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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.

AAAI 2024

ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing

contrastive learning.

bioinformatics

deep learning

technical paper

We are pleased to announce the Thirty-Eighth AAAI Conference on Artificial Intelligence (AAAI-24), which will be held in Vancouver, British Columbia at the Vancouver Convention Centre – West Building from 20-27 February, 2024.

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. AAAI-24 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and a range of other activities to be announced.

We expect for AAAI-24 to be an in-person conference – one author of all accepted papers will be expected to present work in person unless there are exceptional circumstances that prevent this.<br><br><br><br>

In order to access the AAAI-24 event page you need to register [here](https://aaai.org/aaai-conference/registration/)

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. 

Video compression relies heavily on exploiting the temporal redundancy between video frames, which is usually achieved by estimating and using the motion information. The motion information is represented as optical flows in most of the existing deep video compression networks. Indeed, these networks often adopt pre-trained optical flow estimation networks for motion estimation. The optical flows, however, may be less suitable for video compression due to the following two factors. First, the optical flow estimation networks were trained to perform inter-frame prediction as accurately as possible, but the optical flows themselves may cost too many bits to encode. Second, the optical flow estimation networks were trained on synthetic data, and may not generalize well enough to real-world videos. We address the twofold limitations by enhancing the optical flows in two stages: offline and online. In the offline stage, we fine-tune a trained optical flow estimation network with the motion information provided by a traditional (non-deep) video compression scheme, e.g. H.266/VVC, as we believe the motion information of H.266/VVC achieves a better rate-distortion trade-off. In the online stage, we further optimize the latent features of the optical flows with a gradient descent-based algorithm for the video to be compressed, so as to enhance the adaptivity of the optical flows. We conduct experiments on two state-of-the-art deep video compression schemes, DCVC and DCVC-DC. Experimental results demonstrate that the proposed offline and online enhancement together achieves on average 13.4% bitrate saving for DCVC and 4.1% bitrate saving for DCVC-DC on the tested videos, without increasing the model or computational complexity of the decoder side.

Offline and Online Optical Flow Enhancement for Deep Video Compression

This paper investigates a new, practical, but challenging problem named Non-exemplar Online Class-incremental continual Learning (NO-CL), which aims to preserve the discernibility of base classes \emph{without} buffering data examples and efficiently learn novel classes continuously in a \emph{single-pass} (i.e., online) data stream.
The challenges of this task are mainly two-fold: (1) Both base and novel classes suffer from severe catastrophic forgetting as no previous samples are available for replay. (2) As the online data can only be observed once, there is no way to fully re-train the whole model, e.g., re-calibrate the decision boundaries via prototype alignment or feature distillation. In this paper, we propose a novel \underline{\textbf{D}}ual-prototype \underline{\textbf{S}}elf-augment and \underline{\textbf{R}}efinement method (DSR) for NO-CL problem, which consists of two strategies: 1) Dual class prototypes: vanilla and high-dimensional prototypes are exploited to utilize the pre-trained information and obtain robust quasi-orthogonal representations rather than example buffers for both privacy preservation and memory reduction. 
2) Self-augment and refinement: Instead of updating the whole network, we optimize high-dimensional prototypes alternatively with the extra projection module based on self-augment vanilla prototypes, through a bi-level optimization problem. Extensive experiments demonstrate the effectiveness and superiority of the proposed DSR in NO-CL$\footnote{https://github.com/huofushuo/nocl}$.

Non-exemplar Online Class-Incremental Continual Learning via Dual-Prototype Self-Augment and Refinement

In application domains requiring mission-critical decision making, such as finance and robotics, the optimal policy derived by reinforcement learning (RL) often hinges on a preference for risk management. Yet, the dynamic nature of risk measures poses considerable challenges to achieving generalization and adaptation of risk-sensitive policies in the context of RL. In this paper, we propose a risk-conditioned RL model that enables rapid policy adaptation to varying risk measures via a unified risk representation, the Weighted Value-at-Risk (WV@R). To sample risk measures that avoid undue optimism, we construct a risk proposal network employing a conditional adversarial auto-encoder and a normalizing flow. This network establishes coherent representations for risk measures, preserving the continuity in terms of the Wasserstein distance on the risk measures. The normalizing flow is used to support non-crossing quantile regression that obtains valid samples for risk measures, and it is also applied to the agent’s critic to ascertain the preservation of monotonicity in quantile estimations. Through experiments with locomotion, finance, and self-driving scenarios, we show that our model is capable of adapting to a range of risk measures, achieving comparable performance to the baseline models individually trained for each measure. Our model often outperforms the baselines, especially in the cases when exploration is required during training but risk-aversion is favored during evaluation.

Risk-Conditioned Reinforcement Learning: A Generalized Approach for Adapting to Varying Risk Measures

Instruction-following is particularly crucial for large language models (LLMs) to support diverse user requests. While existing work has made progress in aligning LLMs with human preferences, evaluating their capabilities on instruction-following remains a challenge due to complexity and diversity of real-world user instructions. While existing evaluation methods focus on general skills, they suffer from two main shortcomings, i.e., lack of fine-grained task-level evaluation and reliance on singular instruction expression. To address these problems, this paper introduces DINGO, a fine-grained and diverse instruction-following evaluation dataset that has two main advantages: (1) DINGO is based on a manual-annotated, fine-grained and multi-level category tree with 140 nodes derived from real-world user requests; (2) DINGO includes diverse instructions, generated by both GPT-4 and human experts. Through extensive experiments, we demonstrate that DINGO can not only provide more challenging and comprehensive evaluation for LLMs, but also provide task-level fine-grained directions to further improve LLMs.

DINGO: Towards Diverse and Fine-Grained Instruction-Following Evaluation

Discrimination can occur when the underlying unbiased labels are overwritten by an agent with potential bias, resulting in biased datasets that unfairly harm specific groups and cause classifiers to inherit these biases. In this paper, we demonstrate that despite only having access to the biased labels, it is possible to eliminate bias by filtering the fairest instances within the framework of confident learning. In the context of confident learning, low self-confidence usually indicates potential label errors; however, this is not always the case. Instances, particularly those from underrepresented groups, might exhibit low confidence scores for reasons other than labeling errors. To address this limitation, our approach employs truncation of the confidence score and extends the confidence interval of the probabilistic threshold. Additionally, we incorporate with co-teaching paradigm for providing a more robust and reliable selection of fair instances and effectively mitigating the adverse effects of biased labels. Through extensive experimentation and evaluation of various datasets, we demonstrate the efficacy of our approach in promoting fairness and reducing the impact of label bias in machine learning models.

Mitigating Label Bias in Machine Learning: Fairness through Confident Learning

Bioinformatics has always been a prolific domain for generating complex satisfiability and optimization problems. For instance, the synthesis of multi-scale models of biological networks has recently been associated with the resolution of optimization problems mixing Boolean logic and universally quantified linear constraints (OPT+qLP), which can be benchmarked on real-world models. In this paper, we introduce a Counter-Example-Guided Abstraction Refinement (CEGAR) to solve such problems efficiently. Our CEGAR exploits monotone properties inherent to linear optimization in order to generalize counter-examples of Boolean relaxations. We implemented our approach by extending Answer Set Programming (ASP) solver Clingo with a quantified linear constraints propagator. Our prototype enables exploiting independence of sub-formulas to further exploit the generalization of counter-examples. We evaluate the impact of refinement and partitioning on two sets of OPT+qLP problems inspired by system biology. Additionally, we conducted a comparison with the state-of-the-art ASP solver Clingo[lpx] that handles non-quantified linear constraints, showing the advantage of our CEGAR approach for solving large problems.

CEGAR-Based Approach for Solving Combinatorial Optimization Modulo Quantified Linear Arithmetics Problems

The effectiveness of advertising in e-commerce largely depends on the ability of merchants to bid on and win impressions for their targeted users. The bidding procedure is highly complex due to various factors such as market competition, user behavior, and the diverse objectives of advertisers. In this paper we consider the problem at the level of user timelines instead of individual bid requests, manipulating full policies (i.e. pre-defined bidding strategies) and not bid values. In order to optimally allocate policies to users, typical multiple treatments allocation methods solve knapsack-like problems which aim at maximizing an expected value under constraints. In the specific context of online advertising, we argue that optimizing for the probability of success is a more suited objective than expected value maximization, and we introduce the SuccessProbaMax algorithm that aims at finding the policy allocation which is the most likely to outperform a fixed reference policy. Finally, we conduct comprehensive experiments both on synthetic and real-world data to evaluate its performance. The results demonstrate that our proposed algorithm outperforms conventional expected-value maximization algorithms in terms of success rate.

Maximizing the Success Probability of Policy Allocations in Online Systems

In this paper, we present our finding that prepending a Task-Agnostic Prefix Prompt (TAPP) to the input improves the instruction-following ability of various Large Language Models (LLMs) during inference. TAPP is different from canonical prompts for LLMs in that it is a fixed prompt prepended to the beginning of every input regardless of the target task for zero-shot generalization. We observe that both base LLMs (i.e. not fine-tuned to follow instructions) and instruction-tuned models benefit from TAPP, resulting in 34.58% and 12.26% improvement on average, respectively. This implies that the instruction-following ability of LLMs can be improved during inference time with a fixed prompt constructed with simple heuristics. We hypothesize that TAPP assists language models to better estimate the output distribution by focusing more on the instruction of the target task during inference. In other words, such ability does not seem to be sufficiently activated in not only base LLMs but also many instruction-fine-tuned LLMs.

Investigating the Effectiveness of Task-Agnostic Prefix Prompt for Instruction Following

Document-level relation extraction (DocRE) poses the challenge of identifying relationships between entities within a document. Existing approaches rely on logical reasoning or contextual cues from entities. This paper reframes document-level RE as link prediction over a Knowledge Graph (KG) with distinct benefits: 1) Our approach amalgamates entity context and document-derived logical reasoning, enhancing link prediction quality. 2) Predicted links between entities offer interpretability, elucidating employed reasoning. 
We evaluate our approach on benchmark datasets - DocRED, ReDocRED, and DWIE. The results indicate that our proposed method outperforms the state-of-the-art models and suggests that incorporating context-based Knowledge Graph link prediction techniques can enhance the performance of document-level relation extraction models. The code and the models are available at \url{https://anonymous.4open.science/r/DocRE-CED1/}.

Revisiting Document-Level Relation Extraction with Context-Guided Link Prediction

Recent techniques based on Mean Field Games (MFGs) allow the scalable analysis of multi-player games with many similar, rational agents. However, standard MFGs remain limited to homogeneous players that weakly influence each other, and cannot model major players that strongly influence other players, severely limiting the class of problems that can be handled. We propose a novel discrete time version of major-minor MFGs (M3FGs), along with a learning algorithm based on fictitious play and partitioning the probability simplex. Importantly, M3FGs generalize MFGs with common noise and can handle not only random exogeneous environment states but also major players. A key challenge is that the mean field is stochastic and not deterministic as in standard MFGs. Our theoretical investigation verifies both the M3FG model and its algorithmic solution, showing firstly the well-posedness of the M3FG model starting from a finite game of interest, and secondly convergence and approximation guarantees of the fictitious play algorithm. Then, we empirically verify the obtained theoretical results, ablating some of the theoretical assumptions made, and show successful equilibrium learning in three example problems. Overall, we establish a learning framework for a novel and broad class of tractable games.

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ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing

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Offline and Online Optical Flow Enhancement for Deep Video Compression

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ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing

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Offline and Online Optical Flow Enhancement for Deep Video Compression

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PRESENTATIONS

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