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Jan 5

A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce \ourdataset, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. \ourdataset~ consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). \ourdataset~is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with \ourdataset~can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex{huggingface.co/datasets/medexanon/Medex}, and will provide expanded versions as available literature grows.

  • 12 authors
·
Aug 14, 2025

MEG-GPT: A transformer-based foundation model for magnetoencephalography data

Modelling the complex spatiotemporal patterns of large-scale brain dynamics is crucial for neuroscience, but traditional methods fail to capture the rich structure in modalities such as magnetoencephalography (MEG). Recent advances in deep learning have enabled significant progress in other domains, such as language and vision, by using foundation models at scale. Here, we introduce MEG-GPT, a transformer based foundation model that uses time-attention and next time-point prediction. To facilitate this, we also introduce a novel data-driven tokeniser for continuous MEG data, which preserves the high temporal resolution of continuous MEG signals without lossy transformations. We trained MEG-GPT on tokenised brain region time-courses extracted from a large-scale MEG dataset (N=612, eyes-closed rest, Cam-CAN data), and show that the learnt model can generate data with realistic spatio-spectral properties, including transient events and population variability. Critically, it performs well in downstream decoding tasks, improving downstream supervised prediction task, showing improved zero-shot generalisation across sessions (improving accuracy from 0.54 to 0.59) and subjects (improving accuracy from 0.41 to 0.49) compared to a baseline methods. Furthermore, we show the model can be efficiently fine-tuned on a smaller labelled dataset to boost performance in cross-subject decoding scenarios. This work establishes a powerful foundation model for electrophysiological data, paving the way for applications in computational neuroscience and neural decoding.

  • 5 authors
·
Oct 20, 2025

Fire Together Wire Together: A Dynamic Pruning Approach with Self-Supervised Mask Prediction

Dynamic model pruning is a recent direction that allows for the inference of a different sub-network for each input sample during deployment. However, current dynamic methods rely on learning a continuous channel gating through regularization by inducing sparsity loss. This formulation introduces complexity in balancing different losses (e.g task loss, regularization loss). In addition, regularization based methods lack transparent tradeoff hyperparameter selection to realize a computational budget. Our contribution is two-fold: 1) decoupled task and pruning losses. 2) Simple hyperparameter selection that enables FLOPs reduction estimation before training. Inspired by the Hebbian theory in Neuroscience: "neurons that fire together wire together", we propose to predict a mask to process k filters in a layer based on the activation of its previous layer. We pose the problem as a self-supervised binary classification problem. Each mask predictor module is trained to predict if the log-likelihood for each filter in the current layer belongs to the top-k activated filters. The value k is dynamically estimated for each input based on a novel criterion using the mass of heatmaps. We show experiments on several neural architectures, such as VGG, ResNet and MobileNet on CIFAR and ImageNet datasets. On CIFAR, we reach similar accuracy to SOTA methods with 15% and 24% higher FLOPs reduction. Similarly in ImageNet, we achieve lower drop in accuracy with up to 13% improvement in FLOPs reduction.

  • 4 authors
·
Oct 15, 2021

Label Supervised LLaMA Finetuning

The recent success of Large Language Models (LLMs) has gained significant attention in both academia and industry. Substantial efforts have been made to enhance the zero- and few-shot generalization capabilities of open-source LLMs through finetuning. Currently, the prevailing approach is instruction-tuning, which trains LLMs to complete real-world tasks by generating responses guided by natural language instructions. It is worth noticing that such an approach may underperform in sequence and token classification tasks. Unlike text generation tasks, classification tasks have a limited label space, where precise label prediction is more appreciated than generating diverse and human-like responses. Prior research has unveiled that instruction-tuned LLMs cannot outperform BERT, prompting us to explore the potential of leveraging latent representations from LLMs for supervised label prediction. In this paper, we introduce a label-supervised adaptation for LLMs, which aims to finetuning the model with discriminant labels. We evaluate this approach with Label Supervised LLaMA (LS-LLaMA), based on LLaMA-2-7B, a relatively small-scale LLM, and can be finetuned on a single GeForce RTX4090 GPU. We extract latent representations from the final LLaMA layer and project them into the label space to compute the cross-entropy loss. The model is finetuned by Low-Rank Adaptation (LoRA) to minimize this loss. Remarkably, without intricate prompt engineering or external knowledge, LS-LLaMA substantially outperforms LLMs ten times its size in scale and demonstrates consistent improvements compared to robust baselines like BERT-Large and RoBERTa-Large in text classification. Moreover, by removing the causal mask from decoders, LS-unLLaMA achieves the state-of-the-art performance in named entity recognition (NER). Our work will shed light on a novel approach to adapting LLMs for various downstream tasks.

  • 8 authors
·
Oct 2, 2023

Activation Oracles: Training and Evaluating LLMs as General-Purpose Activation Explainers

Large language model (LLM) activations are notoriously difficult to understand, with most existing techniques using complex, specialized methods for interpreting them. Recent work has proposed a simpler approach known as LatentQA: training LLMs to directly accept LLM activations as inputs and answer arbitrary questions about them in natural language. However, prior work has focused on narrow task settings for both training and evaluation. In this paper, we instead take a generalist perspective. We evaluate LatentQA-trained models, which we call Activation Oracles (AOs), in far out-of-distribution settings and examine how performance scales with training data diversity. We find that AOs can recover information fine-tuned into a model (e.g., biographical knowledge or malign propensities) that does not appear in the input text, despite never being trained with activations from a fine-tuned model. Our main evaluations are four downstream tasks where we can compare to prior white- and black-box techniques. We find that even narrowly-trained LatentQA models can generalize well, and that adding additional training datasets (such as classification tasks and a self-supervised context prediction task) yields consistent further improvements. Overall, our best AOs match or exceed prior white-box baselines on all four tasks and are the best method on 3 out of 4. These results suggest that diversified training to answer natural-language queries imparts a general capability to verbalize information about LLM activations.

  • 11 authors
·
Dec 17, 2025

Chain of Thought Imitation with Procedure Cloning

Imitation learning aims to extract high-performance policies from logged demonstrations of expert behavior. It is common to frame imitation learning as a supervised learning problem in which one fits a function approximator to the input-output mapping exhibited by the logged demonstrations (input observations to output actions). While the framing of imitation learning as a supervised input-output learning problem allows for applicability in a wide variety of settings, it is also an overly simplistic view of the problem in situations where the expert demonstrations provide much richer insight into expert behavior. For example, applications such as path navigation, robot manipulation, and strategy games acquire expert demonstrations via planning, search, or some other multi-step algorithm, revealing not just the output action to be imitated but also the procedure for how to determine this action. While these intermediate computations may use tools not available to the agent during inference (e.g., environment simulators), they are nevertheless informative as a way to explain an expert's mapping of state to actions. To properly leverage expert procedure information without relying on the privileged tools the expert may have used to perform the procedure, we propose procedure cloning, which applies supervised sequence prediction to imitate the series of expert computations. This way, procedure cloning learns not only what to do (i.e., the output action), but how and why to do it (i.e., the procedure). Through empirical analysis on navigation, simulated robotic manipulation, and game-playing environments, we show that imitating the intermediate computations of an expert's behavior enables procedure cloning to learn policies exhibiting significant generalization to unseen environment configurations, including those configurations for which running the expert's procedure directly is infeasible.

  • 4 authors
·
May 22, 2022

UniSite: The First Cross-Structure Dataset and Learning Framework for End-to-End Ligand Binding Site Detection

The detection of ligand binding sites for proteins is a fundamental step in Structure-Based Drug Design. Despite notable advances in recent years, existing methods, datasets, and evaluation metrics are confronted with several key challenges: (1) current datasets and methods are centered on individual protein-ligand complexes and neglect that diverse binding sites may exist across multiple complexes of the same protein, introducing significant statistical bias; (2) ligand binding site detection is typically modeled as a discontinuous workflow, employing binary segmentation and subsequent clustering algorithms; (3) traditional evaluation metrics do not adequately reflect the actual performance of different binding site prediction methods. To address these issues, we first introduce UniSite-DS, the first UniProt (Unique Protein)-centric ligand binding site dataset, which contains 4.81 times more multi-site data and 2.08 times more overall data compared to the previously most widely used datasets. We then propose UniSite, the first end-to-end ligand binding site detection framework supervised by set prediction loss with bijective matching. In addition, we introduce Average Precision based on Intersection over Union (IoU) as a more accurate evaluation metric for ligand binding site prediction. Extensive experiments on UniSite-DS and several representative benchmark datasets demonstrate that IoU-based Average Precision provides a more accurate reflection of prediction quality, and that UniSite outperforms current state-of-the-art methods in ligand binding site detection. The dataset and codes will be made publicly available at https://github.com/quanlin-wu/unisite.

  • 4 authors
·
Jun 3, 2025

Semi-supervised Semantics-guided Adversarial Training for Trajectory Prediction

Predicting the trajectories of surrounding objects is a critical task for self-driving vehicles and many other autonomous systems. Recent works demonstrate that adversarial attacks on trajectory prediction, where small crafted perturbations are introduced to history trajectories, may significantly mislead the prediction of future trajectories and induce unsafe planning. However, few works have addressed enhancing the robustness of this important safety-critical task.In this paper, we present a novel adversarial training method for trajectory prediction. Compared with typical adversarial training on image tasks, our work is challenged by more random input with rich context and a lack of class labels. To address these challenges, we propose a method based on a semi-supervised adversarial autoencoder, which models disentangled semantic features with domain knowledge and provides additional latent labels for the adversarial training. Extensive experiments with different types of attacks demonstrate that our Semisupervised Semantics-guided Adversarial Training (SSAT) method can effectively mitigate the impact of adversarial attacks by up to 73% and outperform other popular defense methods. In addition, experiments show that our method can significantly improve the system's robust generalization to unseen patterns of attacks. We believe that such semantics-guided architecture and advancement on robust generalization is an important step for developing robust prediction models and enabling safe decision-making.

  • 5 authors
·
May 27, 2022

DeepSolarEye: Power Loss Prediction and Weakly Supervised Soiling Localization via Fully Convolutional Networks for Solar Panels

The impact of soiling on solar panels is an important and well-studied problem in renewable energy sector. In this paper, we present the first convolutional neural network (CNN) based approach for solar panel soiling and defect analysis. Our approach takes an RGB image of solar panel and environmental factors as inputs to predict power loss, soiling localization, and soiling type. In computer vision, localization is a complex task which typically requires manually labeled training data such as bounding boxes or segmentation masks. Our proposed approach consists of specialized four stages which completely avoids localization ground truth and only needs panel images with power loss labels for training. The region of impact area obtained from the predicted localization masks are classified into soiling types using the webly supervised learning. For improving localization capabilities of CNNs, we introduce a novel bi-directional input-aware fusion (BiDIAF) block that reinforces the input at different levels of CNN to learn input-specific feature maps. Our empirical study shows that BiDIAF improves the power loss prediction accuracy by about 3% and localization accuracy by about 4%. Our end-to-end model yields further improvement of about 24% on localization when learned in a weakly supervised manner. Our approach is generalizable and showed promising results on web crawled solar panel images. Our system has a frame rate of 22 fps (including all steps) on a NVIDIA TitanX GPU. Additionally, we collected first of it's kind dataset for solar panel image analysis consisting 45,000+ images.

  • 5 authors
·
Oct 10, 2017

GeoMAE: Masked Geometric Target Prediction for Self-supervised Point Cloud Pre-Training

This paper tries to address a fundamental question in point cloud self-supervised learning: what is a good signal we should leverage to learn features from point clouds without annotations? To answer that, we introduce a point cloud representation learning framework, based on geometric feature reconstruction. In contrast to recent papers that directly adopt masked autoencoder (MAE) and only predict original coordinates or occupancy from masked point clouds, our method revisits differences between images and point clouds and identifies three self-supervised learning objectives peculiar to point clouds, namely centroid prediction, normal estimation, and curvature prediction. Combined with occupancy prediction, these four objectives yield an nontrivial self-supervised learning task and mutually facilitate models to better reason fine-grained geometry of point clouds. Our pipeline is conceptually simple and it consists of two major steps: first, it randomly masks out groups of points, followed by a Transformer-based point cloud encoder; second, a lightweight Transformer decoder predicts centroid, normal, and curvature for points in each voxel. We transfer the pre-trained Transformer encoder to a downstream peception model. On the nuScene Datset, our model achieves 3.38 mAP improvment for object detection, 2.1 mIoU gain for segmentation, and 1.7 AMOTA gain for multi-object tracking. We also conduct experiments on the Waymo Open Dataset and achieve significant performance improvements over baselines as well.

  • 4 authors
·
May 15, 2023

Mine Your Own vieW: Self-Supervised Learning Through Across-Sample Prediction

State-of-the-art methods for self-supervised learning (SSL) build representations by maximizing the similarity between different transformed "views" of a sample. Without sufficient diversity in the transformations used to create views, however, it can be difficult to overcome nuisance variables in the data and build rich representations. This motivates the use of the dataset itself to find similar, yet distinct, samples to serve as views for one another. In this paper, we introduce Mine Your Own vieW (MYOW), a new approach for self-supervised learning that looks within the dataset to define diverse targets for prediction. The idea behind our approach is to actively mine views, finding samples that are neighbors in the representation space of the network, and then predict, from one sample's latent representation, the representation of a nearby sample. After showing the promise of MYOW on benchmarks used in computer vision, we highlight the power of this idea in a novel application in neuroscience where SSL has yet to be applied. When tested on multi-unit neural recordings, we find that MYOW outperforms other self-supervised approaches in all examples (in some cases by more than 10%), and often surpasses the supervised baseline. With MYOW, we show that it is possible to harness the diversity of the data to build rich views and leverage self-supervision in new domains where augmentations are limited or unknown.

  • 13 authors
·
Feb 19, 2021

Position Prediction as an Effective Pretraining Strategy

Transformers have gained increasing popularity in a wide range of applications, including Natural Language Processing (NLP), Computer Vision and Speech Recognition, because of their powerful representational capacity. However, harnessing this representational capacity effectively requires a large amount of data, strong regularization, or both, to mitigate overfitting. Recently, the power of the Transformer has been unlocked by self-supervised pretraining strategies based on masked autoencoders which rely on reconstructing masked inputs, directly, or contrastively from unmasked content. This pretraining strategy which has been used in BERT models in NLP, Wav2Vec models in Speech and, recently, in MAE models in Vision, forces the model to learn about relationships between the content in different parts of the input using autoencoding related objectives. In this paper, we propose a novel, but surprisingly simple alternative to content reconstruction~-- that of predicting locations from content, without providing positional information for it. Doing so requires the Transformer to understand the positional relationships between different parts of the input, from their content alone. This amounts to an efficient implementation where the pretext task is a classification problem among all possible positions for each input token. We experiment on both Vision and Speech benchmarks, where our approach brings improvements over strong supervised training baselines and is comparable to modern unsupervised/self-supervised pretraining methods. Our method also enables Transformers trained without position embeddings to outperform ones trained with full position information.

  • 10 authors
·
Jul 15, 2022 2

Semi-Supervised Learning for Multi-Task Scene Understanding by Neural Graph Consensus

We address the challenging problem of semi-supervised learning in the context of multiple visual interpretations of the world by finding consensus in a graph of neural networks. Each graph node is a scene interpretation layer, while each edge is a deep net that transforms one layer at one node into another from a different node. During the supervised phase edge networks are trained independently. During the next unsupervised stage edge nets are trained on the pseudo-ground truth provided by consensus among multiple paths that reach the nets' start and end nodes. These paths act as ensemble teachers for any given edge and strong consensus is used for high-confidence supervisory signal. The unsupervised learning process is repeated over several generations, in which each edge becomes a "student" and also part of different ensemble "teachers" for training other students. By optimizing such consensus between different paths, the graph reaches consistency and robustness over multiple interpretations and generations, in the face of unknown labels. We give theoretical justifications of the proposed idea and validate it on a large dataset. We show how prediction of different representations such as depth, semantic segmentation, surface normals and pose from RGB input could be effectively learned through self-supervised consensus in our graph. We also compare to state-of-the-art methods for multi-task and semi-supervised learning and show superior performance.

  • 6 authors
·
Oct 2, 2020 1

GASP: Unifying Geometric and Semantic Self-Supervised Pre-training for Autonomous Driving

Self-supervised pre-training based on next-token prediction has enabled large language models to capture the underlying structure of text, and has led to unprecedented performance on a large array of tasks when applied at scale. Similarly, autonomous driving generates vast amounts of spatiotemporal data, alluding to the possibility of harnessing scale to learn the underlying geometric and semantic structure of the environment and its evolution over time. In this direction, we propose a geometric and semantic self-supervised pre-training method, GASP, that learns a unified representation by predicting, at any queried future point in spacetime, (1) general occupancy, capturing the evolving structure of the 3D scene; (2) ego occupancy, modeling the ego vehicle path through the environment; and (3) distilled high-level features from a vision foundation model. By modeling geometric and semantic 4D occupancy fields instead of raw sensor measurements, the model learns a structured, generalizable representation of the environment and its evolution through time. We validate GASP on multiple autonomous driving benchmarks, demonstrating significant improvements in semantic occupancy forecasting, online mapping, and ego trajectory prediction. Our results demonstrate that continuous 4D geometric and semantic occupancy prediction provides a scalable and effective pre-training paradigm for autonomous driving. For code and additional visualizations, see \href{https://research.zenseact.com/publications/gasp/.

  • 9 authors
·
Mar 19, 2025 2

Self-Supervised Learning of Depth and Camera Motion from 360° Videos

As 360{\deg} cameras become prevalent in many autonomous systems (e.g., self-driving cars and drones), efficient 360{\deg} perception becomes more and more important. We propose a novel self-supervised learning approach for predicting the omnidirectional depth and camera motion from a 360{\deg} video. In particular, starting from the SfMLearner, which is designed for cameras with normal field-of-view, we introduce three key features to process 360{\deg} images efficiently. Firstly, we convert each image from equirectangular projection to cubic projection in order to avoid image distortion. In each network layer, we use Cube Padding (CP), which pads intermediate features from adjacent faces, to avoid image boundaries. Secondly, we propose a novel "spherical" photometric consistency constraint on the whole viewing sphere. In this way, no pixel will be projected outside the image boundary which typically happens in images with normal field-of-view. Finally, rather than naively estimating six independent camera motions (i.e., naively applying SfM-Learner to each face on a cube), we propose a novel camera pose consistency loss to ensure the estimated camera motions reaching consensus. To train and evaluate our approach, we collect a new PanoSUNCG dataset containing a large amount of 360{\deg} videos with groundtruth depth and camera motion. Our approach achieves state-of-the-art depth prediction and camera motion estimation on PanoSUNCG with faster inference speed comparing to equirectangular. In real-world indoor videos, our approach can also achieve qualitatively reasonable depth prediction by acquiring model pre-trained on PanoSUNCG.

  • 8 authors
·
Nov 13, 2018

TEXTRON: Weakly Supervised Multilingual Text Detection through Data Programming

Several recent deep learning (DL) based techniques perform considerably well on image-based multilingual text detection. However, their performance relies heavily on the availability and quality of training data. There are numerous types of page-level document images consisting of information in several modalities, languages, fonts, and layouts. This makes text detection a challenging problem in the field of computer vision (CV), especially for low-resource or handwritten languages. Furthermore, there is a scarcity of word-level labeled data for text detection, especially for multilingual settings and Indian scripts that incorporate both printed and handwritten text. Conventionally, Indian script text detection requires training a DL model on plenty of labeled data, but to the best of our knowledge, no relevant datasets are available. Manual annotation of such data requires a lot of time, effort, and expertise. In order to solve this problem, we propose TEXTRON, a Data Programming-based approach, where users can plug various text detection methods into a weak supervision-based learning framework. One can view this approach to multilingual text detection as an ensemble of different CV-based techniques and DL approaches. TEXTRON can leverage the predictions of DL models pre-trained on a significant amount of language data in conjunction with CV-based methods to improve text detection in other languages. We demonstrate that TEXTRON can improve the detection performance for documents written in Indian languages, despite the absence of corresponding labeled data. Further, through extensive experimentation, we show improvement brought about by our approach over the current State-of-the-art (SOTA) models, especially for handwritten Devanagari text. Code and dataset has been made available at https://github.com/IITB-LEAP-OCR/TEXTRON

  • 5 authors
·
Feb 15, 2024

Anatomically-aware Uncertainty for Semi-supervised Image Segmentation

Semi-supervised learning relaxes the need of large pixel-wise labeled datasets for image segmentation by leveraging unlabeled data. A prominent way to exploit unlabeled data is to regularize model predictions. Since the predictions of unlabeled data can be unreliable, uncertainty-aware schemes are typically employed to gradually learn from meaningful and reliable predictions. Uncertainty estimation methods, however, rely on multiple inferences from the model predictions that must be computed for each training step, which is computationally expensive. Moreover, these uncertainty maps capture pixel-wise disparities and do not consider global information. This work proposes a novel method to estimate segmentation uncertainty by leveraging global information from the segmentation masks. More precisely, an anatomically-aware representation is first learnt to model the available segmentation masks. The learnt representation thereupon maps the prediction of a new segmentation into an anatomically-plausible segmentation. The deviation from the plausible segmentation aids in estimating the underlying pixel-level uncertainty in order to further guide the segmentation network. The proposed method consequently estimates the uncertainty using a single inference from our representation, thereby reducing the total computation. We evaluate our method on two publicly available segmentation datasets of left atria in cardiac MRIs and of multiple organs in abdominal CTs. Our anatomically-aware method improves the segmentation accuracy over the state-of-the-art semi-supervised methods in terms of two commonly used evaluation metrics.

  • 3 authors
·
Oct 24, 2023

Mask-Enhanced Autoregressive Prediction: Pay Less Attention to Learn More

Large Language Models (LLMs) are discovered to suffer from accurately retrieving key information. To address this, we propose Mask-Enhanced Autoregressive Prediction (MEAP), a simple yet effective training paradigm that seamlessly integrates Masked Language Modeling (MLM) into Next-Token Prediction (NTP) to enhance the latter's in-context retrieval capabilities. Specifically, MEAP first randomly masks a small fraction of input tokens and then directly performs the standard next-token prediction autoregressive using a decoder-only Transformer. MEAP eliminates the need for bidirectional attention or encoder-decoder architectures for MLM, incurring no additional computational overhead during pre-training or inference. Intensive experiments demonstrate that MEAP substantially outperforms NTP on key information retrieval and long-context reasoning tasks, while performing on par or better on commonsense reasoning tasks. The benefits of MEAP also extend to supervised fine-tuning, where it shows remarkable advantages in lost-in-the-middle scenarios, outperforming NTP by 11.77 percentage points. Our analysis indicates that MEAP's effectiveness arises from its ability to promote more distinguishable attention scores by concentrating on a reduced set of non-masked tokens. This mechanism improves the model's focus on task-relevant signals while mitigating the influence of peripheral context. These findings position MEAP as a promising training paradigm for large language models.

  • 7 authors
·
Feb 11, 2025 2

Next Edit Prediction: Learning to Predict Code Edits from Context and Interaction History

The rapid advancement of large language models (LLMs) has led to the widespread adoption of AI-powered coding assistants integrated into a development environment. On one hand, low-latency code completion offers completion suggestions but is fundamentally constrained to the cursor's current position. On the other hand, chat-based editing can perform complex modifications, yet forces developers to stop their work, describe the intent in natural language, which causes a context-switch away from the code. This creates a suboptimal user experience, as neither paradigm proactively predicts the developer's next edit in a sequence of related edits. To bridge this gap and provide the seamless code edit suggestion, we introduce the task of Next Edit Prediction, a novel task designed to infer developer intent from recent interaction history to predict both the location and content of the subsequent edit. Specifically, we curate a high-quality supervised fine-tuning dataset and an evaluation benchmark for the Next Edit Prediction task. Then, we conduct supervised fine-tuning on a series of models and performed a comprehensive evaluation of both the fine-tuned models and other baseline models, yielding several novel findings. This work lays the foundation for a new interaction paradigm that proactively collaborate with developers by anticipating their following action, rather than merely reacting to explicit instructions.

  • 5 authors
·
Aug 13, 2025

RoSTE: An Efficient Quantization-Aware Supervised Fine-Tuning Approach for Large Language Models

Supervised fine-tuning is a standard method for adapting pre-trained large language models (LLMs) to downstream tasks. Quantization has been recently studied as a post-training technique for efficient LLM deployment. To obtain quantized fine-tuned LLMs, conventional pipelines would first fine-tune the pre-trained models, followed by post-training quantization. This often yields suboptimal performance as it fails to leverage the synergy between fine-tuning and quantization. To effectively realize low-bit quantization of weights, activations and KV caches in LLMs, we propose an algorithm named Rotated Straight-Through-Estimator (RoSTE), which combines quantization-aware supervised fine-tuning (QA-SFT) with an adaptive rotation strategy that identifies an effective rotation configuration to reduce activation outliers. We provide theoretical insights on RoSTE by analyzing its prediction error when applied to an overparameterized least square quantized training problem. Our findings reveal that the prediction error is directly proportional to the quantization error of the converged weights, which can be effectively managed through an optimized rotation configuration. Experiments on Pythia, Qwen and Llama models of different sizes demonstrate the effectiveness of RoSTE. Compared to existing post-SFT quantization baselines, our method consistently achieves superior performances across various tasks and different LLM architectures. Our code is available at https://github.com/OptimAI-Lab/RoSTE.

  • 7 authors
·
Feb 13, 2025

MetaOcc: Surround-View 4D Radar and Camera Fusion Framework for 3D Occupancy Prediction with Dual Training Strategies

3D occupancy prediction is crucial for autonomous driving perception. Fusion of 4D radar and camera provides a potential solution of robust occupancy prediction on serve weather with least cost. How to achieve effective multi-modal feature fusion and reduce annotation costs remains significant challenges. In this work, we propose MetaOcc, a novel multi-modal occupancy prediction framework that fuses surround-view cameras and 4D radar for comprehensive environmental perception. We first design a height self-attention module for effective 3D feature extraction from sparse radar points. Then, a local-global fusion mechanism is proposed to adaptively capture modality contributions while handling spatio-temporal misalignments. Temporal alignment and fusion module is employed to further aggregate historical feature. Furthermore, we develop a semi-supervised training procedure leveraging open-set segmentor and geometric constraints for pseudo-label generation, enabling robust perception with limited annotations. Extensive experiments on OmniHD-Scenes dataset demonstrate that MetaOcc achieves state-of-the-art performance, surpassing previous methods by significant margins. Notably, as the first semi-supervised 4D radar and camera fusion-based occupancy prediction approach, MetaOcc maintains 92.5% of the fully-supervised performance while using only 50% of ground truth annotations, establishing a new benchmark for multi-modal 3D occupancy prediction. Code and data are available at https://github.com/LucasYang567/MetaOcc.

  • 10 authors
·
Jan 25, 2025

ProtSolM: Protein Solubility Prediction with Multi-modal Features

Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein engineering. Existing methods either construct a supervised learning scheme on small-scale datasets with manually processed physicochemical properties, or blindly apply pre-trained protein language models to extract amino acid interaction information. The scale and quality of available training datasets leave significant room for improvement in terms of accuracy and generalization. To address these research gaps, we propose \sol, a novel deep learning method that combines pre-training and fine-tuning schemes for protein solubility prediction. ProtSolM integrates information from multiple dimensions, including physicochemical properties, amino acid sequences, and protein backbone structures. Our model is trained using \data, the largest solubility dataset that we have constructed. PDBSol includes over 60,000 protein sequences and structures. We provide a comprehensive leaderboard of existing statistical learning and deep learning methods on independent datasets with computational and experimental labels. ProtSolM achieved state-of-the-art performance across various evaluation metrics, demonstrating its potential to significantly advance the accuracy of protein solubility prediction.

  • 4 authors
·
Jun 28, 2024

Extreme Event Prediction with Multi-agent Reinforcement Learning-based Parametrization of Atmospheric and Oceanic Turbulence

Global climate models (GCMs) are the main tools for understanding and predicting climate change. However, due to limited numerical resolutions, these models suffer from major structural uncertainties; e.g., they cannot resolve critical processes such as small-scale eddies in atmospheric and oceanic turbulence. Thus, such small-scale processes have to be represented as a function of the resolved scales via closures (parametrization). The accuracy of these closures is particularly important for capturing climate extremes. Traditionally, such closures are based on heuristics and simplifying assumptions about the unresolved physics. Recently, supervised-learned closures, trained offline on high-fidelity data, have been shown to outperform the classical physics-based closures. However, this approach requires a significant amount of high-fidelity training data and can also lead to instabilities. Reinforcement learning is emerging as a potent alternative for developing such closures as it requires only low-order statistics and leads to stable closures. In Scientific Multi-Agent Reinforcement Learning (SMARL) computational elements serve a dual role of discretization points and learning agents. We leverage SMARL and fundamentals of turbulence physics to learn closures for prototypes of atmospheric and oceanic turbulence. The policy is trained using only the enstrophy spectrum, which is nearly invariant and can be estimated from a few high-fidelity samples (these few samples are far from enough for supervised/offline learning). We show that these closures lead to stable low-resolution simulations that, at a fraction of the cost, can reproduce the high-fidelity simulations' statistics, including the tails of the probability density functions. The results demonstrate the high potential of SMARL for closure modeling for GCMs, especially in the regime of scarce data and indirect observations.

  • 5 authors
·
Dec 1, 2023

Context Autoencoder for Self-Supervised Representation Learning

We present a novel masked image modeling (MIM) approach, context autoencoder (CAE), for self-supervised representation pretraining. We pretrain an encoder by making predictions in the encoded representation space. The pretraining tasks include two tasks: masked representation prediction - predict the representations for the masked patches, and masked patch reconstruction - reconstruct the masked patches. The network is an encoder-regressor-decoder architecture: the encoder takes the visible patches as input; the regressor predicts the representations of the masked patches, which are expected to be aligned with the representations computed from the encoder, using the representations of visible patches and the positions of visible and masked patches; the decoder reconstructs the masked patches from the predicted encoded representations. The CAE design encourages the separation of learning the encoder (representation) from completing the pertaining tasks: masked representation prediction and masked patch reconstruction tasks, and making predictions in the encoded representation space empirically shows the benefit to representation learning. We demonstrate the effectiveness of our CAE through superior transfer performance in downstream tasks: semantic segmentation, object detection and instance segmentation, and classification. The code will be available at https://github.com/Atten4Vis/CAE.

  • 10 authors
·
Feb 7, 2022

Self-Supervised Graph Transformer on Large-Scale Molecular Data

How to obtain informative representations of molecules is a crucial prerequisite in AI-driven drug design and discovery. Recent researches abstract molecules as graphs and employ Graph Neural Networks (GNNs) for molecular representation learning. Nevertheless, two issues impede the usage of GNNs in real scenarios: (1) insufficient labeled molecules for supervised training; (2) poor generalization capability to new-synthesized molecules. To address them both, we propose a novel framework, GROVER, which stands for Graph Representation frOm self-superVised mEssage passing tRansformer. With carefully designed self-supervised tasks in node-, edge- and graph-level, GROVER can learn rich structural and semantic information of molecules from enormous unlabelled molecular data. Rather, to encode such complex information, GROVER integrates Message Passing Networks into the Transformer-style architecture to deliver a class of more expressive encoders of molecules. The flexibility of GROVER allows it to be trained efficiently on large-scale molecular dataset without requiring any supervision, thus being immunized to the two issues mentioned above. We pre-train GROVER with 100 million parameters on 10 million unlabelled molecules -- the biggest GNN and the largest training dataset in molecular representation learning. We then leverage the pre-trained GROVER for molecular property prediction followed by task-specific fine-tuning, where we observe a huge improvement (more than 6% on average) from current state-of-the-art methods on 11 challenging benchmarks. The insights we gained are that well-designed self-supervision losses and largely-expressive pre-trained models enjoy the significant potential on performance boosting.

  • 7 authors
·
Jun 18, 2020

Self-supervised Label Augmentation via Input Transformations

Self-supervised learning, which learns by constructing artificial labels given only the input signals, has recently gained considerable attention for learning representations with unlabeled datasets, i.e., learning without any human-annotated supervision. In this paper, we show that such a technique can be used to significantly improve the model accuracy even under fully-labeled datasets. Our scheme trains the model to learn both original and self-supervised tasks, but is different from conventional multi-task learning frameworks that optimize the summation of their corresponding losses. Our main idea is to learn a single unified task with respect to the joint distribution of the original and self-supervised labels, i.e., we augment original labels via self-supervision of input transformation. This simple, yet effective approach allows to train models easier by relaxing a certain invariant constraint during learning the original and self-supervised tasks simultaneously. It also enables an aggregated inference which combines the predictions from different augmentations to improve the prediction accuracy. Furthermore, we propose a novel knowledge transfer technique, which we refer to as self-distillation, that has the effect of the aggregated inference in a single (faster) inference. We demonstrate the large accuracy improvement and wide applicability of our framework on various fully-supervised settings, e.g., the few-shot and imbalanced classification scenarios.

  • 3 authors
·
Oct 13, 2019

GeoDistill: Geometry-Guided Self-Distillation for Weakly Supervised Cross-View Localization

Cross-view localization, the task of estimating a camera's 3-degrees-of-freedom (3-DoF) pose by aligning ground-level images with satellite images, is crucial for large-scale outdoor applications like autonomous navigation and augmented reality. Existing methods often rely on fully supervised learning, which requires costly ground-truth pose annotations. In this work, we propose GeoDistill, a Geometry guided weakly supervised self distillation framework that uses teacher-student learning with Field-of-View (FoV)-based masking to enhance local feature learning for robust cross-view localization. In GeoDistill, the teacher model localizes a panoramic image, while the student model predicts locations from a limited FoV counterpart created by FoV-based masking. By aligning the student's predictions with those of the teacher, the student focuses on key features like lane lines and ignores textureless regions, such as roads. This results in more accurate predictions and reduced uncertainty, regardless of whether the query images are panoramas or limited FoV images. Our experiments show that GeoDistill significantly improves localization performance across different frameworks. Additionally, we introduce a novel orientation estimation network that predicts relative orientation without requiring precise planar position ground truth. GeoDistill provides a scalable and efficient solution for real-world cross-view localization challenges. Code and model can be found at https://github.com/tongshw/GeoDistill.

  • 5 authors
·
Jul 14, 2025 1

Mixture of Experts Guided by Gaussian Splatters Matters: A new Approach to Weakly-Supervised Video Anomaly Detection

Video Anomaly Detection (VAD) is a challenging task due to the variability of anomalous events and the limited availability of labeled data. Under the Weakly-Supervised VAD (WSVAD) paradigm, only video-level labels are provided during training, while predictions are made at the frame level. Although state-of-the-art models perform well on simple anomalies (e.g., explosions), they struggle with complex real-world events (e.g., shoplifting). This difficulty stems from two key issues: (1) the inability of current models to address the diversity of anomaly types, as they process all categories with a shared model, overlooking category-specific features; and (2) the weak supervision signal, which lacks precise temporal information, limiting the ability to capture nuanced anomalous patterns blended with normal events. To address these challenges, we propose Gaussian Splatting-guided Mixture of Experts (GS-MoE), a novel framework that employs a set of expert models, each specialized in capturing specific anomaly types. These experts are guided by a temporal Gaussian splatting loss, enabling the model to leverage temporal consistency and enhance weak supervision. The Gaussian splatting approach encourages a more precise and comprehensive representation of anomalies by focusing on temporal segments most likely to contain abnormal events. The predictions from these specialized experts are integrated through a mixture-of-experts mechanism to model complex relationships across diverse anomaly patterns. Our approach achieves state-of-the-art performance, with a 91.58% AUC on the UCF-Crime dataset, and demonstrates superior results on XD-Violence and MSAD datasets. By leveraging category-specific expertise and temporal guidance, GS-MoE sets a new benchmark for VAD under weak supervision.

  • 7 authors
·
Aug 8, 2025

Dual Structure-Aware Image Filterings for Semi-supervised Medical Image Segmentation

Semi-supervised image segmentation has attracted great attention recently. The key is how to leverage unlabeled images in the training process. Most methods maintain consistent predictions of the unlabeled images under variations (e.g., adding noise/perturbations, or creating alternative versions) in the image and/or model level. In most image-level variation, medical images often have prior structure information, which has not been well explored. In this paper, we propose novel dual structure-aware image filterings (DSAIF) as the image-level variations for semi-supervised medical image segmentation. Motivated by connected filtering that simplifies image via filtering in structure-aware tree-based image representation, we resort to the dual contrast invariant Max-tree and Min-tree representation. Specifically, we propose a novel connected filtering that removes topologically equivalent nodes (i.e. connected components) having no siblings in the Max/Min-tree. This results in two filtered images preserving topologically critical structure. Applying the proposed DSAIF to mutually supervised networks decreases the consensus of their erroneous predictions on unlabeled images. This helps to alleviate the confirmation bias issue of overfitting to noisy pseudo labels of unlabeled images, and thus effectively improves the segmentation performance. Extensive experimental results on three benchmark datasets demonstrate that the proposed method significantly/consistently outperforms some state-of-the-art methods. The source codes will be publicly available.

  • 7 authors
·
Dec 12, 2023

Unsupervised and semi-supervised co-salient object detection via segmentation frequency statistics

In this paper, we address the detection of co-occurring salient objects (CoSOD) in an image group using frequency statistics in an unsupervised manner, which further enable us to develop a semi-supervised method. While previous works have mostly focused on fully supervised CoSOD, less attention has been allocated to detecting co-salient objects when limited segmentation annotations are available for training. Our simple yet effective unsupervised method US-CoSOD combines the object co-occurrence frequency statistics of unsupervised single-image semantic segmentations with salient foreground detections using self-supervised feature learning. For the first time, we show that a large unlabeled dataset e.g. ImageNet-1k can be effectively leveraged to significantly improve unsupervised CoSOD performance. Our unsupervised model is a great pre-training initialization for our semi-supervised model SS-CoSOD, especially when very limited labeled data is available for training. To avoid propagating erroneous signals from predictions on unlabeled data, we propose a confidence estimation module to guide our semi-supervised training. Extensive experiments on three CoSOD benchmark datasets show that both of our unsupervised and semi-supervised models outperform the corresponding state-of-the-art models by a significant margin (e.g., on the Cosal2015 dataset, our US-CoSOD model has an 8.8% F-measure gain over a SOTA unsupervised co-segmentation model and our SS-CoSOD model has an 11.81% F-measure gain over a SOTA semi-supervised CoSOD model).

  • 5 authors
·
Nov 11, 2023

Self-Supervised Learning with Cluster-Aware-DINO for High-Performance Robust Speaker Verification

Automatic speaker verification task has made great achievements using deep learning approaches with the large-scale manually annotated dataset. However, it's very difficult and expensive to collect a large amount of well-labeled data for system building. In this paper, we propose a novel and advanced self-supervised learning framework which can construct a high performance speaker verification system without using any labeled data. To avoid the impact of false negative pairs, we adopt the self-distillation with no labels (DINO) framework as the initial model, which can be trained without exploiting negative pairs. Then, we introduce a cluster-aware training strategy for DINO to improve the diversity of data. In the iteration learning stage, due to a mass of unreliable labels from clustering, the quality of pseudo labels is important for the system training. This motivates us to propose dynamic loss-gate and label correction (DLG-LC) methods to alleviate the performance degradation caused by unreliable labels. More specifically, we model the loss distribution with GMM and obtain the loss-gate threshold dynamically to distinguish the reliable and unreliable labels. Besides, we adopt the model predictions to correct the unreliable label, for better utilizing the unreliable data rather than dropping them directly. Moreover, we extend the DLG-LC to multi-modality to further improve the performance. The experiments are performed on the commonly used Voxceleb dataset. Compared to the best-known self-supervised speaker verification system, our proposed method obtain 22.17%, 27.94% and 25.56% relative EER improvement on Vox-O, Vox-E and Vox-H test sets, even with fewer iterations, smaller models, and simpler clustering methods. More importantly, the newly proposed system even achieves comparable results with the fully supervised system, but without using any human labeled data.

  • 3 authors
·
Apr 12, 2023

Simple Semi-supervised Knowledge Distillation from Vision-Language Models via $\mathbf{\texttt{D}}$ual-$\mathbf{\texttt{H}}$ead $\mathbf{\texttt{O}}$ptimization

Vision-language models (VLMs) have achieved remarkable success across diverse tasks by leveraging rich textual information with minimal labeled data. However, deploying such large models remains challenging, particularly in resource-constrained environments. Knowledge distillation (KD) offers a well-established solution to this problem; however, recent KD approaches from VLMs often involve multi-stage training or additional tuning, increasing computational overhead and optimization complexity. In this paper, we propose texttt{D}ual-texttt{H}ead texttt{O}ptimization (texttt{DHO}) -- a simple yet effective KD framework that transfers knowledge from VLMs to compact, task-specific models in semi-supervised settings. Specifically, we introduce dual prediction heads that independently learn from labeled data and teacher predictions, and propose to linearly combine their outputs during inference. We observe that DHO mitigates gradient conflicts between supervised and distillation signals, enabling more effective feature learning than single-head KD baselines. As a result, extensive experiments show that DHO consistently outperforms baselines across multiple domains and fine-grained datasets. Notably, on ImageNet, it achieves state-of-the-art performance, improving accuracy by 3% and 0.1% with 1% and 10% labeled data, respectively, while using fewer parameters.

  • 4 authors
·
May 12, 2025 3

Supervised Fine-Tuning or Contrastive Learning? Towards Better Multimodal LLM Reranking

In information retrieval, training reranking models mainly focuses on two types of objectives: metric learning (e.g. contrastive loss to increase the predicted scores on relevant query-document pairs) and classification (binary label prediction of relevance vs. irrelevance). For BERT-style encoders, various studies have shown that contrastive learning (CL) can be more effective than discriminative (classification) learning. However, for large language models (LLMs), classification via supervised fine-tuning (SFT), which predicts ''yes'' (resp. ''no'') token for relevant (resp. irrelevant) pairs, appears more promising as it aligns well with the generative nature of LLMs. This divergence raises a central question: which objective is intrinsically better suited to LLM-based reranking, and what mechanism underlies the difference? In this work, we conduct a comprehensive comparison and analysis between CL and SFT for reranking, taking the universal multimodal retrieval (UMR) as the experimental playground. We first decompose the objectives into two components: weight, which controls the magnitude of those updates, and direction, which guides the model updates, then present a unified framework for understanding their interactions. Through probing experiments, we find that SFT provides a substantially stronger weighting scheme than CL, whereas the preferred scoring direction shows no clear winner. Taken together, these results point to a consistent advantage of SFT over CL for LLM reranking. To further validate our findings, we conduct large-scale training with SFT and present new state-of-the-art rerankers on the MRB benchmark. We also provide ablations on SFT settings and expect our findings to benefit future research and applications in this area.

  • 9 authors
·
Oct 16, 2025

A Benchmark Dataset for Multimodal Prediction of Enzymatic Function Coupling DNA Sequences and Natural Language

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

  • 6 authors
·
Jul 21, 2024

Reasoning-Enhanced Large Language Models for Molecular Property Prediction

Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional machine learning models struggle with task transferability, while specialized molecular language models provide little insight into their decision-making processes. To address these limitations, we propose MPPReasoner, a multimodal large language model that incorporates chemical reasoning for molecular property prediction. Our approach, built upon Qwen2.5-VL-7B-Instruct, integrates molecular images with SMILES strings to enable comprehensive molecular understanding. We develop a two-stage training strategy: supervised fine-tuning (SFT) using 16,000 high-quality reasoning trajectories generated through expert knowledge and multiple teacher models, followed by Reinforcement Learning from Principle-Guided Rewards (RLPGR). RLPGR employs verifiable, rule-based rewards that systematically evaluate chemical principle application, molecular structure analysis, and logical consistency through computational verification. Extensive experiments across 8 datasets demonstrate significant performance improvements, with MPPReasoner outperforming the best baselines by 7.91\% and 4.53\% on in-distribution and out-of-distribution tasks respectively. MPPReasoner exhibits exceptional cross-task generalization and generates chemically sound reasoning paths that provide valuable insights into molecular property analysis, substantially enhancing both interpretability and practical utility for chemists. Code is available at https://anonymous.4open.science/r/MPPReasoner-12687.

  • 12 authors
·
Oct 11, 2025

TeD-SPAD: Temporal Distinctiveness for Self-supervised Privacy-preservation for video Anomaly Detection

Video anomaly detection (VAD) without human monitoring is a complex computer vision task that can have a positive impact on society if implemented successfully. While recent advances have made significant progress in solving this task, most existing approaches overlook a critical real-world concern: privacy. With the increasing popularity of artificial intelligence technologies, it becomes crucial to implement proper AI ethics into their development. Privacy leakage in VAD allows models to pick up and amplify unnecessary biases related to people's personal information, which may lead to undesirable decision making. In this paper, we propose TeD-SPAD, a privacy-aware video anomaly detection framework that destroys visual private information in a self-supervised manner. In particular, we propose the use of a temporally-distinct triplet loss to promote temporally discriminative features, which complements current weakly-supervised VAD methods. Using TeD-SPAD, we achieve a positive trade-off between privacy protection and utility anomaly detection performance on three popular weakly supervised VAD datasets: UCF-Crime, XD-Violence, and ShanghaiTech. Our proposed anonymization model reduces private attribute prediction by 32.25% while only reducing frame-level ROC AUC on the UCF-Crime anomaly detection dataset by 3.69%. Project Page: https://joefioresi718.github.io/TeD-SPAD_webpage/

  • 3 authors
·
Aug 21, 2023

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at https://github.com/QizhiPei/SSM-DTA{Github}.

  • 9 authors
·
Jun 20, 2022

TERA: Self-Supervised Learning of Transformer Encoder Representation for Speech

We introduce a self-supervised speech pre-training method called TERA, which stands for Transformer Encoder Representations from Alteration. Recent approaches often learn by using a single auxiliary task like contrastive prediction, autoregressive prediction, or masked reconstruction. Unlike previous methods, we use alteration along three orthogonal axes to pre-train Transformer Encoders on a large amount of unlabeled speech. The model learns through the reconstruction of acoustic frames from their altered counterpart, where we use a stochastic policy to alter along various dimensions: time, frequency, and magnitude. TERA can be used for speech representations extraction or fine-tuning with downstream models. We evaluate TERA on several downstream tasks, including phoneme classification, keyword spotting, speaker recognition, and speech recognition. We present a large-scale comparison of various self-supervised models. TERA achieves strong performance in the comparison by improving upon surface features and outperforming previous models. In our experiments, we study the effect of applying different alteration techniques, pre-training on more data, and pre-training on various features. We analyze different model sizes and find that smaller models are strong representation learners than larger models, while larger models are more effective for downstream fine-tuning than smaller models. Furthermore, we show the proposed method is transferable to downstream datasets not used in pre-training.

  • 3 authors
·
Jul 12, 2020

Exploring CLIP's Dense Knowledge for Weakly Supervised Semantic Segmentation

Weakly Supervised Semantic Segmentation (WSSS) with image-level labels aims to achieve pixel-level predictions using Class Activation Maps (CAMs). Recently, Contrastive Language-Image Pre-training (CLIP) has been introduced in WSSS. However, recent methods primarily focus on image-text alignment for CAM generation, while CLIP's potential in patch-text alignment remains unexplored. In this work, we propose ExCEL to explore CLIP's dense knowledge via a novel patch-text alignment paradigm for WSSS. Specifically, we propose Text Semantic Enrichment (TSE) and Visual Calibration (VC) modules to improve the dense alignment across both text and vision modalities. To make text embeddings semantically informative, our TSE module applies Large Language Models (LLMs) to build a dataset-wide knowledge base and enriches the text representations with an implicit attribute-hunting process. To mine fine-grained knowledge from visual features, our VC module first proposes Static Visual Calibration (SVC) to propagate fine-grained knowledge in a non-parametric manner. Then Learnable Visual Calibration (LVC) is further proposed to dynamically shift the frozen features towards distributions with diverse semantics. With these enhancements, ExCEL not only retains CLIP's training-free advantages but also significantly outperforms other state-of-the-art methods with much less training cost on PASCAL VOC and MS COCO.

  • 6 authors
·
Mar 25, 2025

Confidence-Weighted Boundary-Aware Learning for Semi-Supervised Semantic Segmentation

Semi-supervised semantic segmentation (SSSS) aims to improve segmentation performance by utilising unlabeled data alongside limited labeled samples. Existing SSSS methods often face challenges such as coupling, where over-reliance on initial labeled data leads to suboptimal learning; confirmation bias, where incorrect predictions reinforce themselves repeatedly; and boundary blur caused by insufficient boundary-awareness and ambiguous edge information. To address these issues, we propose CW-BASS, a novel framework for SSSS. In order to mitigate the impact of incorrect predictions, we assign confidence weights to pseudo-labels. Additionally, we leverage boundary-delineation techniques, which, despite being extensively explored in weakly-supervised semantic segmentation (WSSS) remain under-explored in SSSS. Specifically, our approach: (1) reduces coupling through a confidence-weighted loss function that adjusts the influence of pseudo-labels based on their predicted confidence scores, (2) mitigates confirmation bias with a dynamic thresholding mechanism that learns to filter out pseudo-labels based on model performance, (3) resolves boundary blur with a boundary-aware module that enhances segmentation accuracy near object boundaries, and (4) reduces label noise with a confidence decay strategy that progressively refines pseudo-labels during training. Extensive experiments on the Pascal VOC 2012 and Cityscapes demonstrate that our method achieves state-of-the-art performance. Moreover, using only 1/8 or 12.5\% of labeled data, our method achieves a mIoU of 75.81 on Pascal VOC 2012, highlighting its effectiveness in limited-label settings.

  • 2 authors
·
Feb 20, 2025

Consistent-Teacher: Towards Reducing Inconsistent Pseudo-targets in Semi-supervised Object Detection

In this study, we dive deep into the inconsistency of pseudo targets in semi-supervised object detection (SSOD). Our core observation is that the oscillating pseudo-targets undermine the training of an accurate detector. It injects noise into the student's training, leading to severe overfitting problems. Therefore, we propose a systematic solution, termed ConsistentTeacher, to reduce the inconsistency. First, adaptive anchor assignment~(ASA) substitutes the static IoU-based strategy, which enables the student network to be resistant to noisy pseudo-bounding boxes. Then we calibrate the subtask predictions by designing a 3D feature alignment module~(FAM-3D). It allows each classification feature to adaptively query the optimal feature vector for the regression task at arbitrary scales and locations. Lastly, a Gaussian Mixture Model (GMM) dynamically revises the score threshold of pseudo-bboxes, which stabilizes the number of ground truths at an early stage and remedies the unreliable supervision signal during training. ConsistentTeacher provides strong results on a large range of SSOD evaluations. It achieves 40.0 mAP with ResNet-50 backbone given only 10% of annotated MS-COCO data, which surpasses previous baselines using pseudo labels by around 3 mAP. When trained on fully annotated MS-COCO with additional unlabeled data, the performance further increases to 47.7 mAP. Our code is available at https://github.com/Adamdad/ConsistentTeacher.

  • 9 authors
·
Sep 4, 2022

DetailFlow: 1D Coarse-to-Fine Autoregressive Image Generation via Next-Detail Prediction

This paper presents DetailFlow, a coarse-to-fine 1D autoregressive (AR) image generation method that models images through a novel next-detail prediction strategy. By learning a resolution-aware token sequence supervised with progressively degraded images, DetailFlow enables the generation process to start from the global structure and incrementally refine details. This coarse-to-fine 1D token sequence aligns well with the autoregressive inference mechanism, providing a more natural and efficient way for the AR model to generate complex visual content. Our compact 1D AR model achieves high-quality image synthesis with significantly fewer tokens than previous approaches, i.e. VAR/VQGAN. We further propose a parallel inference mechanism with self-correction that accelerates generation speed by approximately 8x while reducing accumulation sampling error inherent in teacher-forcing supervision. On the ImageNet 256x256 benchmark, our method achieves 2.96 gFID with 128 tokens, outperforming VAR (3.3 FID) and FlexVAR (3.05 FID), which both require 680 tokens in their AR models. Moreover, due to the significantly reduced token count and parallel inference mechanism, our method runs nearly 2x faster inference speed compared to VAR and FlexVAR. Extensive experimental results demonstrate DetailFlow's superior generation quality and efficiency compared to existing state-of-the-art methods.

  • 13 authors
·
May 27, 2025 2

PRDP: Proximal Reward Difference Prediction for Large-Scale Reward Finetuning of Diffusion Models

Reward finetuning has emerged as a promising approach to aligning foundation models with downstream objectives. Remarkable success has been achieved in the language domain by using reinforcement learning (RL) to maximize rewards that reflect human preference. However, in the vision domain, existing RL-based reward finetuning methods are limited by their instability in large-scale training, rendering them incapable of generalizing to complex, unseen prompts. In this paper, we propose Proximal Reward Difference Prediction (PRDP), enabling stable black-box reward finetuning for diffusion models for the first time on large-scale prompt datasets with over 100K prompts. Our key innovation is the Reward Difference Prediction (RDP) objective that has the same optimal solution as the RL objective while enjoying better training stability. Specifically, the RDP objective is a supervised regression objective that tasks the diffusion model with predicting the reward difference of generated image pairs from their denoising trajectories. We theoretically prove that the diffusion model that obtains perfect reward difference prediction is exactly the maximizer of the RL objective. We further develop an online algorithm with proximal updates to stably optimize the RDP objective. In experiments, we demonstrate that PRDP can match the reward maximization ability of well-established RL-based methods in small-scale training. Furthermore, through large-scale training on text prompts from the Human Preference Dataset v2 and the Pick-a-Pic v1 dataset, PRDP achieves superior generation quality on a diverse set of complex, unseen prompts whereas RL-based methods completely fail.

  • 5 authors
·
Feb 13, 2024 1

Mono-ViFI: A Unified Learning Framework for Self-supervised Single- and Multi-frame Monocular Depth Estimation

Self-supervised monocular depth estimation has gathered notable interest since it can liberate training from dependency on depth annotations. In monocular video training case, recent methods only conduct view synthesis between existing camera views, leading to insufficient guidance. To tackle this, we try to synthesize more virtual camera views by flow-based video frame interpolation (VFI), termed as temporal augmentation. For multi-frame inference, to sidestep the problem of dynamic objects encountered by explicit geometry-based methods like ManyDepth, we return to the feature fusion paradigm and design a VFI-assisted multi-frame fusion module to align and aggregate multi-frame features, using motion and occlusion information obtained by the flow-based VFI model. Finally, we construct a unified self-supervised learning framework, named Mono-ViFI, to bilaterally connect single- and multi-frame depth. In this framework, spatial data augmentation through image affine transformation is incorporated for data diversity, along with a triplet depth consistency loss for regularization. The single- and multi-frame models can share weights, making our framework compact and memory-efficient. Extensive experiments demonstrate that our method can bring significant improvements to current advanced architectures. Source code is available at https://github.com/LiuJF1226/Mono-ViFI.

  • 6 authors
·
Jul 19, 2024

K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

  • 7 authors
·
Feb 18, 2025

NyayaAnumana & INLegalLlama: The Largest Indian Legal Judgment Prediction Dataset and Specialized Language Model for Enhanced Decision Analysis

The integration of artificial intelligence (AI) in legal judgment prediction (LJP) has the potential to transform the legal landscape, particularly in jurisdictions like India, where a significant backlog of cases burdens the legal system. This paper introduces NyayaAnumana, the largest and most diverse corpus of Indian legal cases compiled for LJP, encompassing a total of 7,02,945 preprocessed cases. NyayaAnumana, which combines the words "Nyay" (judgment) and "Anuman" (prediction or inference) respectively for most major Indian languages, includes a wide range of cases from the Supreme Court, High Courts, Tribunal Courts, District Courts, and Daily Orders and, thus, provides unparalleled diversity and coverage. Our dataset surpasses existing datasets like PredEx and ILDC, offering a comprehensive foundation for advanced AI research in the legal domain. In addition to the dataset, we present INLegalLlama, a domain-specific generative large language model (LLM) tailored to the intricacies of the Indian legal system. It is developed through a two-phase training approach over a base LLaMa model. First, Indian legal documents are injected using continual pretraining. Second, task-specific supervised finetuning is done. This method allows the model to achieve a deeper understanding of legal contexts. Our experiments demonstrate that incorporating diverse court data significantly boosts model accuracy, achieving approximately 90% F1-score in prediction tasks. INLegalLlama not only improves prediction accuracy but also offers comprehensible explanations, addressing the need for explainability in AI-assisted legal decisions.

  • 6 authors
·
Dec 11, 2024

Background Activation Suppression for Weakly Supervised Object Localization and Semantic Segmentation

Weakly supervised object localization and semantic segmentation aim to localize objects using only image-level labels. Recently, a new paradigm has emerged by generating a foreground prediction map (FPM) to achieve pixel-level localization. While existing FPM-based methods use cross-entropy to evaluate the foreground prediction map and to guide the learning of the generator, this paper presents two astonishing experimental observations on the object localization learning process: For a trained network, as the foreground mask expands, 1) the cross-entropy converges to zero when the foreground mask covers only part of the object region. 2) The activation value continuously increases until the foreground mask expands to the object boundary. Therefore, to achieve a more effective localization performance, we argue for the usage of activation value to learn more object regions. In this paper, we propose a Background Activation Suppression (BAS) method. Specifically, an Activation Map Constraint (AMC) module is designed to facilitate the learning of generator by suppressing the background activation value. Meanwhile, by using foreground region guidance and area constraint, BAS can learn the whole region of the object. In the inference phase, we consider the prediction maps of different categories together to obtain the final localization results. Extensive experiments show that BAS achieves significant and consistent improvement over the baseline methods on the CUB-200-2011 and ILSVRC datasets. In addition, our method also achieves state-of-the-art weakly supervised semantic segmentation performance on the PASCAL VOC 2012 and MS COCO 2014 datasets. Code and models are available at https://github.com/wpy1999/BAS-Extension.

  • 6 authors
·
Sep 22, 2023

CPCM: Contextual Point Cloud Modeling for Weakly-supervised Point Cloud Semantic Segmentation

We study the task of weakly-supervised point cloud semantic segmentation with sparse annotations (e.g., less than 0.1% points are labeled), aiming to reduce the expensive cost of dense annotations. Unfortunately, with extremely sparse annotated points, it is very difficult to extract both contextual and object information for scene understanding such as semantic segmentation. Motivated by masked modeling (e.g., MAE) in image and video representation learning, we seek to endow the power of masked modeling to learn contextual information from sparsely-annotated points. However, directly applying MAE to 3D point clouds with sparse annotations may fail to work. First, it is nontrivial to effectively mask out the informative visual context from 3D point clouds. Second, how to fully exploit the sparse annotations for context modeling remains an open question. In this paper, we propose a simple yet effective Contextual Point Cloud Modeling (CPCM) method that consists of two parts: a region-wise masking (RegionMask) strategy and a contextual masked training (CMT) method. Specifically, RegionMask masks the point cloud continuously in geometric space to construct a meaningful masked prediction task for subsequent context learning. CMT disentangles the learning of supervised segmentation and unsupervised masked context prediction for effectively learning the very limited labeled points and mass unlabeled points, respectively. Extensive experiments on the widely-tested ScanNet V2 and S3DIS benchmarks demonstrate the superiority of CPCM over the state-of-the-art.

  • 8 authors
·
Jul 19, 2023

Graph Self-supervised Learning with Accurate Discrepancy Learning

Self-supervised learning of graph neural networks (GNNs) aims to learn an accurate representation of the graphs in an unsupervised manner, to obtain transferable representations of them for diverse downstream tasks. Predictive learning and contrastive learning are the two most prevalent approaches for graph self-supervised learning. However, they have their own drawbacks. While the predictive learning methods can learn the contextual relationships between neighboring nodes and edges, they cannot learn global graph-level similarities. Contrastive learning, while it can learn global graph-level similarities, its objective to maximize the similarity between two differently perturbed graphs may result in representations that cannot discriminate two similar graphs with different properties. To tackle such limitations, we propose a framework that aims to learn the exact discrepancy between the original and the perturbed graphs, coined as Discrepancy-based Self-supervised LeArning (D-SLA). Specifically, we create multiple perturbations of the given graph with varying degrees of similarity, and train the model to predict whether each graph is the original graph or the perturbed one. Moreover, we further aim to accurately capture the amount of discrepancy for each perturbed graph using the graph edit distance. We validate our D-SLA on various graph-related downstream tasks, including molecular property prediction, protein function prediction, and link prediction tasks, on which ours largely outperforms relevant baselines.

  • 3 authors
·
Feb 7, 2022