De novo peptide sequencing from mass spectrometry (MS) data is a critical task in proteomics research. Traditional de novo algorithms have encountered a bottleneck in accuracy due to the inherent complexity of proteomics data. While deep learning-based methods have shown progress, they reduce the problem to a translation task, potentially overlooking critical nuances between spectra and peptides. In our research, we present ContraNovo, a pioneering algorithm that leverages contrastive learning to extract the relationship between spectra and peptides and incorporates the mass information into peptide decoding, aiming to address these intricacies more efficiently. Through rigorous evaluations on two benchmark datasets, ContraNovo consistently outshines contemporary state-of-the-art solutions, underscoring its promising potential in enhancing de novo peptide sequencing. The source code is available at https://github.com/BEAM-Labs/ContraNovo.
Maxwell-Amp\`{e}re-Nernst-Planck (MANP) equations were recently proposed to model the dynamics of charged particles. In this study, we enhance a numerical algorithm of this system with deep learning tools. The proposed hybrid algorithm provides an automated means to determine a proper approximation for the dummy variables, which can otherwise only be obtained through massive numerical tests. In addition, the original method is validated for 2-dimensional problems. However, when the spatial dimension is one, the original curl-free relaxation component is inapplicable, and the approximation formula for dummy variables, which works well in a 2-dimensional scenario, fails to provide a reasonable output in the 1-dimensional case. The proposed method can be readily generalised to cases with one spatial dimension. Experiments show numerical stability and good convergence to the steady-state solution obtained from Poisson-Boltzmann type equations in the 1-dimensional case. The experiments conducted in the 2-dimensional case indicate that the proposed method preserves the conservation properties.
Large Language Models (LLMs) have recently made significant strides in complex reasoning tasks through the Chain-of-Thought technique. Despite this progress, their reasoning is often constrained by their intrinsic understanding, lacking external insights. To address this, we propose Exchange-of-Thought (EoT), a novel framework that enables cross-model communication during problem-solving. Drawing inspiration from network topology, EoT integrates four unique communication paradigms: Memory, Report, Relay, and Debate. This paper delves into the communication dynamics and volume associated with each paradigm. To counterbalance the risks of incorrect reasoning chains, we implement a robust confidence evaluation mechanism within these communications. Our experiments across diverse complex reasoning tasks demonstrate that EoT significantly surpasses established baselines, underscoring the value of external insights in enhancing LLM performance. Furthermore, we show that EoT achieves these superior results in a cost-effective manner, marking a promising advancement for efficient and collaborative AI problem-solving.
Large language models (LLMs) have formulated a blueprint for the advancement of artificial general intelligence. Its primary objective is to function as a human-centric (helpful, honest, and harmless) assistant. Alignment with humans assumes paramount significance, and reinforcement learning with human feedback (RLHF) emerges as the pivotal technological paradigm underpinning this pursuit. Current technical routes usually include \textbf{reward models} to measure human preferences, \textbf{Proximal Policy Optimization} (PPO) to optimize policy model outputs, and \textbf{process supervision} to improve step-by-step reasoning capabilities. However, due to the challenges of reward design, environment interaction, and agent training, coupled with huge trial and error cost of large language models, there is a significant barrier for AI researchers to motivate the development of technical alignment and safe landing of LLMs. The stable training of RLHF has still been a puzzle. In the first report, we dissect the framework of RLHF, re-evaluate the inner workings of PPO, and explore how the parts comprising PPO algorithms impact policy agent training. We identify policy constraints being the key factor for the effective implementation of the PPO algorithm. Therefore, we explore the PPO-max, an advanced version of PPO algorithm, to efficiently improve the training stability of the policy model. Based on our main results, we perform a comprehensive analysis of RLHF abilities compared with SFT models and ChatGPT. The absence of open-source implementations has posed significant challenges to the investigation of LLMs alignment. Therefore, we are eager to release technical reports, reward models and PPO codes, aiming to make modest contributions to the advancement of LLMs.
Gaussian process regression (GPR) has been a well-known machine learning method for various applications such as uncertainty quantifications (UQ). However, GPR is inherently a data-driven method, which requires sufficiently large dataset. If appropriate physics constraints (e.g. expressed in partial differential equations) can be incorporated, the amount of data can be greatly reduced and the accuracy further improved. In this work, we propose a hybrid data driven-physics constrained Gaussian process regression framework. We encode the physics knowledge with Boltzmann-Gibbs distribution and derive our model through maximum likelihood (ML) approach. We apply deep kernel learning method. The proposed model learns from both data and physics constraints through the training of a deep neural network, which serves as part of the covariance function in GPR. The proposed model achieves good results in high-dimensional problem, and correctly propagate the uncertainty, with very limited labelled data provided.
We present our winning solution to the Open Images 2019 Visual Relationship challenge. This is the largest challenge of its kind to date with nearly 9 million training images. Challenge task consists of detecting objects and identifying relationships between them in complex scenes. Our solution has three stages, first object detection model is fine-tuned for the challenge classes using a novel weight transfer approach. Then, spatio-semantic and visual relationship models are trained on candidate object pairs. Finally, features and model predictions are combined to generate the final relationship prediction. Throughout the challenge we focused on minimizing the hardware requirements of our architecture. Specifically, our weight transfer approach enables much faster optimization, allowing the entire architecture to be trained on a single GPU in under two days. In addition to efficient optimization, our approach also achieves superior accuracy winning first place out of over 200 teams, and outperforming the second place team by over $5\%$ on the held-out private leaderboard.
We present our solution to Landmark Image Retrieval Challenge 2019. This challenge was based on the large Google Landmarks Dataset V2[9]. The goal was to retrieve all database images containing the same landmark for every provided query image. Our solution is a combination of global and local models to form an initial KNN graph. We then use a novel extension of the recently proposed graph traversal method EGT [1] referred to as semi-supervised EGT to refine the graph and retrieve better candidates.
Augmented reality is an emerging technology in many application domains. Among them is the beauty industry, where live virtual try-on of beauty products is of great importance. In this paper, we address the problem of live hair color augmentation. To achieve this goal, hair needs to be segmented quickly and accurately. We show how a modified MobileNet CNN architecture can be used to segment the hair in real-time. Instead of training this network using large amounts of accurate segmentation data, which is difficult to obtain, we use crowd sourced hair segmentation data. While such data is much simpler to obtain, the segmentations there are noisy and coarse. Despite this, we show how our system can produce accurate and fine-detailed hair mattes, while running at over 30 fps on an iPad Pro tablet.
Motivated by the lossy compression of an active-vision video stream, we consider the problem of finding the rate-distortion function of an arbitrarily varying source (AVS) composed of a finite number of subsources with known distributions. Berger's paper `The Source Coding Game', \emph{IEEE Trans. Inform. Theory}, 1971, solves this problem under the condition that the adversary is allowed only strictly causal access to the subsource realizations. We consider the case when the adversary has access to the subsource realizations non-causally. Using the type-covering lemma, this new rate-distortion function is determined to be the maximum of the IID rate-distortion function over a set of source distributions attainable by the adversary. We then extend the results to allow for partial or noisy observations of subsource realizations. We further explore the model by attempting to find the rate-distortion function when the adversary is actually helpful. Finally, a bound is developed on the uniform continuity of the IID rate-distortion function for finite-alphabet sources. The bound is used to give a sufficient number of distributions that need to be sampled to compute the rate-distortion function of an AVS to within a certain accuracy. The bound is also used to give a rate of convergence for the estimate of the rate-distortion function for an unknown IID finite-alphabet source .