Molecular dynamics plays a pivotal role in elucidating the dynamic behavior of molecules, providing essential insights into the temporal evolution of complex systems, such as understanding the conformational changes, interactions, and thermodynamic properties of molecules. It is thus important for fields ranging from drug discovery to materials science. The potential energy surface serves as the underlying landscape dictating the dynamics of a molecular system, and making an accurate representation of it is crucial for studying the dynamics of molecules through numerical simulations. Ab initio methods like Density Functional Theory (DFT) provide high accuracy by accounting for the electronic structure of atoms. Yet their high computational demands pose a significant challenge for efficient utilization, particularly in the context of large many-body systems. On the other hand, forces can be computed using empirical interatomic potentials tailored to specific environments, bypassing the electronic structures of the system. This approach significantly reduces the computational cost compared to ab initio methods. As there is a wide variety of interactions in molecular systems (bonded or non-bonded interactions), finding the appropriate functional forms can be challenging.

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing and conducting chemical reactions to synthesize new compounds with desired properties and applications. Current approaches, however, often neglect the critical role of multiple molecule graph interaction in understanding chemical reactions, leading to suboptimal performance in synthetic chemistry tasks. This study introduces PRESTO(Progressive Pretraining Enhances Synthetic Chemistry Outcomes), a new framework that bridges the molecule-text modality gap by integrating a comprehensive benchmark of pretraining strategies and dataset configurations. It progressively improves multimodal LLMs through cross-modal alignment and multi-graph understanding. Our extensive experiments demonstrate that PRESTO offers competitive results in downstream synthetic chemistry tasks. The code can be found at https://github.com/IDEA-XL/PRESTO.

Accurate representation of procedures in restricted scenarios, such as non-standardized scientific experiments, requires precise depiction of constraints. Unfortunately, Domain-specific Language (DSL), as an effective tool to express constraints structurally, often requires case-by-case hand-crafting, necessitating customized, labor-intensive efforts. To overcome this challenge, we introduce the AutoDSL framework to automate DSL-based constraint design across various domains. Utilizing domain specified experimental protocol corpora, AutoDSL optimizes syntactic constraints and abstracts semantic constraints. Quantitative and qualitative analyses of the DSLs designed by AutoDSL across five distinct domains highlight its potential as an auxiliary module for language models, aiming to improve procedural planning and execution.

Machine Learning (ML) for Mineral Prospectivity Mapping (MPM) remains a challenging problem as it requires the analysis of associations between large-scale multi-modal geospatial data and few historical mineral commodity observations (positive labels). Recent MPM works have explored Deep Learning (DL) as a modeling tool with more representation capacity. However, these overparameterized methods may be more prone to overfitting due to their reliance on scarce labeled data. While a large quantity of unlabeled geospatial data exists, no prior MPM works have considered using such information in a self-supervised manner. Our MPM approach uses a masked image modeling framework to pretrain a backbone neural network in a self-supervised manner using unlabeled geospatial data alone. After pretraining, the backbone network provides feature extraction for downstream MPM tasks. We evaluated our approach alongside existing methods to assess mineral prospectivity of Mississippi Valley Type (MVT) and Clastic-Dominated (CD) Lead-Zinc deposits in North America and Australia. Our results demonstrate that self-supervision promotes robustness in learned features, improving prospectivity predictions. Additionally, we leverage explainable artificial intelligence techniques to demonstrate that individual predictions can be interpreted from a geological perspective.

Large Language Models (LLMs) have demonstrated impressive capabilities for generalizing in unseen tasks. In the Named Entity Recognition (NER) task, recent advancements have seen the remarkable improvement of LLMs in a broad range of entity domains via instruction tuning, by adopting entity-centric schema. In this work, we explore the potential enhancement of the existing methods by incorporating negative instances into training. Our experiments reveal that negative instances contribute to remarkable improvements by (1) introducing contextual information, and (2) clearly delineating label boundaries. Furthermore, we introduce an efficient longest common subsequence (LCS) matching algorithm, which is tailored to transform unstructured predictions into structured entities. By integrating these components, we present GNER, a Generative NER system that shows improved zero-shot performance across unseen entity domains. Our comprehensive evaluation illustrates our system's superiority, surpassing state-of-the-art (SoTA) methods by 9 $F_1$ score in zero-shot evaluation.

Significant advancements in the field of wood species identification are needed worldwide to support sustainable timber trade. In this work we contribute to automate the identification of wood species via high-resolution macroscopic images of timber. The main challenge of this problem is that fine-grained patterns in timber are crucial in order to accurately identify wood species, and these patterns are not properly learned by traditional convolutional neural networks (CNNs) trained on low/medium resolution images. We propose a Timber Deep Learning Identification with Patch-based Inference Voting methodology, abbreviated TDLI-PIV methodology. Our proposal exploits the concept of patching and the availability of high-resolution macroscopic images of timber in order to overcome the inherent challenges that CNNs face in timber identification. The TDLI-PIV methodology is able to capture fine-grained patterns in timber and, moreover, boosts robustness and prediction accuracy via a collaborative voting inference process. In this work we also introduce a new data set of marcroscopic images of timber, called GOIMAI-Phase-I, which has been obtained using optical magnification in order to capture fine-grained details, which contrasts to the other datasets that are publicly available. More concretely, images in GOIMAI-Phase-I are taken with a smartphone with a 24x magnifying lens attached to the camera. Our data set contains 2120 images of timber and covers 37 legally protected wood species. Our experiments have assessed the performance of the TDLI-PIV methodology, involving the comparison with other methodologies available in the literature, exploration of data augmentation methods and the effect that the dataset size has on the accuracy of TDLI-PIV.

Coarse-graining is a molecular modeling technique in which an atomistic system is represented in a simplified fashion that retains the most significant system features that contribute to a target output, while removing the degrees of freedom that are less relevant. This reduction in model complexity allows coarse-grained molecular simulations to reach increased spatial and temporal scales compared to corresponding all-atom models. A core challenge in coarse-graining is to construct a force field that represents the interactions in the new representation in a way that preserves the atomistic-level properties. Many approaches to building coarse-grained force fields have limited transferability between different thermodynamic conditions as a result of averaging over internal fluctuations at a specific thermodynamic state point. Here, we use a graph-convolutional neural network architecture, the Hierarchically Interacting Particle Neural Network with Tensor Sensitivity (HIP-NN-TS), to develop a highly automated training pipeline for coarse grained force fields which allows for studying the transferability of coarse-grained models based on the force-matching approach. We show that this approach not only yields highly accurate force fields, but also that these force fields are more transferable through a variety of thermodynamic conditions. These results illustrate the potential of machine learning techniques such as graph neural networks to improve the construction of transferable coarse-grained force fields.

"Jailbreak" is a major safety concern of Large Language Models (LLMs), which occurs when malicious prompts lead LLMs to produce harmful outputs, raising issues about the reliability and safety of LLMs. Therefore, an effective evaluation of jailbreaks is very crucial to develop its mitigation strategies. However, our research reveals that many jailbreaks identified by current evaluations may actually be hallucinations-erroneous outputs that are mistaken for genuine safety breaches. This finding suggests that some perceived vulnerabilities might not represent actual threats, indicating a need for more precise red teaming benchmarks. To address this problem, we propose the $\textbf{B}$enchmark for reli$\textbf{AB}$ilit$\textbf{Y}$ and jail$\textbf{B}$reak ha$\textbf{L}$l$\textbf{U}$cination $\textbf{E}$valuation (BabyBLUE). BabyBLUE introduces a specialized validation framework including various evaluators to enhance existing jailbreak benchmarks, ensuring outputs are useful malicious instructions. Additionally, BabyBLUE presents a new dataset as an augmentation to the existing red teaming benchmarks, specifically addressing hallucinations in jailbreaks, aiming to evaluate the true potential of jailbroken LLM outputs to cause harm to human society.

Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reproducibility, and task singularity. Firstly, the absence of standardization can lead to unfair comparisons and inconclusive insights. To address this dilemma, we propose CBGBench, a comprehensive benchmark for SBDD, that unifies the task as a generative heterogeneous graph completion, analogous to fill-in-the-blank of the 3D complex binding graph. By categorizing existing methods based on their attributes, CBGBench facilitates a modular and extensible framework that implements various cutting-edge methods. Secondly, a single task on \textit{de novo} molecule generation can hardly reflect their capabilities. To broaden the scope, we have adapted these models to a range of tasks essential in drug design, which are considered sub-tasks within the graph fill-in-the-blank tasks. These tasks include the generative designation of \textit{de novo} molecules, linkers, fragments, scaffolds, and sidechains, all conditioned on the structures of protein pockets. Our evaluations are conducted with fairness, encompassing comprehensive perspectives on interaction, chemical properties, geometry authenticity, and substructure validity. We further provide the pre-trained versions of the state-of-the-art models and deep insights with analysis from empirical studies. The codebase for CBGBench is publicly accessible at \url{https://github.com/Edapinenut/CBGBench}.

Cosine similarity is widely used to measure the similarity between two embeddings, while interpretations based on angle and correlation coefficient are common. In this study, we focus on the interpretable axes of embeddings transformed by Independent Component Analysis (ICA), and propose a novel interpretation of cosine similarity as the sum of semantic similarities over axes. To investigate this, we first show experimentally that unnormalized embeddings contain norm-derived artifacts. We then demonstrate that normalized ICA-transformed embeddings exhibit sparsity, with a few large values in each axis and across embeddings, thereby enhancing interpretability by delineating clear semantic contributions. Finally, to validate our interpretation, we perform retrieval experiments using ideal embeddings with and without specific semantic components.