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We introduce Predictive Batch Scheduling (PBS), a novel training optimization technique that accelerates language model convergence by dynamically prioritizing high-loss samples during batch construction. Unlike curriculum learning…

Rapid determination of molecular structures can greatly accelerate workflows across many chemical disciplines. However, elucidating structure using only one-dimensional (1D) NMR spectra, the most readily accessible data, remains an…

Deep learning models for anticipating the products of organic reactions have found many use cases, including validating retrosynthetic pathways and constraining synthesis-based molecular design tools. Despite compelling performance on…

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our…

Anticancer peptides (ACPs) are a group of peptides that exhibite antineoplastic properties. The utilization of ACPs in cancer prevention can present a viable substitute for conventional cancer therapeutics, as they possess a higher degree…

We present an Expectation-Maximization (EM) Regularized Deep Learning (EMReDL) model for weakly supervised tumor segmentation. The proposed framework is tailored to glioblastoma, a type of malignant tumor characterized by its diffuse…

We show that large language model (LLMs) can be transformed via supervised fine-tuning (SFT) of engineered prompts into SmileyLlama for exploring the chemical space of drug molecules. We benchmark SmileyLlama against pre-trained LLMs and…

Vulnerability analysis is crucial for software security. This work focuses on using pre-training techniques to enhance the understanding of vulnerable code and boost vulnerability analysis. The code understanding ability of a pre-trained…

For large libraries of small molecules, exhaustive combinatorial chemical screens become infeasible to perform when considering a range of disease models, assay conditions, and dose ranges. Deep learning models have achieved state of the…

Prediction of toxicity levels of chemical compounds is an important issue in Quantitative Structure-Activity Relationship (QSAR) modeling. Although toxicity prediction has achieved significant progress in recent times through deep learning,…

Purpose: Large Language Models (LLMs) like GPT (Generative Pre-trained Transformer) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI are increasingly recognized for their potential in the field of cheminformatics,…

Deep Learning (DL) can predict biomarkers directly from digitized cancer histology in a weakly-supervised setting. Recently, the prediction of continuous biomarkers through regression-based DL has seen an increasing interest. Nonetheless,…

Finetuning a Large Language Model (LLM) is crucial for generating results towards specific objectives. This research delves into the realm of drug optimization and introduce a novel reinforcement learning algorithm to finetune a drug…

Glioblastoma, a highly aggressive brain tumor with diverse molecular and pathological features, poses a diagnostic challenge due to its heterogeneity. Accurate diagnosis and assessment of this heterogeneity are essential for choosing the…

Recent deep learning frameworks in histopathology, particularly multiple instance learning (MIL) combined with pathology foundational models (PFMs), have shown strong performance. However, PFMs exhibit limitations on certain cancer or…

In this study, we generate and maintain a database of 10 million virtual lipids through METiS's in-house de novo lipid generation algorithms and lipid virtual screening techniques. These virtual lipids serve as a corpus for pre-training,…

Recent advances in Language Models have enabled the protein modeling community with a powerful tool since protein sequences can be represented as text. Specifically, by taking advantage of Transformers, sequence-to-property prediction will…

Theoretical predictions of NMR chemical shifts from first-principles can greatly facilitate experimental interpretation and structure identification. However, accurate prediction of chemical shifts using the best coupled cluster methods can…

We cast retrosynthesis as a machine translation problem by introducing a special Tensor2Tensor, an entire attention-based and fully data-driven model. Given a data set comprising about 50,000 diverse reactions extracted from USPTO patents,…

This study aims to develop a deep learning model for predicting the binding affinity of ligands targeting the Peroxisome Proliferator-Activated Receptor (PPAR) family, using 2D molecular descriptors. A dataset of 3,764 small molecules with…