PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding

Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely unaddressed due to the difficulty in capturing the complex and sometimes unstable structures of peptides. This study introduces a novel multi-view contrastive learning framework PepHarmony for the sequence-based peptide encoding task. PepHarmony innovatively combines both sequence- and structure-level information into a sequence-level encoding module through contrastive learning. We carefully select datasets from the Protein Data Bank (PDB) and AlphaFold database to encompass a broad spectrum of peptide sequences and structures. The experimental data highlights PepHarmony's exceptional capability in capturing the intricate relationship between peptide sequences and structures compared with the baseline and fine-tuned models. The robustness of our model is confirmed through extensive ablation studies, which emphasize the crucial roles of contrastive loss and strategic data sorting in enhancing predictive performance. The proposed PepHarmony framework serves as a notable contribution to peptide representations, and offers valuable insights for future applications in peptide drug discovery and peptide engineering. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/PepHarmony or http://www.healthinformaticslab.org/supp/.

FedNS: A Fast Sketching Newton-Type Algorithm for Federated Learning

Recent Newton-type federated learning algorithms have demonstrated linear convergence with respect to the communication rounds. However, communicating Hessian matrices is often unfeasible due to their quadratic communication complexity. In this paper, we introduce a novel approach to tackle this issue while still achieving fast convergence rates. Our proposed method, named as Federated Newton Sketch methods (FedNS), approximates the centralized Newton's method by communicating the sketched square-root Hessian instead of the exact Hessian. To enhance communication efficiency, we reduce the sketch size to match the effective dimension of the Hessian matrix. We provide convergence analysis based on statistical learning for the federated Newton sketch approaches. Specifically, our approaches reach super-linear convergence rates w.r.t. the communication rounds for the first time. We validate the effectiveness of our algorithms through various experiments, which coincide with our theoretical findings.

Semantic Complete Scene Forecasting from a 4D Dynamic Point Cloud Sequence

We study a new problem of semantic complete scene forecasting (SCSF) in this work. Given a 4D dynamic point cloud sequence, our goal is to forecast the complete scene corresponding to the future next frame along with its semantic labels. To tackle this challenging problem, we properly model the synergetic relationship between future forecasting and semantic scene completion through a novel network named SCSFNet. SCSFNet leverages a hybrid geometric representation for high-resolution complete scene forecasting. To leverage multi-frame observation as well as the understanding of scene dynamics to ease the completion task, SCSFNet introduces an attention-based skip connection scheme. To ease the need to model occlusion variations and to better focus on the occluded part, SCSFNet utilizes auxiliary visibility grids to guide the forecasting task. To evaluate the effectiveness of SCSFNet, we conduct experiments on various benchmarks including two large-scale indoor benchmarks we contributed and the outdoor SemanticKITTI benchmark. Extensive experiments show SCSFNet outperforms baseline methods on multiple metrics by a large margin, and also prove the synergy between future forecasting and semantic scene completion.

PepLand: a large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids

In recent years, the scientific community has become increasingly interested on peptides with non-canonical amino acids due to their superior stability and resistance to proteolytic degradation. These peptides present promising modifications to biological, pharmacological, and physiochemical attributes in both endogenous and engineered peptides. Notwithstanding their considerable advantages, the scientific community exhibits a conspicuous absence of an effective pre-trained model adept at distilling feature representations from such complex peptide sequences. We herein propose PepLand, a novel pre-training architecture for representation and property analysis of peptides spanning both canonical and non-canonical amino acids. In essence, PepLand leverages a comprehensive multi-view heterogeneous graph neural network tailored to unveil the subtle structural representations of peptides. Empirical validations underscore PepLand's effectiveness across an array of peptide property predictions, encompassing protein-protein interactions, permeability, solubility, and synthesizability. The rigorous evaluation confirms PepLand's unparalleled capability in capturing salient synthetic peptide features, thereby laying a robust foundation for transformative advances in peptide-centric research domains. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/pepland

What Truly Matters in Trajectory Prediction for Autonomous Driving?

In the autonomous driving system, trajectory prediction plays a vital role in ensuring safety and facilitating smooth navigation. However, we observe a substantial discrepancy between the accuracy of predictors on fixed datasets and their driving performance when used in downstream tasks. This discrepancy arises from two overlooked factors in the current evaluation protocols of trajectory prediction: 1) the dynamics gap between the dataset and real driving scenario; and 2) the computational efficiency of predictors. In real-world scenarios, prediction algorithms influence the behavior of autonomous vehicles, which, in turn, alter the behaviors of other agents on the road. This interaction results in predictor-specific dynamics that directly impact prediction results. As other agents' responses are predetermined on datasets, a significant dynamics gap arises between evaluations conducted on fixed datasets and actual driving scenarios. Furthermore, focusing solely on accuracy fails to address the demand for computational efficiency, which is critical for the real-time response required by the autonomous driving system. Therefore, in this paper, we demonstrate that an interactive, task-driven evaluation approach for trajectory prediction is crucial to reflect its efficacy for autonomous driving.

ChatGPT or Grammarly? Evaluating ChatGPT on Grammatical Error Correction Benchmark

ChatGPT is a cutting-edge artificial intelligence language model developed by OpenAI, which has attracted a lot of attention due to its surprisingly strong ability in answering follow-up questions. In this report, we aim to evaluate ChatGPT on the Grammatical Error Correction(GEC) task, and compare it with commercial GEC product (e.g., Grammarly) and state-of-the-art models (e.g., GECToR). By testing on the CoNLL2014 benchmark dataset, we find that ChatGPT performs not as well as those baselines in terms of the automatic evaluation metrics (e.g., $F_{0.5}$ score), particularly on long sentences. We inspect the outputs and find that ChatGPT goes beyond one-by-one corrections. Specifically, it prefers to change the surface expression of certain phrases or sentence structure while maintaining grammatical correctness. Human evaluation quantitatively confirms this and suggests that ChatGPT produces less under-correction or mis-correction issues but more over-corrections. These results demonstrate that ChatGPT is severely under-estimated by the automatic evaluation metrics and could be a promising tool for GEC.

Matching-based Term Semantics Pre-training for Spoken Patient Query Understanding

Medical Slot Filling (MSF) task aims to convert medical queries into structured information, playing an essential role in diagnosis dialogue systems. However, the lack of sufficient term semantics learning makes existing approaches hard to capture semantically identical but colloquial expressions of terms in medical conversations. In this work, we formalize MSF into a matching problem and propose a Term Semantics Pre-trained Matching Network (TSPMN) that takes both terms and queries as input to model their semantic interaction. To learn term semantics better, we further design two self-supervised objectives, including Contrastive Term Discrimination (CTD) and Matching-based Mask Term Modeling (MMTM). CTD determines whether it is the masked term in the dialogue for each given term, while MMTM directly predicts the masked ones. Experimental results on two Chinese benchmarks show that TSPMN outperforms strong baselines, especially in few-shot settings.

Video Instance Shadow Detection

Video instance shadow detection aims to simultaneously detect, segment, associate, and track paired shadow-object associations in videos. This work has three key contributions to the task. First, we design SSIS-Track, a new framework to extract shadow-object associations in videos with paired tracking and without category specification; especially, we strive to maintain paired tracking even the objects/shadows are temporarily occluded for several frames. Second, we leverage both labeled images and unlabeled videos, and explore temporal coherence by augmenting the tracking ability via an association cycle consistency loss to optimize SSIS-Track's performance. Last, we build $\textit{SOBA-VID}$, a new dataset with 232 unlabeled videos of ${5,863}$ frames for training and 60 labeled videos of ${1,182}$ frames for testing. Experimental results show that SSIS-Track surpasses baselines built from SOTA video tracking and instance-shadow-detection methods by a large margin. In the end, we showcase several video-level applications.

Semi-Supervised Convolutive NMF for Automatic Music Transcription

Automatic Music Transcription, which consists in transforming an audio recording of a musical performance into symbolic format, remains a difficult Music Information Retrieval task. In this work, we propose a semi-supervised approach using low-rank matrix factorization techniques, in particular Convolutive Nonnegative Matrix Factorization. In the semi-supervised setting, only a single recording of each individual notes is required. We show on the MAPS dataset that the proposed semi-supervised CNMF method performs better than state-of-the-art low-rank factorization techniques and a little worse than supervised deep learning state-of-the-art methods, while however suffering from generalization issues.

Unbalanced Optimal Transport through Non-negative Penalized Linear Regression

This paper addresses the problem of Unbalanced Optimal Transport (UOT) in which the marginal conditions are relaxed (using weighted penalties in lieu of equality) and no additional regularization is enforced on the OT plan. In this context, we show that the corresponding optimization problem can be reformulated as a non-negative penalized linear regression problem. This reformulation allows us to propose novel algorithms inspired from inverse problems and nonnegative matrix factorization. In particular, we consider majorization-minimization which leads in our setting to efficient multiplicative updates for a variety of penalties. Furthermore, we derive for the first time an efficient algorithm to compute the regularization path of UOT with quadratic penalties. The proposed algorithm provides a continuity of piece-wise linear OT plans converging to the solution of balanced OT (corresponding to infinite penalty weights). We perform several numerical experiments on simulated and real data illustrating the new algorithms, and provide a detailed discussion about more sophisticated optimization tools that can further be used to solve OT problems thanks to our reformulation.