Molecular Property Prediction (MPP) is a critical task in computational drug discovery, aimed at identifying molecules with desirable pharmacological and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties. Machine learning models have been widely used in this fast-growing field, with two types of models being commonly employed: traditional non-deep models and deep models.

Finding new drugs is getting harder and harder. One of the hopes of drug discovery is to use machine learning models to predict molecular properties.

SSL based on persistent homology (PH), a mathematical tool for modeling topological features of data that persist across multiple scales.

The Tanimoto coefficient is commonly used to measure the similarity between molecules represented as discrete fingerprints, either as a distance metric or a positive definite kernel.

However, identifying the original base model of an LLM is challenging due to potential parameter alterations. In thisstudy, we introduce HuRef, a human-readable fingerprint for LLMs that uniquely identifies the base model without interfering with training or exposing model parameters to the public.We first observe that the vector direction of LLM parameters remains stable after the model has converged during pretraining, with negligible perturbations through subsequent training steps, including continued pretraining, supervised fine-tuning, and RLHF, which makes it a sufficient conditionto identify the base model.The necessity is validated by continuing to train an LLM with an extra term to drive away the model parameters' direction and the model becomes damaged. However, this direction is vulnerable to simple attacks like dimension permutation or matrix rotation, which significantly change it without affecting performance. To address this, leveraging the Transformer structure, we systematically analyze potential attacks and define three invariant terms that identify an LLM's base model. Due to the potential risk of information leakage, we cannot publish invariant terms directly. Instead, we map them to a Gaussian vector using an encoder, then convert it into a natural image using StyleGAN2, and finally publish the image. In our black-box setting, all fingerprinting steps are internally conducted by the LLMs owners. To ensure the published fingerprints are honestly generated, we introduced Zero-Knowledge Proof (ZKP).Experimental results across various LLMs demonstrate the effectiveness of our method.

In computer-aided drug discovery (CADD), virtual screening (VS) is used for comparing a library of compounds against known active ligands to identify the drug candidates that are most likely to bind to a molecular target. Most VS methods to date have focused on using canonical compound representations (e.g., SMILES strings, Morgan fingerprints) or generating alternative fingerprints of the compounds by training progressively more complex variational autoencoders (VAEs) and graph neural networks (GNNs). Although VAEs and GNNs led to significant improvements in VS performance, these methods suffer from reduced performance when scaling to large virtual compound datasets. The performance of these methods has shown only incremental improvements in the past few years. To address this problem, we developed a novel method using multiparameter persistence (MP) homology that produces topological fingerprints of the compounds as multidimensional vectors. Our primary contribution is framing the VS process as a new topology-based graph ranking problem by partitioning a compound into chemical substructures informed by the periodic properties of its atoms and extracting their persistent homology features at multiple resolution levels. We show that the margin loss fine-tuning of pretrained Triplet networks attains highly competitive results in differentiating between compounds in the embedding space and ranking their likelihood of becoming effective drug candidates. We further establish theoretical guarantees for the stability properties of our proposed MP signatures, and demonstrate that our models, enhanced by the MP signatures, outperform state-of-the-art methods on benchmark datasets by a wide and highly statistically significant margin (e.g., 93\% gain for Cleves-Jain and 54\% gain for DUD-E Diverse dataset).

Components of machine learning systems are not (yet) perceived as security hotspots. Secure coding practices, such as ensuring that no execution paths depend on confidential inputs, have not yet been adopted by ML developers. We initiate the study of code security of ML systems by investigating how nucleus sampling---a popular approach for generating text, used for applications such as auto-completion---unwittingly leaks texts typed by users. Our main result is that the series of nucleus sizes for many natural English word sequences is a unique fingerprint. We then show how an attacker can infer typed text by measuring these fingerprints via a suitable side channel (e.g., cache access times), explain how this attack could help de-anonymize anonymous texts, and discuss defenses.

Understanding and predicting polymer solubility in various solvents is critical for applications ranging from recycling to pharmaceutical formulation. This work presents a deep learning framework that predicts polymer solubility, expressed as weight percent (wt%), directly from SMILES representations of both polymers and solvents. A dataset of 8,049 polymer solvent pairs at 25 deg C was constructed from calibrated molecular dynamics simulations (Zhou et al., 2023), and molecular descriptors and fingerprints were combined into a 2,394 feature representation per sample. A fully connected neural network with six hidden layers was trained using the Adam optimizer and evaluated using mean squared error loss, achieving strong agreement between predicted and actual solubility values. Generalizability was demonstrated using experimentally measured data from the Materials Genome Project, where the model maintained high accuracy on 25 unseen polymer solvent combinations. These findings highlight the viability of SMILES based machine learning models for scalable solubility prediction and high-throughput solvent screening, supporting applications in green chemistry, polymer processing, and materials design.

Science Archaeology Who built Scandinavia's oldest wooden plank boat? An ancient fingerprint offers clues. Archeologists are closer to solving the Hjortspring Boat's mysteries. Breakthroughs, discoveries, and DIY tips sent every weekday. Archaeologists examining an ancient boat discovered in Denmark over a century ago are getting some help from a clue usually associated with crime scenes .