Ding Wang

Dingshuo Chen, Zhixun Li, Yuyan Ni et al.

With the emergence of various molecular tasks and massive datasets, how to perform efficient training has become an urgent yet under-explored issue in the area. Data pruning (DP), as an oft-stated approach to saving training burdens, filters out less influential samples to form a coreset for training. However, the increasing reliance on pretrained models for molecular tasks renders traditional in-domain DP methods incompatible. Therefore, we propose a Molecular data Pruning framework for enhanced Generalization (MolPeg), which focuses on the source-free data pruning scenario, where data pruning is applied with pretrained models. By maintaining two models with different updating paces during training, we introduce a novel scoring function to measure the informativeness of samples based on the loss discrepancy. As a plug-and-play framework, MolPeg realizes the perception of both source and target domain and consistently outperforms existing DP methods across four downstream tasks. Remarkably, it can surpass the performance obtained from full-dataset training, even when pruning up to 60-70% of the data on HIV and PCBA dataset. Our work suggests that the discovery of effective data-pruning metrics could provide a viable path to both enhanced efficiency and superior generalization in transfer learning.

Andrew Smart, Ben Hutchinson, Lameck Mbangula Amugongo et al.

Large Language Models (LLMs) have rapidly increased in size and apparent capabilities in the last three years, but their training data is largely English text. There is growing interest in multilingual LLMs, and various efforts are striving for models to accommodate languages of communities outside of the Global North, which include many languages that have been historically underrepresented in digital realms. These languages have been coined as "low resource languages" or "long-tail languages", and LLMs performance on these languages is generally poor. While expanding the use of LLMs to more languages may bring many potential benefits, such as assisting cross-community communication and language preservation, great care must be taken to ensure that data collection on these languages is not extractive and that it does not reproduce exploitative practices of the past. Collecting data from languages spoken by previously colonized people, indigenous people, and non-Western languages raises many complex sociopolitical and ethical questions, e.g., around consent, cultural safety, and data sovereignty. Furthermore, linguistic complexity and cultural nuances are often lost in LLMs. This position paper builds on recent scholarship, and our own work, and outlines several relevant social, cultural, and ethical considerations and potential ways to mitigate them through qualitative research, community partnerships, and participatory design approaches. We provide twelve recommendations for consideration when collecting language data on underrepresented language communities outside of the Global North.

Erika Yilin Zheng, Yu Yan, Baradwaj Simha Sankar et al.

Existing machine learning methods for molecular (e.g., gene) embeddings are restricted to specific tasks or data modalities, limiting their effectiveness within narrow domains. As a result, they fail to capture the full breadth of gene functions and interactions across diverse biological contexts. In this study, we have systematically evaluated knowledge representations of biomolecules across multiple dimensions representing a task-agnostic manner spanning three major data sources, including omics experimental data, literature-derived text data, and knowledge graph-based representations. To distinguish between meaningful biological signals from chance correlations, we devised an adjusted variant of Singular Vector Canonical Correlation Analysis (SVCCA) that quantifies signal redundancy and complementarity across different data modalities and sources. These analyses reveal that existing embeddings capture largely non-overlapping molecular signals, highlighting the value of embedding integration. Building on this insight, we propose Platform for Representation and Integration of multimodal Molecular Embeddings (PRISME), a machine learning based workflow using an autoencoder to integrate these heterogeneous embeddings into a unified multimodal representation. We validated this approach across various benchmark tasks, where PRISME demonstrated consistent performance, and outperformed individual embedding methods in missing value imputations. This new framework supports comprehensive modeling of biomolecules, advancing the development of robust, broadly applicable multimodal embeddings optimized for downstream biomedical machine learning applications.