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.

How Transformers Implement Induction Heads: Approximation and Optimization Analysis

Transformers have demonstrated exceptional in-context learning capabilities, yet the theoretical understanding of the underlying mechanisms remain limited. A recent work (Elhage et al., 2021) identified a "rich" in-context mechanism known as induction head, contrasting with "lazy" $n$-gram models that overlook long-range dependencies. In this work, we provide both approximation and optimization analyses of how transformers implement induction heads. In the approximation analysis, we formalize both standard and generalized induction head mechanisms, and examine how transformers can efficiently implement them, with an emphasis on the distinct role of each transformer submodule. For the optimization analysis, we study the training dynamics on a synthetic mixed target, composed of a 4-gram and an in-context 2-gram component. This setting enables us to precisely characterize the entire training process and uncover an {\em abrupt transition} from lazy (4-gram) to rich (induction head) mechanisms as training progresses.

Uni-ELF: A Multi-Level Representation Learning Framework for Electrolyte Formulation Design

Advancements in lithium battery technology heavily rely on the design and engineering of electrolytes. However, current schemes for molecular design and recipe optimization of electrolytes lack an effective computational-experimental closed loop and often fall short in accurately predicting diverse electrolyte formulation properties. In this work, we introduce Uni-ELF, a novel multi-level representation learning framework to advance electrolyte design. Our approach involves two-stage pretraining: reconstructing three-dimensional molecular structures at the molecular level using the Uni-Mol model, and predicting statistical structural properties (e.g., radial distribution functions) from molecular dynamics simulations at the mixture level. Through this comprehensive pretraining, Uni-ELF is able to capture intricate molecular and mixture-level information, which significantly enhances its predictive capability. As a result, Uni-ELF substantially outperforms state-of-the-art methods in predicting both molecular properties (e.g., melting point, boiling point, synthesizability) and formulation properties (e.g., conductivity, Coulombic efficiency). Moreover, Uni-ELF can be seamlessly integrated into an automatic experimental design workflow. We believe this innovative framework will pave the way for automated AI-based electrolyte design and engineering.

$\text{Memory}^3$: Language Modeling with Explicit Memory

The training and inference of large language models (LLMs) are together a costly process that transports knowledge from raw data to meaningful computation. Inspired by the memory hierarchy of the human brain, we reduce this cost by equipping LLMs with explicit memory, a memory format cheaper than model parameters and text retrieval-augmented generation (RAG). Conceptually, with most of its knowledge externalized to explicit memories, the LLM can enjoy a smaller parameter size, training cost, and inference cost, all proportional to the amount of remaining "abstract knowledge". As a preliminary proof of concept, we train from scratch a 2.4B LLM, which achieves better performance than much larger LLMs as well as RAG models, and maintains higher decoding speed than RAG. The model is named $\text{Memory}^3$, since explicit memory is the third form of memory in LLMs after implicit memory (model parameters) and working memory (context key-values). We introduce a memory circuitry theory to support the externalization of knowledge, and present novel techniques including a memory sparsification mechanism that makes storage tractable and a two-stage pretraining scheme that facilitates memory formation.

Uni-Mol2: Exploring Molecular Pretraining Model at Scale

In recent years, pretraining models have made significant advancements in the fields of natural language processing (NLP), computer vision (CV), and life sciences. The significant advancements in NLP and CV are predominantly driven by the expansion of model parameters and data size, a phenomenon now recognized as the scaling laws. However, research exploring scaling law in molecular pretraining models remains unexplored. In this work, we present Uni-Mol2 , an innovative molecular pretraining model that leverages a two-track transformer to effectively integrate features at the atomic level, graph level, and geometry structure level. Along with this, we systematically investigate the scaling law within molecular pretraining models, characterizing the power-law correlations between validation loss and model size, dataset size, and computational resources. Consequently, we successfully scale Uni-Mol2 to 1.1 billion parameters through pretraining on 800 million conformations, making it the largest molecular pretraining model to date. Extensive experiments show consistent improvement in the downstream tasks as the model size grows. The Uni-Mol2 with 1.1B parameters also outperforms existing methods, achieving an average 27% improvement on the QM9 and 14% on COMPAS-1D dataset.

Improving Generalization and Convergence by Enhancing Implicit Regularization

In this work, we propose an Implicit Regularization Enhancement (IRE) framework to accelerate the discovery of flat solutions in deep learning, thereby improving generalization and convergence. Specifically, IRE decouples the dynamics of flat and sharp directions, which boosts the sharpness reduction along flat directions while maintaining the training stability in sharp directions. We show that IRE can be practically incorporated with {\em generic base optimizers} without introducing significant computational overload. Experiments show that IRE consistently improves the generalization performance for image classification tasks across a variety of benchmark datasets (CIFAR-10/100, ImageNet) and models (ResNets and ViTs). Surprisingly, IRE also achieves a $2\times$ {\em speed-up} compared to AdamW in the pre-training of Llama models (of sizes ranging from 60M to 229M) on datasets including Wikitext-103, Minipile, and Openwebtext. Moreover, we provide theoretical guarantees, showing that IRE can substantially accelerate the convergence towards flat minima in Sharpness-aware Minimization (SAM).

Coarse-graining conformational dynamics with multi-dimensional generalized Langevin equation: how, when, and why

A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained conformational dynamics. Constrained by the fluctuation-dissipation theorem, the approach can build coarse-grained models in dynamical consistency with all-atom molecular dynamics. We also propose practical criteria for AIGLE to enforce long-term dynamical consistency. Case studies of a toy polymer, with 20 coarse-grained sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling coarse-grained conformational dynamics in practice.

Understanding the Expressive Power and Mechanisms of Transformer for Sequence Modeling

We conduct a systematic study of the approximation properties of Transformer for sequence modeling with long, sparse and complicated memory. We investigate the mechanisms through which different components of Transformer, such as the dot-product self-attention, positional encoding and feed-forward layer, affect its expressive power, and we study their combined effects through establishing explicit approximation rates. Our study reveals the roles of critical parameters in the Transformer, such as the number of layers and the number of attention heads, and these insights also provide natural suggestions for alternative architectures.

Anchor function: a type of benchmark functions for studying language models

Understanding transformer-based language models is becoming increasingly crucial, particularly as they play pivotal roles in advancing towards artificial general intelligence. However, language model research faces significant challenges, especially for academic research groups with constrained resources. These challenges include complex data structures, unknown target functions, high computational costs and memory requirements, and a lack of interpretability in the inference process, etc. Drawing a parallel to the use of simple models in scientific research, we propose the concept of an anchor function. This is a type of benchmark function designed for studying language models in learning tasks that follow an "anchor-key" pattern. By utilizing the concept of an anchor function, we can construct a series of functions to simulate various language tasks. The anchor function plays a role analogous to that of mice in diabetes research, particularly suitable for academic research. We demonstrate the utility of the anchor function with an example, revealing two basic operations by attention structures in language models: shifting tokens and broadcasting one token from one position to many positions. These operations are also commonly observed in large language models. The anchor function framework, therefore, opens up a series of valuable and accessible research questions for further exploration, especially for theoretical study.

Learning Free Terminal Time Optimal Closed-loop Control of Manipulators

This paper presents a novel approach to learning free terminal time closed-loop control for robotic manipulation tasks, enabling dynamic adjustment of task duration and control inputs to enhance performance. We extend the supervised learning approach, namely solving selected optimal open-loop problems and utilizing them as training data for a policy network, to the free terminal time scenario. Three main challenges are addressed in this extension. First, we introduce a marching scheme that enhances the solution quality and increases the success rate of the open-loop solver by gradually refining time discretization. Second, we extend the QRnet in Nakamura-Zimmerer et al. (2021b) to the free terminal time setting to address discontinuity and improve stability at the terminal state. Third, we present a more automated version of the initial value problem (IVP) enhanced sampling method from previous work (Zhang et al., 2022) to adaptively update the training dataset, significantly improving its quality. By integrating these techniques, we develop a closed-loop policy that operates effectively over a broad domain with varying optimal time durations, achieving near globally optimal total costs.