arXiv subjects

Jemma Daniel

Publications and source records attributed to Jemma Daniel.

3 recordsLinked to original sources

arXiv2025

De novo peptide sequencing rescoring and FDR estimation with Winnow

Machine learning has markedly advanced de novo peptide sequencing (DNS) for mass spectrometry-based proteomics. DNS tools offer a reliable way to identify peptides without relying on reference databases, extending proteomic analysis and unlocking applications into less-charted regions of the proteome. However, they still face a key limitation. DNS tools lack principled methods for estimating false discovery rates (FDR) and instead rely on model-specific confidence scores that are often miscalibrated. This limits trust in results, hinders cross-model comparisons and reduces validation success. Here we present Winnow, a model-agnostic framework for estimating FDR from calibrated DNS outputs. Winnow maps raw model scores to calibrated confidences using a neural network trained on peptide-spectrum match (PSM)-derived features. From these calibrated scores, Winnow computes PSM-specific error metrics and an experiment-wide FDR estimate using a novel decoy-free FDR estimator. It supports both zero-shot and dataset-specific calibration, enabling flexible application via direct inference, fine-tuning, or training a custom model. We demonstrate that, when applied to InstaNovo predictions, Winnow's calibrator improves recall at fixed FDR thresholds, and its FDR estimator tracks true error rates when benchmarked against reference proteomes and database search. Winnow ensures accurate FDR control across datasets, helping unlock the full potential of DNS.

q-bio.QM↗

arXiv2024

Multi-Agent Reinforcement Learning with Selective State-Space Models

The Transformer model has demonstrated success across a wide range of domains, including in Multi-Agent Reinforcement Learning (MARL) where the Multi-Agent Transformer (MAT) has emerged as a leading algorithm in the field. However, a significant drawback of Transformer models is their quadratic computational complexity relative to input size, making them computationally expensive when scaling to larger inputs. This limitation restricts MAT's scalability in environments with many agents. Recently, State-Space Models (SSMs) have gained attention due to their computational efficiency, but their application in MARL remains unexplored. In this work, we investigate the use of Mamba, a recent SSM, in MARL and assess whether it can match the performance of MAT while providing significant improvements in efficiency. We introduce a modified version of MAT that incorporates standard and bi-directional Mamba blocks, as well as a novel "cross-attention" Mamba block. Extensive testing shows that our Multi-Agent Mamba (MAM) matches the performance of MAT across multiple standard multi-agent environments, while offering superior scalability to larger agent scenarios. This is significant for the MARL community, because it indicates that SSMs could replace Transformers without compromising performance, whilst also supporting more effective scaling to higher numbers of agents. Our project page is available at https://sites.google.com/view/multi-agent-mamba .

cs.LG↗

arXiv2024

Sable: a Performant, Efficient and Scalable Sequence Model for MARL

As multi-agent reinforcement learning (MARL) progresses towards solving larger and more complex problems, it becomes increasingly important that algorithms exhibit the key properties of (1) strong performance, (2) memory efficiency, and (3) scalability. In this work, we introduce Sable, a performant, memory-efficient, and scalable sequence modeling approach to MARL. Sable works by adapting the retention mechanism in Retentive Networks (Sun et al., 2023) to achieve computationally efficient processing of multi-agent observations with long context memory for temporal reasoning. Through extensive evaluations across six diverse environments, we demonstrate how Sable is able to significantly outperform existing state-of-the-art methods in a large number of diverse tasks (34 out of 45 tested). Furthermore, Sable maintains performance as we scale the number of agents, handling environments with more than a thousand agents while exhibiting a linear increase in memory usage. Finally, we conduct ablation studies to isolate the source of Sable's performance gains and confirm its efficient computational memory usage.

cs.LG↗