Leveraging State Space Models in Long Range Genomics

Long-range dependencies are critical for understanding genomic structure and function, yet most conventional methods struggle with them. Widely adopted transformer-based models, while excelling at short-context tasks, are limited by the attention module's quadratic computational complexity and inability to extrapolate to sequences longer than those seen in training. In this work, we explore State Space Models (SSMs) as a promising alternative by benchmarking two SSM-inspired architectures, Caduceus and Hawk, on long-range genomics modeling tasks under conditions parallel to a 50M parameter transformer baseline. We discover that SSMs match transformer performance and exhibit impressive zero-shot extrapolation across multiple tasks, handling contexts 10 to 100 times longer than those seen during training, indicating more generalizable representations better suited for modeling the long and complex human genome. Moreover, we demonstrate that these models can efficiently process sequences of 1M tokens on a single GPU, allowing for modeling entire genomic regions at once, even in labs with limited compute. Our findings establish SSMs as efficient and scalable for long-context genomic analysis.

ACE: A LLM-based Negotiation Coaching System

The growing prominence of LLMs has led to an increase in the development of AI tutoring systems. These systems are crucial in providing underrepresented populations with improved access to valuable education. One important area of education that is unavailable to many learners is strategic bargaining related to negotiation. To address this, we develop a LLM-based Assistant for Coaching nEgotiation (ACE). ACE not only serves as a negotiation partner for users but also provides them with targeted feedback for improvement. To build our system, we collect a dataset of negotiation transcripts between MBA students. These transcripts come from trained negotiators and emulate realistic bargaining scenarios. We use the dataset, along with expert consultations, to design an annotation scheme for detecting negotiation mistakes. ACE employs this scheme to identify mistakes and provide targeted feedback to users. To test the effectiveness of ACE-generated feedback, we conducted a user experiment with two consecutive trials of negotiation and found that it improves negotiation performances significantly compared to a system that doesn't provide feedback and one which uses an alternative method of providing feedback.