Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling

3D molecule generation is crucial for drug discovery and material science, requiring models to process complex multi-modalities, including atom types, chemical bonds, and 3D coordinates. A key challenge is integrating these modalities of different shapes while maintaining SE(3) equivariance for 3D coordinates. To achieve this, existing approaches typically maintain separate latent spaces for invariant and equivariant modalities, reducing efficiency in both training and sampling. In this work, we propose \textbf{U}nified Variational \textbf{A}uto-\textbf{E}ncoder for \textbf{3D} Molecular Latent Diffusion Modeling (\textbf{UAE-3D}), a multi-modal VAE that compresses 3D molecules into latent sequences from a unified latent space, while maintaining near-zero reconstruction error. This unified latent space eliminates the complexities of handling multi-modality and equivariance when performing latent diffusion modeling. We demonstrate this by employing the Diffusion Transformer--a general-purpose diffusion model without any molecular inductive bias--for latent generation. Extensive experiments on GEOM-Drugs and QM9 datasets demonstrate that our method significantly establishes new benchmarks in both \textit{de novo} and conditional 3D molecule generation, achieving leading efficiency and quality.

Multimodal Language Modeling for High-Accuracy Single Cell Transcriptomics Analysis and Generation

Pre-trained language models (PLMs) have revolutionized scientific research, yet their application to single-cell analysis remains limited. Text PLMs cannot process single-cell RNA sequencing data, while cell PLMs lack the ability to handle free text, restricting their use in multimodal tasks. Existing efforts to bridge these modalities often suffer from information loss or inadequate single-modal pre-training, leading to suboptimal performances. To address these challenges, we propose Single-Cell MultiModal Generative Pre-trained Transformer (scMMGPT), a unified PLM for joint cell and text modeling. scMMGPT effectively integrates the state-of-the-art cell and text PLMs, facilitating cross-modal knowledge sharing for improved performance. To bridge the text-cell modality gap, scMMGPT leverages dedicated cross-modal projectors, and undergoes extensive pre-training on 27 million cells -- the largest dataset for multimodal cell-text PLMs to date. This large-scale pre-training enables scMMGPT to excel in joint cell-text tasks, achieving an 84\% relative improvement of textual discrepancy for cell description generation, 20.5\% higher accuracy for cell type annotation, and 4\% improvement in $k$-NN accuracy for text-conditioned pseudo-cell generation, outperforming baselines.

Route Sparse Autoencoder to Interpret Large Language Models

Mechanistic interpretability of large language models (LLMs) aims to uncover the internal processes of information propagation and reasoning. Sparse autoencoders (SAEs) have demonstrated promise in this domain by extracting interpretable and monosemantic features. However, prior works primarily focus on feature extraction from a single layer, failing to effectively capture activations that span multiple layers. In this paper, we introduce Route Sparse Autoencoder (RouteSAE), a new framework that integrates a routing mechanism with a shared SAE to efficiently extract features from multiple layers. It dynamically assigns weights to activations from different layers, incurring minimal parameter overhead while achieving high interpretability and flexibility for targeted feature manipulation. We evaluate RouteSAE through extensive experiments on Llama-3.2-1B-Instruct. Specifically, under the same sparsity constraint of 64, RouteSAE extracts 22.5% more features than baseline SAEs while achieving a 22.3% higher interpretability score. These results underscore the potential of RouteSAE as a scalable and effective method for LLM interpretability, with applications in feature discovery and model intervention. Our codes are available at https://github.com/swei2001/RouteSAEs.

NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language Models (LMs), which can generate 100% valid molecules and leverage the billion-scale 1D molecule datasets. To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. NExT-Mol uses an extensively pretrained molecule LM for 1D molecule generation, and subsequently predicts the generated molecule's 3D conformers with a 3D diffusion model. We enhance NExT-Mol's performance by scaling up the LM's model size, refining the diffusion neural architecture, and applying 1D to 3D transfer learning. Notably, our 1D molecule LM significantly outperforms baselines in distributional similarity while ensuring validity, and our 3D diffusion model achieves leading performances in conformer prediction. Given these improvements in 1D and 3D modeling, NExT-Mol achieves a 26% relative improvement in 3D FCD for de novo 3D generation on GEOM-DRUGS, and a 13% average relative gain for conditional 3D generation on QM9-2014. Our codes and pretrained checkpoints are available at https://github.com/acharkq/NExT-Mol.

PatchRec: Multi-Grained Patching for Efficient LLM-based Sequential Recommendation

Large Language Models for sequential recommendation (LLM4SR), which transform user-item interactions into language modeling, have shown promising results. However, due to the limitations of context window size and the computational costs associated with Large Language Models (LLMs), current approaches primarily truncate user history by only considering the textual information of items from the most recent interactions in the input prompt. This truncation fails to fully capture the long-term behavioral patterns of users. To address this, we propose a multi-grained patching framework -- PatchRec. It compresses the textual tokens of an item title into a compact item patch, and further compresses multiple item patches into a denser session patch, with earlier interactions being compressed to a greater degree. The framework consists of two stages: (1) Patch Pre-training, which familiarizes LLMs with item-level compression patterns, and (2) Patch Fine-tuning, which teaches LLMs to model sequences at multiple granularities. Through this simple yet effective approach, empirical results demonstrate that PatchRec outperforms existing methods, achieving significant performance gains with fewer tokens fed to the LLM. Specifically, PatchRec shows up to a 32% improvement in HR@20 on the Goodreads dataset over uncompressed baseline, while using only 7% of the tokens. This multi-grained sequence modeling paradigm, with an adjustable compression ratio, enables LLMs to be efficiently deployed in real-world recommendation systems that handle extremely long user behavior sequences.

Intelligent System for Automated Molecular Patent Infringement Assessment

Automated drug discovery offers significant potential for accelerating the development of novel therapeutics by substituting labor-intensive human workflows with machine-driven processes. However, a critical bottleneck persists in the inability of current automated frameworks to assess whether newly designed molecules infringe upon existing patents, posing significant legal and financial risks. We introduce PatentFinder, a novel tool-enhanced and multi-agent framework that accurately and comprehensively evaluates small molecules for patent infringement. It incorporates both heuristic and model-based tools tailored for decomposed subtasks, featuring: MarkushParser, which is capable of optical chemical structure recognition of molecular and Markush structures, and MarkushMatcher, which enhances large language models' ability to extract substituent groups from molecules accurately. On our benchmark dataset MolPatent-240, PatentFinder outperforms baseline approaches that rely solely on large language models, demonstrating a 13.8\% increase in F1-score and a 12\% rise in accuracy. Experimental results demonstrate that PatentFinder mitigates label bias to produce balanced predictions and autonomously generates detailed, interpretable patent infringement reports. This work not only addresses a pivotal challenge in automated drug discovery but also demonstrates the potential of decomposing complex scientific tasks into manageable subtasks for specialized, tool-augmented agents.

Unleashing the Power of Data Synthesis in Visual Localization

Visual localization, which estimates a camera's pose within a known scene, is a long-standing challenge in vision and robotics. Recent end-to-end methods that directly regress camera poses from query images have gained attention for fast inference. However, existing methods often struggle to generalize to unseen views. In this work, we aim to unleash the power of data synthesis to promote the generalizability of pose regression. Specifically, we lift real 2D images into 3D Gaussian Splats with varying appearance and deblurring abilities, which are then used as a data engine to synthesize more posed images. To fully leverage the synthetic data, we build a two-branch joint training pipeline, with an adversarial discriminator to bridge the syn-to-real gap. Experiments on established benchmarks show that our method outperforms state-of-the-art end-to-end approaches, reducing translation and rotation errors by 50% and 21.6% on indoor datasets, and 35.56% and 38.7% on outdoor datasets. We also validate the effectiveness of our method in dynamic driving scenarios under varying weather conditions. Notably, as data synthesis scales up, our method exhibits a growing ability to interpolate and extrapolate training data for localizing unseen views. Project Page: https://ai4ce.github.io/RAP/

Multiview Scene Graph

A proper scene representation is central to the pursuit of spatial intelligence where agents can robustly reconstruct and efficiently understand 3D scenes. A scene representation is either metric, such as landmark maps in 3D reconstruction, 3D bounding boxes in object detection, or voxel grids in occupancy prediction, or topological, such as pose graphs with loop closures in SLAM or visibility graphs in SfM. In this work, we propose to build Multiview Scene Graphs (MSG) from unposed images, representing a scene topologically with interconnected place and object nodes. The task of building MSG is challenging for existing representation learning methods since it needs to jointly address both visual place recognition, object detection, and object association from images with limited fields of view and potentially large viewpoint changes. To evaluate any method tackling this task, we developed an MSG dataset and annotation based on a public 3D dataset. We also propose an evaluation metric based on the intersection-over-union score of MSG edges. Moreover, we develop a novel baseline method built on mainstream pretrained vision models, combining visual place recognition and object association into one Transformer decoder architecture. Experiments demonstrate our method has superior performance compared to existing relevant baselines.

Text-guided Diffusion Model for 3D Molecule Generation

The de novo generation of molecules with targeted properties is crucial in biology, chemistry, and drug discovery. Current generative models are limited to using single property values as conditions, struggling with complex customizations described in detailed human language. To address this, we propose the text guidance instead, and introduce TextSMOG, a new Text-guided Small Molecule Generation Approach via 3D Diffusion Model which integrates language and diffusion models for text-guided small molecule generation. This method uses textual conditions to guide molecule generation, enhancing both stability and diversity. Experimental results show TextSMOG's proficiency in capturing and utilizing information from textual descriptions, making it a powerful tool for generating 3D molecular structures in response to complex textual customizations.

SciLitLLM: How to Adapt LLMs for Scientific Literature Understanding

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks.cIn this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. Our contributions are threefold: (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for supervised fine-tuning in less-represented scientific domains. (3) SciLitLLM achieves promising performance improvements on scientific literature understanding benchmarks.