a capability that carries profound implications for molecular graphs due to the staggering number of potential molecules and the high cost of obtaining labels. However, GSSL methods are designed not for optimisation within a specific domain but rather for transferability across a variety of downstream tasks. This broad applicability complicates their evaluation. Addressing this challenge, we present "Molecular Graph Representation Evaluation" (MOLGRAPHEVAL), generating detailed profiles of molecular graph embeddings with interpretable and diversified attributes. MOLGRAPHEVAL offers a suite of probing tasks grouped into three categories: (i) generic graph, (ii) molecular substructure, and (iii) embedding space properties. By leveraging MOLGRAPHEVAL to benchmark existing GSSL methods against both current downstream datasets and our suite of tasks, we uncover significant inconsistencies between inferences drawn solely from existing datasets and those derived from more nuanced probing. These findings suggest that current evaluation methodologies fail to capture the entirety of the landscape.Comment: update result

A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks

UniDistill: A Universal Cross-Modality Knowledge Distillation Framework for 3D Object Detection in Bird's-Eye View

In the field of 3D object detection for autonomous driving, the sensor portfolio including multi-modality and single-modality is diverse and complex. Since the multi-modal methods have system complexity while the accuracy of single-modal ones is relatively low, how to make a tradeoff between them is difficult. In this work, we propose a universal cross-modality knowledge distillation framework (UniDistill) to improve the performance of single-modality detectors. Specifically, during training, UniDistill projects the features of both the teacher and the student detector into Bird's-Eye-View (BEV), which is a friendly representation for different modalities. Then, three distillation losses are calculated to sparsely align the foreground features, helping the student learn from the teacher without introducing additional cost during inference. Taking advantage of the similar detection paradigm of different detectors in BEV, UniDistill easily supports LiDAR-to-camera, camera-to-LiDAR, fusion-to-LiDAR and fusion-to-camera distillation paths. Furthermore, the three distillation losses can filter the effect of misaligned background information and balance between objects of different sizes, improving the distillation effectiveness. Extensive experiments on nuScenes demonstrate that UniDistill effectively improves the mAP and NDS of student detectors by 2.0%~3.2%

ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedback

Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reaction and retrosynthesis. While drug editing, a critical task in the drug discovery pipeline, remains largely unexplored. To bridge this gap, we propose ChatDrug, a framework to facilitate the systematic investigation of drug editing using LLMs. ChatDrug jointly leverages a prompt module, a retrieval and domain feedback (ReDF) module, and a conversation module to streamline effective drug editing. We empirically show that ChatDrug reaches the best performance on 33 out of 39 drug editing tasks, encompassing small molecules, peptides, and proteins. We further demonstrate, through 10 case studies, that ChatDrug can successfully identify the key substructures (e.g., the molecule functional groups, peptide motifs, and protein structures) for manipulation, generating diverse and valid suggestions for drug editing. Promisingly, we also show that ChatDrug can offer insightful explanations from a domain-specific perspective, enhancing interpretability and enabling informed decision-making. This research sheds light on the potential of ChatGPT and conversational LLMs for drug editing. It paves the way for a more efficient and collaborative drug discovery pipeline, contributing to the advancement of pharmaceutical research and development