TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models

Navigating the vast chemical space of druggable compounds is a formidable challenge in drug discovery, where generative models are increasingly employed to identify viable candidates. Conditional 3D structure-based drug design (3D-SBDD) models, which take into account complex three-dimensional interactions and molecular geometries, are particularly promising. Scaffold hopping is an efficient strategy that facilitates the identification of similar active compounds by strategically modifying the core structure of molecules, effectively narrowing the wide chemical space and enhancing the discovery of drug-like products. However, the practical application of 3D-SBDD generative models is hampered by their slow processing speeds. To address this bottleneck, we introduce TurboHopp, an accelerated pocket-conditioned 3D scaffold hopping model that merges the strategic effectiveness of traditional scaffold hopping with rapid generation capabilities of consistency models. This synergy not only enhances efficiency but also significantly boosts generation speeds, achieving up to 30 times faster inference speed as well as superior generation quality compared to existing diffusion-based models, establishing TurboHopp as a powerful tool in drug discovery. Supported by faster inference speed, we further optimize our model, using Reinforcement Learning for Consistency Models (RLCM), to output desirable molecules. We demonstrate the broad applicability of TurboHopp across multiple drug discovery scenarios, underscoring its potential in diverse molecular settings.

Learning-enabled Flexible Job-shop Scheduling for Scalable Smart Manufacturing

In smart manufacturing systems (SMSs), flexible job-shop scheduling with transportation constraints (FJSPT) is essential to optimize solutions for maximizing productivity, considering production flexibility based on automated guided vehicles (AGVs). Recent developments in deep reinforcement learning (DRL)-based methods for FJSPT have encountered a scale generalization challenge. These methods underperform when applied to environment at scales different from their training set, resulting in low-quality solutions. To address this, we introduce a novel graph-based DRL method, named the Heterogeneous Graph Scheduler (HGS). Our method leverages locally extracted relational knowledge among operations, machines, and vehicle nodes for scheduling, with a graph-structured decision-making framework that reduces encoding complexity and enhances scale generalization. Our performance evaluation, conducted with benchmark datasets, reveals that the proposed method outperforms traditional dispatching rules, meta-heuristics, and existing DRL-based approaches in terms of makespan performance, even on large-scale instances that have not been experienced during training.

MolPLA: A Molecular Pretraining Framework for Learning Cores, R-Groups and their Linker Joints

Molecular core structures and R-groups are essential concepts in drug development. Integration of these concepts with conventional graph pre-training approaches can promote deeper understanding in molecules. We propose MolPLA, a novel pre-training framework that employs masked graph contrastive learning in understanding the underlying decomposable parts inmolecules that implicate their core structure and peripheral R-groups. Furthermore, we formulate an additional framework that grants MolPLA the ability to help chemists find replaceable R-groups in lead optimization scenarios. Experimental results on molecular property prediction show that MolPLA exhibits predictability comparable to current state-of-the-art models. Qualitative analysis implicate that MolPLA is capable of distinguishing core and R-group sub-structures, identifying decomposable regions in molecules and contributing to lead optimization scenarios by rationally suggesting R-group replacements given various query core templates. The code implementation for MolPLA and its pre-trained model checkpoint is available at https://github.com/dmis-lab/MolPLA

Camera-Driven Representation Learning for Unsupervised Domain Adaptive Person Re-identification

We present a novel unsupervised domain adaption method for person re-identification (reID) that generalizes a model trained on a labeled source domain to an unlabeled target domain. We introduce a camera-driven curriculum learning (CaCL) framework that leverages camera labels of person images to transfer knowledge from source to target domains progressively. To this end, we divide target domain dataset into multiple subsets based on the camera labels, and initially train our model with a single subset (i.e., images captured by a single camera). We then gradually exploit more subsets for training, according to a curriculum sequence obtained with a camera-driven scheduling rule. The scheduler considers maximum mean discrepancies (MMD) between each subset and the source domain dataset, such that the subset closer to the source domain is exploited earlier within the curriculum. For each curriculum sequence, we generate pseudo labels of person images in a target domain to train a reID model in a supervised way. We have observed that the pseudo labels are highly biased toward cameras, suggesting that person images obtained from the same camera are likely to have the same pseudo labels, even for different IDs. To address the camera bias problem, we also introduce a camera-diversity (CD) loss encouraging person images of the same pseudo label, but captured across various cameras, to involve more for discriminative feature learning, providing person representations robust to inter-camera variations. Experimental results on standard benchmarks, including real-to-real and synthetic-to-real scenarios, demonstrate the effectiveness of our framework.

Extracting Structured Seed-Mediated Gold Nanorod Growth Procedures from Literature with GPT-3

Although gold nanorods have been the subject of much research, the pathways for controlling their shape and thereby their optical properties remain largely heuristically understood. Although it is apparent that the simultaneous presence of and interaction between various reagents during synthesis control these properties, computational and experimental approaches for exploring the synthesis space can be either intractable or too time-consuming in practice. This motivates an alternative approach leveraging the wealth of synthesis information already embedded in the body of scientific literature by developing tools to extract relevant structured data in an automated, high-throughput manner. To that end, we present an approach using the powerful GPT-3 language model to extract structured multi-step seed-mediated growth procedures and outcomes for gold nanorods from unstructured scientific text. GPT-3 prompt completions are fine-tuned to predict synthesis templates in the form of JSON documents from unstructured text input with an overall accuracy of $86\%$. The performance is notable, considering the model is performing simultaneous entity recognition and relation extraction. We present a dataset of 11,644 entities extracted from 1,137 papers, resulting in 268 papers with at least one complete seed-mediated gold nanorod growth procedure and outcome for a total of 332 complete procedures.

Structured information extraction from complex scientific text with fine-tuned large language models

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

Decomposed Knowledge Distillation for Class-Incremental Semantic Segmentation

Class-incremental semantic segmentation (CISS) labels each pixel of an image with a corresponding object/stuff class continually. To this end, it is crucial to learn novel classes incrementally without forgetting previously learned knowledge. Current CISS methods typically use a knowledge distillation (KD) technique for preserving classifier logits, or freeze a feature extractor, to avoid the forgetting problem. The strong constraints, however, prevent learning discriminative features for novel classes. We introduce a CISS framework that alleviates the forgetting problem and facilitates learning novel classes effectively. We have found that a logit can be decomposed into two terms. They quantify how likely an input belongs to a particular class or not, providing a clue for a reasoning process of a model. The KD technique, in this context, preserves the sum of two terms (i.e., a class logit), suggesting that each could be changed and thus the KD does not imitate the reasoning process. To impose constraints on each term explicitly, we propose a new decomposed knowledge distillation (DKD) technique, improving the rigidity of a model and addressing the forgetting problem more effectively. We also introduce a novel initialization method to train new classifiers for novel classes. In CISS, the number of negative training samples for novel classes is not sufficient to discriminate old classes. To mitigate this, we propose to transfer knowledge of negatives to the classifiers successively using an auxiliary classifier, boosting the performance significantly. Experimental results on standard CISS benchmarks demonstrate the effectiveness of our framework.

OIMNet++: Prototypical Normalization and Localization-aware Learning for Person Search

We address the task of person search, that is, localizing and re-identifying query persons from a set of raw scene images. Recent approaches are typically built upon OIMNet, a pioneer work on person search, that learns joint person representations for performing both detection and person re-identification (reID) tasks. To obtain the representations, they extract features from pedestrian proposals, and then project them on a unit hypersphere with L2 normalization. These methods also incorporate all positive proposals, that sufficiently overlap with the ground truth, equally to learn person representations for reID. We have found that 1) the L2 normalization without considering feature distributions degenerates the discriminative power of person representations, and 2) positive proposals often also depict background clutter and person overlaps, which could encode noisy features to person representations. In this paper, we introduce OIMNet++ that addresses the aforementioned limitations. To this end, we introduce a novel normalization layer, dubbed ProtoNorm, that calibrates features from pedestrian proposals, while considering a long-tail distribution of person IDs, enabling L2 normalized person representations to be discriminative. We also propose a localization-aware feature learning scheme that encourages better-aligned proposals to contribute more in learning discriminative representations. Experimental results and analysis on standard person search benchmarks demonstrate the effectiveness of OIMNet++.

Learning by Aligning: Visible-Infrared Person Re-identification using Cross-Modal Correspondences

We address the problem of visible-infrared person re-identification (VI-reID), that is, retrieving a set of person images, captured by visible or infrared cameras, in a cross-modal setting. Two main challenges in VI-reID are intra-class variations across person images, and cross-modal discrepancies between visible and infrared images. Assuming that the person images are roughly aligned, previous approaches attempt to learn coarse image- or rigid part-level person representations that are discriminative and generalizable across different modalities. However, the person images, typically cropped by off-the-shelf object detectors, are not necessarily well-aligned, which distract discriminative person representation learning. In this paper, we introduce a novel feature learning framework that addresses these problems in a unified way. To this end, we propose to exploit dense correspondences between cross-modal person images. This allows to address the cross-modal discrepancies in a pixel-level, suppressing modality-related features from person representations more effectively. This also encourages pixel-wise associations between cross-modal local features, further facilitating discriminative feature learning for VI-reID. Extensive experiments and analyses on standard VI-reID benchmarks demonstrate the effectiveness of our approach, which significantly outperforms the state of the art.

HVPR: Hybrid Voxel-Point Representation for Single-stage 3D Object Detection

We address the problem of 3D object detection, that is, estimating 3D object bounding boxes from point clouds. 3D object detection methods exploit either voxel-based or point-based features to represent 3D objects in a scene. Voxel-based features are efficient to extract, while they fail to preserve fine-grained 3D structures of objects. Point-based features, on the other hand, represent the 3D structures more accurately, but extracting these features is computationally expensive. We introduce in this paper a novel single-stage 3D detection method having the merit of both voxel-based and point-based features. To this end, we propose a new convolutional neural network (CNN) architecture, dubbed HVPR, that integrates both features into a single 3D representation effectively and efficiently. Specifically, we augment the point-based features with a memory module to reduce the computational cost. We then aggregate the features in the memory, semantically similar to each voxel-based one, to obtain a hybrid 3D representation in a form of a pseudo image, allowing to localize 3D objects in a single stage efficiently. We also propose an Attentive Multi-scale Feature Module (AMFM) that extracts scale-aware features considering the sparse and irregular patterns of point clouds. Experimental results on the KITTI dataset demonstrate the effectiveness and efficiency of our approach, achieving a better compromise in terms of speed and accuracy.