MOTIVATION: The current paradigm of deep learning models for the joint representation of molecules and text primarily relies on 1D or 2D molecular formats, neglecting significant 3D structural information that offers valuable physical insight. This narrow focus inhibits the models' versatility and adaptability across a wide range of modalities. Conversely, the limited research focusing on explicit 3D representation tends to overlook textual data within the biomedical domain. RESULTS: We present a unified pre-trained language model, MolLM, that concurrently captures 2D and 3D molecular information alongside biomedical text. MolLM consists of a text Transformer encoder and a molecular Transformer encoder, designed to encode both 2D and 3D molecular structures. To support MolLM's self-supervised pre-training, we constructed 160K molecule-text pairings. Employing contrastive learning as a supervisory signal for learning, MolLM demonstrates robust molecular representation capabilities across four downstream tasks, including cross-modal molecule and text matching, property prediction, captioning, and text-prompted molecular editing. Through ablation, we demonstrate that the inclusion of explicit 3D representations improves performance in these downstream tasks. AVAILABILITY AND IMPLEMENTATION: Our code, data, pre-trained model weights, and examples of using our model are all available at https://github.com/gersteinlab/MolLM. In particular, we provide Jupyter Notebooks offering step-by-step guidance on how to use MolLM to extract embeddings for both molecules and text.

Large Language Models (LLMs) have become integral to numerous domains, significantly advancing applications in data management, mining, and analysis. Their profound capabilities in processing and interpreting complex language data, however, bring to light pressing concerns regarding data privacy, especially the risk of unintentional training data leakage. Despite the critical nature of this issue, there has been no existing literature to offer a comprehensive assessment of data privacy risks in LLMs. Addressing this gap, our paper introduces LLM-PBE, a toolkit crafted specifically for the systematic evaluation of data privacy risks in LLMs. LLM-PBE is designed to analyze privacy across the entire lifecycle of LLMs, incorporating diverse attack and defense strategies, and handling various data types and metrics. Through detailed experimentation with multiple LLMs, LLM-PBE facilitates an in-depth exploration of data privacy concerns, shedding light on influential factors such as model size, data characteristics, and evolving temporal dimensions. This study not only enriches the understanding of privacy issues in LLMs but also serves as a vital resource for future research in the field. Aimed at enhancing the breadth of knowledge in this area, the findings, resources, and our full technical report are made available at https://llm-pbe.github.io/, providing an open platform for academic and practical advancements in LLM privacy assessment.

We present a method for optimization-based recovery of eye motion from rolling shutter video of the retina. Our approach formulates eye tracking as an optimization problem that jointly estimates the retina’s motion and appearance using convex optimization and a constrained version of gradient descent. By incorporating the rolling shutter imaging model into the formulation of our joint optimization, we achieve state-of-the-art accuracy both offline and in real-time. We apply our method to retina video captured with an adaptive optics scanning laser ophthalmoscope (AOSLO), demonstrating eye tracking at 1 kHz with accuracies below one arcminute—over an order of magnitude higher than conventional eye tracking systems.