Drug discovery is a complex process that involves multiple scenarios and stages, such as fragment-constrained molecule generation, hit generation and lead optimization. However, existing molecular generative models can only tackle one or two of these scenarios and lack the flexibility to address various aspects of the drug discovery pipeline. In this paper, we present Generalist Molecular generative model (GenMol), a versatile framework that addresses these limitations by applying discrete diffusion to the Sequential Attachment-based Fragment Embedding (SAFE) molecular representation. GenMol generates SAFE sequences through non-autoregressive bidirectional parallel decoding, thereby allowing utilization of a molecular context that does not rely on the specific token ordering and enhanced computational efficiency. Moreover, under the discrete diffusion framework, we introduce fragment remasking, a strategy that optimizes molecules by replacing fragments with masked tokens and regenerating them, enabling effective exploration of chemical space. GenMol significantly outperforms the previous GPT-based model trained on SAFE representations in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These experimental results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language models (pLM) training on hundreds of graphical processing units (GPUs). We introduce the BioNeMo Framework to facilitate the training of computational biology and chemistry AI models across hundreds of GPUs. Its modular design allows the integration of individual components, such as data loaders, into existing workflows and is open to community contributions. We detail technical features of the BioNeMo Framework through use cases such as pLM pre-training and fine-tuning. On 256 NVIDIA A100s, BioNeMo Framework trains a three billion parameter BERT-based pLM on over one trillion tokens in 4.2 days. The BioNeMo Framework is open-source and free for everyone to use.

High quality labeled datasets have allowed deep learning to achieve impressive results on many sound analysis tasks. Yet, it is labor-intensive to accurately annotate large amount of audio data, and the dataset may contain noisy labels in the practical settings. Meanwhile, the deep neural networks are susceptive to those incorrect labeled data because of their outstanding memorization ability. In this paper, we present a novel framework, named CrossFilter, to combat the noisy labels problem for audio tagging. Multiple representations (such as, Logmel and MFCC) are used as the input of our framework for providing more complementary information of the audio. Then, though the cooperation and interaction of two neural networks, we divide the dataset into curated and noisy subsets by incrementally pick out the possibly correctly labeled data from the noisy data. Moreover, our approach leverages the multi-task learning on curated and noisy subsets with different loss function to fully utilize the entire dataset. The noisy-robust loss function is employed to alleviate the adverse effects of incorrect labels. On both the audio tagging datasets FSDKaggle2018 and FSDKaggle2019, empirical results demonstrate the performance improvement compared with other competing approaches. On FSDKaggle2018 dataset, our method achieves state-of-the-art performance and even surpasses the ensemble models.

In recent years, dynamically growing data and incrementally growing number of classes pose new challenges to large-scale data classification research. Most traditional methods struggle to balance the precision and computational burden when data and its number of classes increased. However, some methods are with weak precision, and the others are time-consuming. In this paper, we propose an incremental learning method, namely, heterogeneous incremental Nearest Class Mean Random Forest (hi-RF), to handle this issue. It is a heterogeneous method that either replaces trees or updates trees leaves in the random forest adaptively, to reduce the computational time in comparable performance, when data of new classes arrive. Specifically, to keep the accuracy, one proportion of trees are replaced by new NCM decision trees; to reduce the computational load, the rest trees are updated their leaves probabilities only. Most of all, out-of-bag estimation and out-of-bag boosting are proposed to balance the accuracy and the computational efficiency. Fair experiments were conducted and demonstrated its comparable precision with much less computational time.