MassSpecGym: A benchmark for the discovery and identification of molecules

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: \textit{de novo} molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at \url{https://github.com/pluskal-lab/MassSpecGym}.

Dataset and Lessons Learned from the 2024 SaTML LLM Capture-the-Flag Competition

Large language model systems face important security risks from maliciously crafted messages that aim to overwrite the system's original instructions or leak private data. To study this problem, we organized a capture-the-flag competition at IEEE SaTML 2024, where the flag is a secret string in the LLM system prompt. The competition was organized in two phases. In the first phase, teams developed defenses to prevent the model from leaking the secret. During the second phase, teams were challenged to extract the secrets hidden for defenses proposed by the other teams. This report summarizes the main insights from the competition. Notably, we found that all defenses were bypassed at least once, highlighting the difficulty of designing a successful defense and the necessity for additional research to protect LLM systems. To foster future research in this direction, we compiled a dataset with over 137k multi-turn attack chats and open-sourced the platform.

Self-Supervised Traversability Prediction by Learning to Reconstruct Safe Terrain

Navigating off-road with a fast autonomous vehicle depends on a robust perception system that differentiates traversable from non-traversable terrain. Typically, this depends on a semantic understanding which is based on supervised learning from images annotated by a human expert. This requires a significant investment in human time, assumes correct expert classification, and small details can lead to misclassification. To address these challenges, we propose a method for predicting high- and low-risk terrains from only past vehicle experience in a self-supervised fashion. First, we develop a tool that projects the vehicle trajectory into the front camera image. Second, occlusions in the 3D representation of the terrain are filtered out. Third, an autoencoder trained on masked vehicle trajectory regions identifies low- and high-risk terrains based on the reconstruction error. We evaluated our approach with two models and different bottleneck sizes with two different training and testing sites with a fourwheeled off-road vehicle. Comparison with two independent test sets of semantic labels from similar terrain as training sites demonstrates the ability to separate the ground as low-risk and the vegetation as high-risk with 81.1% and 85.1% accuracy.

PrePARE: Predictive Proprioception for Agile Failure Event Detection in Robotic Exploration of Extreme Terrains

Legged robots can traverse a wide variety of terrains, some of which may be challenging for wheeled robots, such as stairs or highly uneven surfaces. However, quadruped robots face stability challenges on slippery surfaces. This can be resolved by adjusting the robot's locomotion by switching to more conservative and stable locomotion modes, such as crawl mode (where three feet are in contact with the ground always) or amble mode (where one foot touches down at a time) to prevent potential falls. To tackle these challenges, we propose an approach to learn a model from past robot experience for predictive detection of potential failures. Accordingly, we trigger gait switching merely based on proprioceptive sensory information. To learn this predictive model, we propose a semi-supervised process for detecting and annotating ground truth slip events in two stages: We first detect abnormal occurrences in the time series sequences of the gait data using an unsupervised anomaly detector, and then, the anomalies are verified with expert human knowledge in a replay simulation to assert the event of a slip. These annotated slip events are then used as ground truth examples to train an ensemble decision learner for predicting slip probabilities across terrains for traversability. We analyze our model on data recorded by a legged robot on multiple sites with slippery terrain. We demonstrate that a potential slip event can be predicted up to 720 ms ahead of a potential fall with an average precision greater than 0.95 and an average F-score of 0.82. Finally, we validate our approach in real-time by deploying it on a legged robot and switching its gait mode based on slip event detection.