DNABERT-S: Learning Species-Aware DNA Embedding with Genome Foundation Models

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C$^2$LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.

MPRE: Multi-perspective Patient Representation Extractor for Disease Prediction

Patient representation learning based on electronic health records (EHR) is a critical task for disease prediction. This task aims to effectively extract useful information on dynamic features. Although various existing works have achieved remarkable progress, the model performance can be further improved by fully extracting the trends, variations, and the correlation between the trends and variations in dynamic features. In addition, sparse visit records limit the performance of deep learning models. To address these issues, we propose the Multi-perspective Patient Representation Extractor (MPRE) for disease prediction. Specifically, we propose Frequency Transformation Module (FTM) to extract the trend and variation information of dynamic features in the time-frequency domain, which can enhance the feature representation. In the 2D Multi-Extraction Network (2D MEN), we form the 2D temporal tensor based on trend and variation. Then, the correlations between trend and variation are captured by the proposed dilated operation. Moreover, we propose the First-Order Difference Attention Mechanism (FODAM) to calculate the contributions of differences in adjacent variations to the disease diagnosis adaptively. To evaluate the performance of MPRE and baseline methods, we conduct extensive experiments on two real-world public datasets. The experiment results show that MPRE outperforms state-of-the-art baseline methods in terms of AUROC and AUPRC.

3D Pose Estimation of Two Interacting Hands from a Monocular Event Camera

3D hand tracking from a monocular video is a very challenging problem due to hand interactions, occlusions, left-right hand ambiguity, and fast motion. Most existing methods rely on RGB inputs, which have severe limitations under low-light conditions and suffer from motion blur. In contrast, event cameras capture local brightness changes instead of full image frames and do not suffer from the described effects. Unfortunately, existing image-based techniques cannot be directly applied to events due to significant differences in the data modalities. In response to these challenges, this paper introduces the first framework for 3D tracking of two fast-moving and interacting hands from a single monocular event camera. Our approach tackles the left-right hand ambiguity with a novel semi-supervised feature-wise attention mechanism and integrates an intersection loss to fix hand collisions. To facilitate advances in this research domain, we release a new synthetic large-scale dataset of two interacting hands, Ev2Hands-S, and a new real benchmark with real event streams and ground-truth 3D annotations, Ev2Hands-R. Our approach outperforms existing methods in terms of the 3D reconstruction accuracy and generalises to real data under severe light conditions.

AfriMTE and AfriCOMET: Empowering COMET to Embrace Under-resourced African Languages

Despite the progress we have recorded in scaling multilingual machine translation (MT) models and evaluation data to several under-resourced African languages, it is difficult to measure accurately the progress we have made on these languages because evaluation is often performed on n-gram matching metrics like BLEU that often have worse correlation with human judgments. Embedding-based metrics such as COMET correlate better; however, lack of evaluation data with human ratings for under-resourced languages, complexity of annotation guidelines like Multidimensional Quality Metrics (MQM), and limited language coverage of multilingual encoders have hampered their applicability to African languages. In this paper, we address these challenges by creating high-quality human evaluation data with a simplified MQM guideline for error-span annotation and direct assessment (DA) scoring for 13 typologically diverse African languages. Furthermore, we develop AfriCOMET, a COMET evaluation metric for African languages by leveraging DA training data from high-resource languages and African-centric multilingual encoder (AfroXLM-Roberta) to create the state-of-the-art evaluation metric for African languages MT with respect to Spearman-rank correlation with human judgments (+0.406).

Prompt Optimisation with Random Sampling

Using the generative nature of a language model to generate task-relevant separators has shown competitive results compared to human-curated prompts like "TL;DR". We demonstrate that even randomly chosen tokens from the vocabulary as separators can achieve near-state-of-the-art performance. We analyse this phenomenon in detail using three different random generation strategies, establishing that the language space is rich with potential good separators, regardless of the underlying language model size. These observations challenge the common assumption that an effective prompt should be human-readable or task-relevant. Experimental results show that using random separators leads to an average 16% relative improvement across nine text classification tasks on seven language models, compared to human-curated separators, and is on par with automatic prompt searching methods.

Synslator: An Interactive Machine Translation Tool with Online Learning

Interactive machine translation (IMT) has emerged as a progression of the computer-aided translation paradigm, where the machine translation system and the human translator collaborate to produce high-quality translations. This paper introduces Synslator, a user-friendly computer-aided translation (CAT) tool that not only supports IMT, but is adept at online learning with real-time translation memories. To accommodate various deployment environments for CAT services, Synslator integrates two different neural translation models to handle translation memories for online learning. Additionally, the system employs a language model to enhance the fluency of translations in an interactive mode. In evaluation, we have confirmed the effectiveness of online learning through the translation models, and have observed a 13% increase in post-editing efficiency with the interactive functionalities of Synslator. A tutorial video is available at:https://youtu.be/K0vRsb2lTt8.

Multi-level Asymmetric Contrastive Learning for Medical Image Segmentation Pre-training

Contrastive learning, which is a powerful technique for learning image-level representations from unlabeled data, leads a promising direction to dealing with the dilemma between large-scale pre-training and limited labeled data. However, most existing contrastive learning strategies are designed mainly for downstream tasks of natural images, therefore they are sub-optimal and even worse than learning from scratch when directly applied to medical images whose downstream tasks are usually segmentation. In this work, we propose a novel asymmetric contrastive learning framework named JCL for medical image segmentation with self-supervised pre-training. Specifically, (1) A novel asymmetric contrastive learning strategy is proposed to pre-train both encoder and decoder simultaneously in one-stage to provide better initialization for segmentation models. (2) A multi-level contrastive loss is designed to take the correspondence among feature-level, image-level and pixel-level projections, respectively into account to make sure multi-level representations can be learned by the encoder and decoder during pre-training. (3) Experiments on multiple medical image datasets indicate our JCL framework outperforms existing SOTA contrastive learning strategies.

Online Multi-Contact Receding Horizon Planning via Value Function Approximation

Planning multi-contact motions in a receding horizon fashion requires a value function to guide the planning with respect to the future, e.g., building momentum to traverse large obstacles. Traditionally, the value function is approximated by computing trajectories in a prediction horizon (never executed) that foresees the future beyond the execution horizon. However, given the non-convex dynamics of multi-contact motions, this approach is computationally expensive. To enable online Receding Horizon Planning (RHP) of multi-contact motions, we find efficient approximations of the value function. Specifically, we propose a trajectory-based and a learning-based approach. In the former, namely RHP with Multiple Levels of Model Fidelity, we approximate the value function by computing the prediction horizon with a convex relaxed model. In the latter, namely Locally-Guided RHP, we learn an oracle to predict local objectives for locomotion tasks, and we use these local objectives to construct local value functions for guiding a short-horizon RHP. We evaluate both approaches in simulation by planning centroidal trajectories of a humanoid robot walking on moderate slopes, and on large slopes where the robot cannot maintain static balance. Our results show that locally-guided RHP achieves the best computation efficiency (95\%-98.6\% cycles converge online). This computation advantage enables us to demonstrate online receding horizon planning of our real-world humanoid robot Talos walking in dynamic environments that change on-the-fly.

Non-parametric, Nearest-neighbor-assisted Fine-tuning for Neural Machine Translation

Non-parametric, k-nearest-neighbor algorithms have recently made inroads to assist generative models such as language models and machine translation decoders. We explore whether such non-parametric models can improve machine translation models at the fine-tuning stage by incorporating statistics from the kNN predictions to inform the gradient updates for a baseline translation model. There are multiple methods which could be used to incorporate kNN statistics and we investigate gradient scaling by a gating mechanism, the kNN's ground truth probability, and reinforcement learning. For four standard in-domain machine translation datasets, compared with classic fine-tuning, we report consistent improvements of all of the three methods by as much as 1.45 BLEU and 1.28 BLEU for German-English and English-German translations respectively. Through qualitative analysis, we found particular improvements when it comes to translating grammatical relations or function words, which results in increased fluency of our model.

ADELT: Transpilation Between Deep Learning Frameworks

We propose Adversarial DEep Learning Transpiler (ADELT) for source-to-source transpilation between deep learning frameworks. Unlike prior approaches, we decouple the transpilation of code skeletons and the mapping of API keywords (an API function name or a parameter name). ADELT transpile code skeletons using few-shot prompting on big language models. Based on contextual embeddings extracted by a BERT for code, we train aligned API embeddings in a domain-adversarial setup, upon which we generate a dictionary for keyword translation. The model is trained on our unlabeled DL corpus from web crawl data, without using any hand-crafted rules and parallel data. Our method outperforms state-of-the-art transpilers on multiple transpilation pairs including PyTorch-Keras and PyTorch-MXNet by 15.9pts and 12.0pts in exact match scores respectively.