Michael Morris Danziger

Jonas Zausinger, Lars Pennig, Anamarija Kozina et al.

While language models have exceptional capabilities at text generation, they lack a natural inductive bias for emitting numbers and thus struggle in tasks involving quantitative reasoning, especially arithmetic. One fundamental limitation is the nature of the cross-entropy (CE) loss, which assumes a nominal scale and thus cannot convey proximity between generated number tokens. In response, we here present a regression-like loss that operates purely on token level. Our proposed Number Token Loss (NTL) comes in two flavors and minimizes either the $L_p$ norm or the Wasserstein distance between the numerical values of the real and predicted number tokens. NTL can easily be added to any language model and extend the CE objective during training without runtime overhead. We evaluate the proposed scheme on various mathematical datasets and find that it consistently improves performance in math-related tasks. In a direct comparison on a regression task, we find that NTL can match the performance of a regression head, despite operating on token level. Finally, we scale NTL up to 3B parameter models and observe improved performance, demonstrating its potential for seamless integration into LLMs. We hope to inspire LLM developers to improve their pretraining objectives and distribute NTL as a minimalistic and lightweight PyPI package $ntloss$: https://github.com/ai4sd/number-token-loss. Development code for full paper reproduction is available separately.

Yoav Kan-Tor, Michael Morris Danziger, Eden Zohar et al.

The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types. However, comparing the performance of these models consistently has proven to be a challenge due to differences in training data and downstream tasks. To tackle this problem, we developed an architecture-agnostic benchmarking approach that, instead of evaluating the models directly, leverages entity representation vectors from each model and trains simple predictive models for each benchmarking task. This ensures that all types of models are evaluated using the same input and output types. Here we focus on gene properties collected from professionally curated bioinformatics databases. These gene properties are categorized into five major groups: genomic properties, regulatory functions, localization, biological processes, and protein properties. Overall, we define hundreds of tasks based on these databases, which include binary, multi-label, and multi-class classification tasks. We apply these benchmark tasks to evaluate expression-based models, large language models, protein language models, DNA-based models, and traditional baselines. Our findings suggest that text-based models and protein language models generally outperform expression-based models in genomic properties and regulatory functions tasks, whereas expression-based models demonstrate superior performance in localization tasks. These results should aid in the development of more informed artificial intelligence strategies for biological understanding and therapeutic discovery. To ensure the reproducibility and transparency of our findings, we have made the source code and benchmark data publicly accessible for further investigation and expansion at github.com/BiomedSciAI/gene-benchmark.