Hongyu Guo

Hongyu Guo, Hao Li, He Cao et al.

Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers. This masks a critical failure mode: a model may output the correct molecule, product, or option while its reasoning violates chemical logic. Existing process-level evaluators are hard to scale because LLM judges and human step-level process annotation are costly, inconsistent, and vulnerable to hallucination. We introduce ChemCoTBench-V2, a rule-verifiable diagnostic benchmark for low-cost, auditable evaluation of structured, verifier-addressable chemical reasoning traces. It spans molecular understanding, molecule editing, molecular optimization, and reaction prediction, with 5,620 evaluation samples across 18 reporting tasks. Models must expose key intermediate steps in expert-designed templates, and those steps are checked with deterministic chemistry rules and, for closed-answer tasks, reference traces rather than another LLM judge. Open-ended molecular optimization is evaluated with oracle-verifiable state constraints rather than strict trace matching. The benchmark reports three separate signals: final-answer correctness, template adherence, and step-wise verifier correctness over expert-refined intermediate commitments. Experiments on frontier models reveal a persistent gap between final-answer success and structured-reasoning-state consistency: models often follow the requested format while failing chemical-step checks, or answer correctly with weak supporting reasoning. ChemCoTBench-V2 enables fine-grained model comparison and identifies the concrete step at which the trace first violates the verifier.

Shengchao Liu, Weitao Du, Yanjing Li et al.

Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these scientific problems, molecules serve as the fundamental building blocks, and machine learning has emerged as a highly effective and powerful tool for modeling their geometric structures. Nevertheless, due to the rapidly evolving process of the field and the knowledge gap between science (e.g., physics, chemistry, & biology) and machine learning communities, a benchmarking study on geometrical representation for such data has not been conducted. To address such an issue, in this paper, we first provide a unified view of the current symmetry-informed geometric methods, classifying them into three main categories: invariance, equivariance with spherical frame basis, and equivariance with vector frame basis. Then we propose a platform, coined Geom3D, which enables benchmarking the effectiveness of geometric strategies. Geom3D contains 16 advanced symmetry-informed geometric representation models and 14 geometric pretraining methods over 46 diverse datasets, including small molecules, proteins, and crystalline materials. We hope that Geom3D can, on the one hand, eliminate barriers for machine learning researchers interested in exploring scientific problems; and, on the other hand, provide valuable guidance for researchers in computational chemistry, structural biology, and materials science, aiding in the informed selection of representation techniques for specific applications.

Fang Sun, Zhihao Zhan, Hongyu Guo et al.

Designing molecules that bind to specific target proteins is a fundamental task in drug discovery. Recent models leverage geometric constraints to generate ligand molecules that bind cohesively with specific protein pockets. However, these models cannot effectively generate 3D molecules with 2D skeletal curtailments and property constraints, which are pivotal to drug potency and development. To tackle this challenge, we propose GraphVF, a variational flow-based framework that combines 2D topology and 3D geometry, for controllable generation of binding 3D molecules. Empirically, our method achieves state-of-the-art binding affinity and realistic sub-structural layouts for protein-specific generation. In particular, GraphVF represents the first controllable geometry-aware, protein-specific molecule generation method, which can generate binding 3D molecules with tailored sub-structures and physio-chemical properties. Our code is available at https://github.com/Franco-Solis/GraphVF-code.

Shengchao Liu, Hongyu Guo, Jian Tang

Molecular representation pretraining is critical in various applications for drug and material discovery due to the limited number of labeled molecules, and most existing work focuses on pretraining on 2D molecular graphs. However, the power of pretraining on 3D geometric structures has been less explored. This is owing to the difficulty of finding a sufficient proxy task that can empower the pretraining to effectively extract essential features from the geometric structures. Motivated by the dynamic nature of 3D molecules, where the continuous motion of a molecule in the 3D Euclidean space forms a smooth potential energy surface, we propose GeoSSL, a 3D coordinate denoising pretraining framework to model such an energy landscape. Further by leveraging an SE(3)-invariant score matching method, we propose GeoSSL-DDM in which the coordinate denoising proxy task is effectively boiled down to denoising the pairwise atomic distances in a molecule. Our comprehensive experiments confirm the effectiveness and robustness of our proposed method.

Shengchao Liu, Yanjing Li, Zhuoxinran Li et al.

Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level functionalities. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP which aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that creates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We quantitatively verify the effectiveness of ProteinDT on three challenging tasks: (1) over 90% accuracy for text-guided protein generation; (2) best hit ratio on 12 zero-shot text-guided protein editing tasks; (3) superior performance on four out of six protein property prediction benchmarks.

Xinyu Yuan, Xixian Liu, Jianan Zhao et al.

Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved conditions. A promising recent direction leverages large language models (LLMs) as "virtual cell" simulators-using stepwise, knowledge-grounded mechanistic reasoning to infer differential expression-pointing toward an interpretable, knowledge-driven paradigm that transcends purely data-driven approaches. However, we find that plausibility is not prediction: despite producing biologically plausible explanations, these methods fail to capture perturbation-specific effects: systematically overestimating differential expression, often underperforming a simple gene-frequency baseline in aggregate evaluations, and collapsing to chance-level performance at the per-gene level. This reveals a reliance on intrinsic gene response tendencies rather than true perturbation reasoning. We trace this failure to how evidence is presented: existing methods evaluate perturbation-gene pairs in isolation, without exposing how related perturbations differ in their effects on the same gene. To address this limitation, we introduce CORE (Contrastive Organization of Relational Evidence), which reframes prediction as a comparison task by organizing evidence into positive and negative outcomes from related perturbations. Using a biomedical knowledge graph for evidence retrieval, CORE improves calibration and substantially boosts perturbation-specific prediction in both LLM-based and non-LLM settings: for example, on drug-perturbation data, CORE-Reasoning improves Qwen3.5-9B aggregate metrics by up to 28.6%, while on generic perturbation data, CORE-Voting raises macro-per-gene AUROC from chance to 0.703 in average across four cell lines. This highlights contrastive evidence organization as essential to reliable LLM-based perturbation reasoning

Shengchao Liu, Divin Yan, Weitao Du et al.

Artificial intelligence models have shown great potential in structure-based drug design, generating ligands with high binding affinities. However, existing models have often overlooked a crucial physical constraint: atoms must maintain a minimum pairwise distance to avoid separation violation, a phenomenon governed by the balance of attractive and repulsive forces. To mitigate such separation violations, we propose NucleusDiff. It models the interactions between atomic nuclei and their surrounding electron clouds by enforcing the distance constraint between the nuclei and manifolds. We quantitatively evaluate NucleusDiff using the CrossDocked2020 dataset and a COVID-19 therapeutic target, demonstrating that NucleusDiff reduces violation rate by up to 100.00% and enhances binding affinity by up to 22.16%, surpassing state-of-the-art models for structure-based drug design. We also provide qualitative analysis through manifold sampling, visually confirming the effectiveness of NucleusDiff in reducing separation violations and improving binding affinities.

Hongyu Guo, Kun Xie, Mehdi Keyvan-Ekbatani

Lane changes are complex driving behaviors and frequently involve safety-critical situations. This study aims to develop a lane-change-related evasive behavior model, which can facilitate the development of safety-aware traffic simulations and predictive collision avoidance systems. Large-scale connected vehicle data from the Safety Pilot Model Deployment (SPMD) program were used for this study. A new surrogate safety measure, two-dimensional time-to-collision (2D-TTC), was proposed to identify the safety-critical situations during lane changes. The validity of 2D-TTC was confirmed by showing a high correlation between the detected conflict risks and the archived crashes. A deep deterministic policy gradient (DDPG) algorithm, which could learn the sequential decision-making process over continuous action spaces, was used to model the evasive behaviors in the identified safety-critical situations. The results showed the superiority of the proposed model in replicating both the longitudinal and lateral evasive behaviors.

Stephen Obadinma, Hongyu Guo, Xiaodan Zhu

Recent work has demonstrated that using parameter efficient tuning techniques such as prefix tuning (or P-tuning) on pretrained language models can yield performance that is comparable or superior to fine-tuning while dramatically reducing trainable parameters. Nevertheless, the effectiveness of such methods under the context of data augmentation, a common strategy to improve learning under low data regimes, has not been fully explored. In this paper, we examine the effectiveness of several popular task-agnostic data augmentation techniques, i.e., EDA, Back Translation, and Mixup, when using two general parameter efficient tuning methods, P-tuning v2 and LoRA, under data scarcity. We show that data augmentation can be used to boost the performance of P-tuning and LoRA models, but the effectiveness of each technique varies and certain methods can lead to a notable degradation in performance, particularly when using larger models and on harder tasks. We further analyze the sentence representations of P-tuning compared to fine-tuning to help understand the above behaviour, and reveal how P-tuning generally presents a more limited ability to separate the sentence embeddings from different classes of augmented data. In addition, it displays poorer performance on heavily altered data. However, we demonstrate that by adding a simple contrastive loss function it can help mitigate such issues for prefix tuning, resulting in sizable improvements to augmented data performance.

Xinyu Yuan, Xixian Liu, Ya Shi Zhang et al.

Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).

Jianan Zhao, Xixian Liu, Zhihao Zhan et al.

Long-context DNA models are limited by token-mixing cost and by how compression allocates representational budget across the genome. Existing approaches operate close to base-pair resolution, apply fixed downsampling, or learn content-dependent chunks without an explicit genomic budget, making long-context pretraining expensive and difficult to control. We introduce GeneZip, a region-aware DNA compression framework that combines H-Net-style dynamic routing with a Region-Aware Ratio (RAR) objective and bounded routing. GeneZip uses static gene-structure annotations during compression training to specify region-wise base-pairs-per-token (BPT) targets; at inference time, it compresses raw unseen DNA without annotations. GeneZip provides three main benefits. First, it is effective: GeneZip variants achieve the best validation PPL among encoder-based compressors, with GeneZip-70M operating at 137.6 BPT, and across four reproducible DNALongBench tasks--contact map prediction, eQTL prediction, enhancer-target gene prediction, and transcription-initiation signal prediction--GeneZip obtains the best average rank among compared sequence models. Second, it is redundancy-aware: a post-hoc RepeatMasker/TRF analysis shows that, without repeat supervision, GeneZip assigns higher local BPT to TE-derived interspersed repeats and tandem repeats, two major classes of repetitive DNA sequence redundancy. Third, it is efficient: by reducing the effective token-mixing length, GeneZip enables longer-context and larger-capacity pretraining, including 128K-context and 636M-parameter variants on a single A100 80GB GPU, and fine-tunes the eQTL task 50.4x faster than JanusDNA (50 vs. 2520 minutes). These results establish GeneZip as an effective, redundancy-aware, and efficient compression interface for long-context DNA modeling.

Hongyu Guo

Wheat is one of the most significant crop species with an annual worldwide grain production of 700 million tonnes. Assessing the production of wheat spikes can help us measure the grain production. Thus, detecting and characterizing spikes from images of wheat fields is an essential component in a wheat breeding process. In this study, we propose three wheat head counting networks (WHCNet\_1, WHCNet\_2 and WHCNet\_3) to accurately estimate the wheat head count from an individual image and construct high quality density map, which illustrates the distribution of wheat heads in the image. The WHCNets are composed of two major components: a convolutional neural network (CNN) as the front-end for wheat head image feature extraction and a CNN with skip connections for the back-end to generate high-quality density maps. The dataset used in this study is the Global Wheat Head Detection (GWHD) dataset, which is a large, diverse, and well-labelled dataset of wheat images and built by a joint international collaborative effort. We compare our methods with CSRNet, a deep learning method which developed for highly congested scenes understanding and performing accurate count estimation as well as presenting high quality density maps. By taking the advantage of the skip connections between CNN layers, WHCNets integrate features from low CNN layers to high CNN layers, thus, the output density maps have both high spatial resolution and detailed representations of the input images. The experiments showed that our methods outperformed CSRNet in terms of the evaluation metrics, mean absolute error (MAE) and the root mean squared error (RMSE) with smaller model sizes. The code has been deposited on GitHub (\url{https://github.com/hyguozz}).

Hongyu Guo, Sun Sun

Augmented graphs play a vital role in regularizing Graph Neural Networks (GNNs), which leverage information exchange along edges in graphs, in the form of message passing, for learning. Due to their effectiveness, simple edge and node manipulations (e.g., addition and deletion) have been widely used in graph augmentation. Nevertheless, such common augmentation techniques can dramatically change the semantics of the original graph, causing overaggressive augmentation and thus under-fitting in the GNN learning. To address this problem arising from dropping or adding graph edges and nodes, we propose SoftEdge, which assigns random weights to a portion of the edges of a given graph for augmentation. The synthetic graph generated by SoftEdge maintains the same nodes and their connectivities as the original graph, thus mitigating the semantic changes of the original graph. We empirically show that this simple method obtains superior accuracy to popular node and edge manipulation approaches and notable resilience to the accuracy degradation with the GNN depth.

Zhanghan Ni, Yanjing Li, Zeju Qiu et al.

Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43\% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8\% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available at: https://github.com/ZhanghanNi/RigidSSL.git.

Zixuan Liu, Ziqiao Wang, Hongyu Guo et al.

Mixup, which creates synthetic training instances by linearly interpolating random sample pairs, is a simple and yet effective regularization technique to boost the performance of deep models trained with SGD. In this work, we report a previously unobserved phenomenon in Mixup training: on a number of standard datasets, the performance of Mixup-trained models starts to decay after training for a large number of epochs, giving rise to a U-shaped generalization curve. This behavior is further aggravated when the size of original dataset is reduced. To help understand such a behavior of Mixup, we show theoretically that Mixup training may introduce undesired data-dependent label noises to the synthesized data. Via analyzing a least-square regression problem with a random feature model, we explain why noisy labels may cause the U-shaped curve to occur: Mixup improves generalization through fitting the clean patterns at the early training stage, but as training progresses, Mixup becomes over-fitting to the noise in the synthetic data. Extensive experiments are performed on a variety of benchmark datasets, validating this explanation.

Ziqi Chen, Martin Renqiang Min, Hongyu Guo et al.

T cells monitor the health status of cells by identifying foreign peptides displayed on their surface. T-cell receptors (TCRs), which are protein complexes found on the surface of T cells, are able to bind to these peptides. This process is known as TCR recognition and constitutes a key step for immune response. Optimizing TCR sequences for TCR recognition represents a fundamental step towards the development of personalized treatments to trigger immune responses killing cancerous or virus-infected cells. In this paper, we formulated the search for these optimized TCRs as a reinforcement learning (RL) problem, and presented a framework TCRPPO with a mutation policy using proximal policy optimization. TCRPPO mutates TCRs into effective ones that can recognize given peptides. TCRPPO leverages a reward function that combines the likelihoods of mutated sequences being valid TCRs measured by a new scoring function based on deep autoencoders, with the probabilities of mutated sequences recognizing peptides from a peptide-TCR interaction predictor. We compared TCRPPO with multiple baseline methods and demonstrated that TCRPPO significantly outperforms all the baseline methods to generate positive binding and valid TCRs. These results demonstrate the potential of TCRPPO for both precision immunotherapy and peptide-recognizing TCR motif discovery.

Stephen Obadinma, Xiaodan Zhu, Hongyu Guo

In this work, we highlight and perform a comprehensive study on calibration attacks, a form of adversarial attacks that aim to trap victim models to be heavily miscalibrated without altering their predicted labels, hence endangering the trustworthiness of the models and follow-up decision making based on their confidence. We propose four typical forms of calibration attacks: underconfidence, overconfidence, maximum miscalibration, and random confidence attacks, conducted in both black-box and white-box setups. We demonstrate that the attacks are highly effective on both convolutional and attention-based models: with a small number of queries, they seriously skew confidence without changing the predictive performance. Given the potential danger, we further investigate the effectiveness of a wide range of adversarial defence and recalibration methods, including our proposed defences specifically designed for calibration attacks to mitigate the harm. From the ECE and KS scores, we observe that there are still significant limitations in handling calibration attacks. To the best of our knowledge, this is the first dedicated study that provides a comprehensive investigation on calibration-focused attacks. We hope this study helps attract more attention to these types of attacks and hence hamper their potential serious damages. To this end, this work also provides detailed analyses to understand the characteristics of the attacks. Our code is available at https://github.com/PhenetOs/CalibrationAttack

Xiangzhao Hao, Kuan Zhu, Hongyu Guo et al.

Using natural language to query visual information is a fundamental need in real-world applications. Text-Image Retrieval (TIR) retrieves a target image from a gallery based on an image-level description, while Referring Expression Comprehension (REC) localizes a target object within a given image using an instance-level description. However, real-world applications often present more complex demands. Users typically query an instance-level description across a large gallery and expect to receive both relevant image and the corresponding instance location. In such scenarios, TIR struggles with fine-grained descriptions and object-level localization, while REC is limited in its ability to efficiently search large galleries and lacks an effective ranking mechanism. In this paper, we introduce a new task called \textbf{Referring Expression Instance Retrieval (REIR)}, which supports both instance-level retrieval and localization based on fine-grained referring expressions. First, we propose a large-scale benchmark for REIR, named REIRCOCO, constructed by prompting advanced vision-language models to generate high-quality referring expressions for instances in the MSCOCO and RefCOCO datasets. Second, we present a baseline method, Contrastive Language-Instance Alignment with Relation Experts (CLARE), which employs a dual-stream architecture to address REIR in an end-to-end manner. Given a referring expression, the textual branch encodes it into a query embedding. The visual branch detects candidate objects and extracts their instance-level visual features. The most similar candidate to the query is selected for bounding box prediction. CLARE is first trained on object detection and REC datasets to establish initial grounding capabilities, then optimized via Contrastive Language-Instance Alignment (CLIA) for improved retrieval across images. We will release our code and benchmark publicly.

Haorui Li, Weitao Du, Yuqiang Li et al.

Transformer-based autoregressive models have emerged as a unifying paradigm across modalities such as text and images, but their extension to 3D molecule generation remains underexplored. The gap stems from two fundamental challenges: (1) tokenizing molecules into a canonical 1D sequence of tokens that is invariant to both SE(3) transformations and atom index permutations, and (2) designing an architecture capable of modeling hybrid atom-based tokens that couple discrete atom types with continuous 3D coordinates. To address these challenges, we introduce InertialAR. InertialAR devises a canonical tokenization that aligns molecules to their inertial frames and reorders atoms to ensure SE(3) and permutation invariance. Moreover, InertialAR equips the attention mechanism with geometric awareness via geometric rotary positional encoding (GeoRoPE). In addition, it utilizes a hierarchical autoregressive paradigm to predict the next atom-based token, predicting the atom type first and then its 3D coordinates via Diffusion loss. Experimentally, InertialAR achieves state-of-the-art performance on 7 of the 10 evaluation metrics for unconditional molecule generation across QM9, GEOM-Drugs, and B3LYP. Moreover, it significantly outperforms strong baselines in controllable generation for targeted chemical functionality, attaining state-of-the-art results across all 5 metrics.

Yadong Li, Jun Liu, Tao Zhang et al.

We introduce Baichuan-Omni-1.5, an omni-modal model that not only has omni-modal understanding capabilities but also provides end-to-end audio generation capabilities. To achieve fluent and high-quality interaction across modalities without compromising the capabilities of any modality, we prioritized optimizing three key aspects. First, we establish a comprehensive data cleaning and synthesis pipeline for multimodal data, obtaining about 500B high-quality data (text, audio, and vision). Second, an audio-tokenizer (Baichuan-Audio-Tokenizer) has been designed to capture both semantic and acoustic information from audio, enabling seamless integration and enhanced compatibility with MLLM. Lastly, we designed a multi-stage training strategy that progressively integrates multimodal alignment and multitask fine-tuning, ensuring effective synergy across all modalities. Baichuan-Omni-1.5 leads contemporary models (including GPT4o-mini and MiniCPM-o 2.6) in terms of comprehensive omni-modal capabilities. Notably, it achieves results comparable to leading models such as Qwen2-VL-72B across various multimodal medical benchmarks.

Jiarui Lu, Xiaoyin Chen, Stephen Zhewen Lu et al.

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally expensive. Recently, deep generative models have shown promise in generating protein conformations as a more efficient alternative. However, these methods predominantly rely on the diffusion process within a 3D geometric space, which typically centers around the vicinity of metastable states and is often inefficient in terms of runtime. In this paper, we introduce Structure Language Modeling (SLM) as a novel framework for efficient protein conformation generation. Specifically, the protein structures are first encoded into a compact latent space using a discrete variational auto-encoder, followed by conditional language modeling that effectively captures sequence-specific conformation distributions. This enables a more efficient and interpretable exploration of diverse ensemble modes compared to existing methods. Based on this general framework, we instantiate SLM with various popular LM architectures as well as proposing the ESMDiff, a novel BERT-like structure language model fine-tuned from ESM3 with masked diffusion. We verify our approach in various scenarios, including the equilibrium dynamics of BPTI, conformational change pairs, and intrinsically disordered proteins. SLM provides a highly efficient solution, offering a 20-100x speedup than existing methods in generating diverse conformations, shedding light on promising avenues for future research.

Yiwei Lu, Guojun Zhang, Sun Sun et al.

In self-supervised contrastive learning, a widely-adopted objective function is InfoNCE, which uses the heuristic cosine similarity for the representation comparison, and is closely related to maximizing the Kullback-Leibler (KL)-based mutual information. In this paper, we aim at answering two intriguing questions: (1) Can we go beyond the KL-based objective? (2) Besides the popular cosine similarity, can we design a better similarity function? We provide answers to both questions by generalizing the KL-based mutual information to the $f$-Mutual Information in Contrastive Learning ($f$-MICL) using the $f$-divergences. To answer the first question, we provide a wide range of $f$-MICL objectives which share the nice properties of InfoNCE (e.g., alignment and uniformity), and meanwhile result in similar or even superior performance. For the second question, assuming that the joint feature distribution is proportional to the Gaussian kernel, we derive an $f$-Gaussian similarity with better interpretability and empirical performance. Finally, we identify close relationships between the $f$-MICL objective and several popular InfoNCE-based objectives. Using benchmark tasks from both vision and natural language, we empirically evaluate $f$-MICL with different $f$-divergences on various architectures (SimCLR, MoCo, and MoCo v3) and datasets. We observe that $f$-MICL generally outperforms the benchmarks and the best-performing $f$-divergence is task and dataset dependent.

Luke Rivard, Sun Sun, Hongyu Guo et al.

We introduce NeuralOS, a neural framework that simulates graphical user interfaces (GUIs) of operating systems by directly predicting screen frames in response to user inputs such as mouse movements, clicks, and keyboard events. NeuralOS combines a recurrent neural network (RNN), which tracks computer state, with a diffusion-based neural renderer that generates screen images. The model is trained on a large-scale dataset of Ubuntu XFCE recordings, which include both randomly generated interactions and realistic interactions produced by AI agents. Experiments show that NeuralOS successfully renders realistic GUI sequences, accurately captures mouse interactions, and reliably predicts state transitions like application launches. Although modeling fine-grained keyboard interactions precisely remains challenging, NeuralOS offers a step toward creating fully adaptive, generative neural interfaces for future human-computer interaction systems.

Mingjing Li, Huihui Zhou, Xiaofeng Xu et al.

There is a growing necessity for edge training to adapt to dynamically changing environment. Neuromorphic computing represents a significant pathway for high-efficiency intelligent computation in energy-constrained edges, but existing neuromorphic architectures lack the ability of directly training spiking neural networks (SNNs) based on backpropagation. We develop a multi-core neuromorphic architecture with Feedforward-Propagation, Back-Propagation, and Weight-Gradient engines in each core, supporting high efficient parallel computing at both the engine and core levels. It combines various data flows and sparse computation optimization by fully leveraging the sparsity in SNN training, obtaining a high energy efficiency of 1.05TFLOPS/W@ FP16 @ 28nm, 55 ~ 85% reduction of DRAM access compared to A100 GPU in SNN trainings, and a 20-core deep SNN training and a 5-worker federated learning on FPGAs. Our study develops the first multi-core neuromorphic architecture supporting the direct SNN training, facilitating the neuromorphic computing in edge-learnable applications.

Félix Therrien, Jamal Abou Haibeh, Divya Sharma et al.

Solid-state electrolyte batteries are expected to replace liquid electrolyte lithium-ion batteries in the near future thanks to their higher theoretical energy density and improved safety. However, their adoption is currently hindered by their lower effective ionic conductivity, a quantity that governs charge and discharge rates. Identifying highly ion-conductive materials using conventional theoretical calculations and experimental validation is both time-consuming and resource-intensive. While machine learning holds the promise to expedite this process, relevant ionic conductivity and structural data is scarce. Here, we present OBELiX, a database of $\sim$600 synthesized solid electrolyte materials and their experimentally measured room temperature ionic conductivities gathered from literature and curated by domain experts. Each material is described by their measured composition, space group and lattice parameters. A full-crystal description in the form of a crystallographic information file (CIF) is provided for $\sim$320 structures for which atomic positions were available. We discuss various statistics and features of the dataset and provide training and testing splits carefully designed to avoid data leakage. Finally, we benchmark seven existing ML models on the task of predicting ionic conductivity and discuss their performance. The goal of this work is to facilitate the use of machine learning for solid-state electrolyte materials discovery.

Hongyu Guo

Analogical reasoning, the transfer of relational structures across contexts (e.g., planet is to sun as electron is to nucleus), is fundamental to scientific discovery. Yet human insight is often constrained by domain expertise and surface-level biases, limiting access to deeper, structure-driven analogies both within and across disciplines. Large language models (LLMs), trained on vast cross-domain data, present a promising yet underexplored tool for analogical reasoning in science. Here, we demonstrate that LLMs can generate novel battery materials by (1) retrieving cross-domain analogs and analogy-guided exemplars to steer exploration beyond conventional dopant substitutions, and (2) constructing in-domain analogical templates from few labeled examples to guide targeted exploitation. These explicit analogical reasoning strategies yield candidates outside established compositional spaces and outperform standard prompting baselines. Our findings position LLMs as interpretable, expert-like hypothesis generators that leverage analogy-driven generalization for scientific innovation.

Hongyu Guo, Kuan Zhu, Xiangzhao Hao et al.

Few-shot fine-grained visual classification (FGVC) aims to leverage limited data to enable models to discriminate subtly distinct categories. Recent works mostly finetuned the pre-trained visual language models to achieve performance gain, yet suffering from overfitting and weak generalization. To deal with this, we introduce UniFGVC, a universal training-free framework that reformulates few-shot FGVC as multimodal retrieval. First, we propose the Category-Discriminative Visual Captioner (CDV-Captioner) to exploit the open-world knowledge of multimodal large language models (MLLMs) to generate a structured text description that captures the fine-grained attribute features distinguishing closely related classes. CDV-Captioner uses chain-of-thought prompting and visually similar reference images to reduce hallucination and enhance discrimination of generated captions. Using it we can convert each image into an image-description pair, enabling more comprehensive feature representation, and construct the multimodal category templates using few-shot samples for the subsequent retrieval pipeline. Then, off-the-shelf vision and text encoders embed query and template pairs, and FGVC is accomplished by retrieving the nearest template in the joint space. UniFGVC ensures broad compatibility with diverse MLLMs and encoders, offering reliable generalization and adaptability across few-shot FGVC scenarios. Extensive experiments on 12 FGVC benchmarks demonstrate its consistent superiority over prior few-shot CLIP-based methods and even several fully-supervised MLLMs-based approaches.

Yuanhao Shen, Daniel Xavier de Sousa, Ricardo Marçal et al.

Recent advancements in Large Language Models (LLMs) have revealed their impressive ability to perform multi-step, logic-driven reasoning across complex domains, positioning them as powerful tools and collaborators in scientific discovery while challenging the long-held view that inspiration-driven ideation is uniquely human. However, the lack of a dedicated benchmark that evaluates LLMs' ability to develop ideas in Interdisciplinary Research (IDR) settings poses a critical barrier to fully understanding their strengths and limitations. To address this gap, we introduce IDRBench -- a pioneering benchmark featuring an expert annotated dataset and a suite of tasks tailored to evaluate LLMs' capabilities in proposing valuable research ideas from different scientific domains for interdisciplinary research. This benchmark aims to provide a systematic framework for assessing LLM performance in complex, cross-domain scientific research. Our dataset consists of scientific publications sourced from the ArXiv platform covering six distinct disciplines, and is annotated by domain experts with diverse academic backgrounds. To ensure high-quality annotations, we emphasize clearly defined dimensions that characterize authentic interdisciplinary research. The design of evaluation tasks in IDRBench follows a progressive, real-world perspective, reflecting the natural stages of interdisciplinary research development, including 1) IDR Paper Identification, 2) IDR Idea Integration, and 3) IDR Idea Recommendation. Using IDRBench, we construct baselines across 10 LLMs and observe that despite fostering some level of IDR awareness, LLMs still struggle to produce quality IDR ideas. These findings could not only spark new research directions, but also help to develop next-generation LLMs that excel in interdisciplinary research.

Max Ku, Sun Sun, Hongyu Guo et al.

We introduce DisProtEdit, a controllable protein editing framework that leverages dual-channel natural language supervision to learn disentangled representations of structural and functional properties. Unlike prior approaches that rely on joint holistic embeddings, DisProtEdit explicitly separates semantic factors, enabling modular and interpretable control. To support this, we construct SwissProtDis, a large-scale multimodal dataset where each protein sequence is paired with two textual descriptions, one for structure and one for function, automatically decomposed using a large language model. DisProtEdit aligns protein and text embeddings using alignment and uniformity objectives, while a disentanglement loss promotes independence between structural and functional semantics. At inference time, protein editing is performed by modifying one or both text inputs and decoding from the updated latent representation. Experiments on protein editing and representation learning benchmarks demonstrate that DisProtEdit performs competitively with existing methods while providing improved interpretability and controllability. On a newly constructed multi-attribute editing benchmark, the model achieves a both-hit success rate of up to 61.7%, highlighting its effectiveness in coordinating simultaneous structural and functional edits.

Shengchao Liu, Weitao Du, Hannan Xu et al.

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of improving the efficiency of MD simulations through better numerical methods and, more recently, by utilizing machine learning (ML) methods. Yet, challenges remain, such as accurate modeling of extended-timescale simulations. To address this issue, we propose NeuralMD, the first ML surrogate that can facilitate numerical MD and provide accurate simulations in protein-ligand binding dynamics. We propose a principled approach that incorporates a novel physics-informed multi-grained group symmetric framework. Specifically, we propose (1) the BindingNet model that satisfies group symmetry using vector frames and captures the multi-level protein-ligand interactions, and (2) an augmented neural differential equation solver that learns the trajectory under Newtonian mechanics. For the experiment, we design ten single-trajectory and three multi-trajectory binding simulation tasks. We demonstrate the efficiency and effectiveness of NeuralMD, achieving over 1K$\times$ speedup compared to standard numerical MD simulations. NeuralMD also outperforms all other ML approaches, achieving up to 15$\times$ reduction in reconstruction error and 70% increase in validity. Additionally, we qualitatively illustrate that the oscillations in the predicted trajectories align more closely with ground-truth dynamics than those of other machine-learning methods. We believe NeuralMD paves the foundation for a new research paradigm in simulating protein-ligand dynamics.

Shengchao Liu, Jiongxiao Wang, Yijin Yang et al.

Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reaction and retrosynthesis. While drug editing, a critical task in the drug discovery pipeline, remains largely unexplored. To bridge this gap, we propose ChatDrug, a framework to facilitate the systematic investigation of drug editing using LLMs. ChatDrug jointly leverages a prompt module, a retrieval and domain feedback (ReDF) module, and a conversation module to streamline effective drug editing. We empirically show that ChatDrug reaches the best performance on 33 out of 39 drug editing tasks, encompassing small molecules, peptides, and proteins. We further demonstrate, through 10 case studies, that ChatDrug can successfully identify the key substructures (e.g., the molecule functional groups, peptide motifs, and protein structures) for manipulation, generating diverse and valid suggestions for drug editing. Promisingly, we also show that ChatDrug can offer insightful explanations from a domain-specific perspective, enhancing interpretability and enabling informed decision-making. This research sheds light on the potential of ChatGPT and conversational LLMs for drug editing. It paves the way for a more efficient and collaborative drug discovery pipeline, contributing to the advancement of pharmaceutical research and development.

Shengchao Liu, Weitao Du, Zhiming Ma et al.

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

Hongyu Guo, Yongyi Mao

We present a simple and yet effective interpolation-based regularization technique, aiming to improve the generalization of Graph Neural Networks (GNNs) on supervised graph classification. We leverage Mixup, an effective regularizer for vision, where random sample pairs and their labels are interpolated to create synthetic images for training. Unlike images with grid-like coordinates, graphs have arbitrary structure and topology, which can be very sensitive to any modification that alters the graph's semantic meanings. This posts two unanswered questions for Mixup-like regularization schemes: Can we directly mix up a pair of graph inputs? If so, how well does such mixing strategy regularize the learning of GNNs? To answer these two questions, we propose ifMixup, which first adds dummy nodes to make two graphs have the same input size and then simultaneously performs linear interpolation between the aligned node feature vectors and the aligned edge representations of the two graphs. We empirically show that such simple mixing schema can effectively regularize the classification learning, resulting in superior predictive accuracy to popular graph augmentation and GNN methods.

Shengchao Liu, Hanchen Wang, Weiyang Liu et al.

Molecular graph representation learning is a fundamental problem in modern drug and material discovery. Molecular graphs are typically modeled by their 2D topological structures, but it has been recently discovered that 3D geometric information plays a more vital role in predicting molecular functionalities. However, the lack of 3D information in real-world scenarios has significantly impeded the learning of geometric graph representation. To cope with this challenge, we propose the Graph Multi-View Pre-training (GraphMVP) framework where self-supervised learning (SSL) is performed by leveraging the correspondence and consistency between 2D topological structures and 3D geometric views. GraphMVP effectively learns a 2D molecular graph encoder that is enhanced by richer and more discriminative 3D geometry. We further provide theoretical insights to justify the effectiveness of GraphMVP. Finally, comprehensive experiments show that GraphMVP can consistently outperform existing graph SSL methods.

Hongyu Guo

Label Smoothing (LS) improves model generalization through penalizing models from generating overconfident output distributions. For each training sample the LS strategy smooths the one-hot encoded training signal by distributing its distribution mass over the non-ground truth classes. We extend this technique by considering example pairs, coined PLS. PLS first creates midpoint samples by averaging random sample pairs and then learns a smoothing distribution during training for each of these midpoint samples, resulting in midpoints with high uncertainty labels for training. We empirically show that PLS significantly outperforms LS, achieving up to 30% of relative classification error reduction. We also visualize that PLS produces very low winning softmax scores for both in and out of distribution samples.

Sun Sun, Hongyu Guo

Leveraging the framework of Optimal Transport, we introduce a new family of generative autoencoders with a learnable prior, called Symmetric Wasserstein Autoencoders (SWAEs). We propose to symmetrically match the joint distributions of the observed data and the latent representation induced by the encoder and the decoder. The resulting algorithm jointly optimizes the modelling losses in both the data and the latent spaces with the loss in the data space leading to the denoising effect. With the symmetric treatment of the data and the latent representation, the algorithm implicitly preserves the local structure of the data in the latent space. To further improve the quality of the latent representation, we incorporate a reconstruction loss into the objective, which significantly benefits both the generation and reconstruction. We empirically show the superior performance of SWAEs over the state-of-the-art generative autoencoders in terms of classification, reconstruction, and generation.

Hangrui Bi, Hengyi Wang, Chence Shi et al.

Reliably predicting the products of chemical reactions presents a fundamental challenge in synthetic chemistry. Existing machine learning approaches typically produce a reaction product by sequentially forming its subparts or intermediate molecules. Such autoregressive methods, however, not only require a pre-defined order for the incremental construction but preclude the use of parallel decoding for efficient computation. To address these issues, we devise a non-autoregressive learning paradigm that predicts reaction in one shot. Leveraging the fact that chemical reactions can be described as a redistribution of electrons in molecules, we formulate a reaction as an arbitrary electron flow and predict it with a novel multi-pointer decoding network. Experiments on the USPTO-MIT dataset show that our approach has established a new state-of-the-art top-1 accuracy and achieves at least 27 times inference speedup over the state-of-the-art methods. Also, our predictions are easier for chemists to interpret owing to predicting the electron flows.

Minghao Xu, Hang Wang, Bingbing Ni et al.

This paper studies unsupervised/self-supervised whole-graph representation learning, which is critical in many tasks such as molecule properties prediction in drug and material discovery. Existing methods mainly focus on preserving the local similarity structure between different graph instances but fail to discover the global semantic structure of the entire data set. In this paper, we propose a unified framework called Local-instance and Global-semantic Learning (GraphLoG) for self-supervised whole-graph representation learning. Specifically, besides preserving the local similarities, GraphLoG introduces the hierarchical prototypes to capture the global semantic clusters. An efficient online expectation-maximization (EM) algorithm is further developed for learning the model. We evaluate GraphLoG by pre-training it on massive unlabeled graphs followed by fine-tuning on downstream tasks. Extensive experiments on both chemical and biological benchmark data sets demonstrate the effectiveness of the proposed approach.

Hongyu Guo

Label Smoothing (LS) is an effective regularizer to improve the generalization of state-of-the-art deep models. For each training sample the LS strategy smooths the one-hot encoded training signal by distributing its distribution mass over the non ground-truth classes, aiming to penalize the networks from generating overconfident output distributions. This paper introduces a novel label smoothing technique called Pairwise Label Smoothing (PLS). The PLS takes a pair of samples as input. Smoothing with a pair of ground-truth labels enables the PLS to preserve the relative distance between the two truth labels while further soften that between the truth labels and the other targets, resulting in models producing much less confident predictions than the LS strategy. Also, unlike current LS methods, which typically require to find a global smoothing distribution mass through cross-validation search, PLS automatically learns the distribution mass for each input pair during training. We empirically show that PLS significantly outperforms LS and the baseline models, achieving up to 30% of relative classification error reduction. We also visually show that when achieving such accuracy gains the PLS tends to produce very low winning softmax scores.

Chence Shi, Minkai Xu, Hongyu Guo et al.

A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of reaction templates, which are very computationally expensive and also suffer from the problem of coverage. In this paper, we propose a novel template-free approach called G2Gs by transforming a target molecular graph into a set of reactant molecular graphs. G2Gs first splits the target molecular graph into a set of synthons by identifying the reaction centers, and then translates the synthons to the final reactant graphs via a variational graph translation framework. Experimental results show that G2Gs significantly outperforms existing template-free approaches by up to 63% in terms of the top-1 accuracy and achieves a performance close to that of state-of-the-art template based approaches, but does not require domain knowledge and is much more scalable.

Masoumeh Soflaei, Hongyu Guo, Ali Al-Bashabsheh et al.

We consider the problem of learning a neural network classifier. Under the information bottleneck (IB) principle, we associate with this classification problem a representation learning problem, which we call "IB learning". We show that IB learning is, in fact, equivalent to a special class of the quantization problem. The classical results in rate-distortion theory then suggest that IB learning can benefit from a "vector quantization" approach, namely, simultaneously learning the representations of multiple input objects. Such an approach assisted with some variational techniques, result in a novel learning framework, "Aggregated Learning", for classification with neural network models. In this framework, several objects are jointly classified by a single neural network. The effectiveness of this framework is verified through extensive experiments on standard image recognition and text classification tasks.

Hongyu Guo, Khalique Newaz, Scott Emrich et al.

As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally classifies the structures of proteins into pre-defined groups. We develop a weighted network that depicts the protein structures, and more importantly, we propose the first graphlet-based measure that applies to weighted networks. Further, we develop a deep neural network (DNN) composed of both convolutional and recurrent layers to use this measure for classification. Put together, our approach shows dramatic improvements in performance over existing graphlet-based approaches on 36 real datasets. Even comparing with the state-of-the-art approach, it almost halves the classification error. In addition to protein structure networks, our weighted-graphlet measure and DNN classifier can potentially be applied to classification of other weighted networks in computational biology as well as in other domains.

Junfan Chen, Richong Zhang, Yongyi Mao et al.

Distant supervision for relation extraction enables one to effectively acquire structured relations out of very large text corpora with less human efforts. Nevertheless, most of the prior-art models for such tasks assume that the given text can be noisy, but their corresponding labels are clean. Such unrealistic assumption is contradictory with the fact that the given labels are often noisy as well, thus leading to significant performance degradation of those models on real-world data. To cope with this challenge, we propose a novel label-denoising framework that combines neural network with probabilistic modelling, which naturally takes into account the noisy labels during learning. We empirically demonstrate that our approach significantly improves the current art in uncovering the ground-truth relation labels.

Guillaume P. Archambault, Yongyi Mao, Hongyu Guo et al.

In this work, we explain the working mechanism of MixUp in terms of adversarial training. We introduce a new class of adversarial training schemes, which we refer to as directional adversarial training, or DAT. In a nutshell, a DAT scheme perturbs a training example in the direction of another example but keeps its original label as the training target. We prove that MixUp is equivalent to a special subclass of DAT, in that it has the same expected loss function and corresponds to the same optimization problem asymptotically. This understanding not only serves to explain the effectiveness of MixUp, but also reveals a more general family of MixUp schemes, which we call Untied MixUp. We prove that the family of Untied MixUp schemes is equivalent to the entire class of DAT schemes. We establish empirically the existence of Untied Mixup schemes which improve upon MixUp.

Hongyu Guo, Yongyi Mao, Richong Zhang

Mixup, a recent proposed data augmentation method through linearly interpolating inputs and modeling targets of random samples, has demonstrated its capability of significantly improving the predictive accuracy of the state-of-the-art networks for image classification. However, how this technique can be applied to and what is its effectiveness on natural language processing (NLP) tasks have not been investigated. In this paper, we propose two strategies for the adaption of Mixup on sentence classification: one performs interpolation on word embeddings and another on sentence embeddings. We conduct experiments to evaluate our methods using several benchmark datasets. Our studies show that such interpolation strategies serve as an effective, domain independent data augmentation approach for sentence classification, and can result in significant accuracy improvement for both CNN and LSTM models.

Hongyu Guo, Yongyi Mao, Richong Zhang

MixUp is a recently proposed data-augmentation scheme, which linearly interpolates a random pair of training examples and correspondingly the one-hot representations of their labels. Training deep neural networks with such additional data is shown capable of significantly improving the predictive accuracy of the current art. The power of MixUp, however, is primarily established empirically and its working and effectiveness have not been explained in any depth. In this paper, we develop an understanding for MixUp as a form of "out-of-manifold regularization", which imposes certain "local linearity" constraints on the model's input space beyond the data manifold. This analysis enables us to identify a limitation of MixUp, which we call "manifold intrusion". In a nutshell, manifold intrusion in MixUp is a form of under-fitting resulting from conflicts between the synthetic labels of the mixed-up examples and the labels of original training data. Such a phenomenon usually happens when the parameters controlling the generation of mixing policies are not sufficiently fine-tuned on the training data. To address this issue, we propose a novel adaptive version of MixUp, where the mixing policies are automatically learned from the data using an additional network and objective function designed to avoid manifold intrusion. The proposed regularizer, AdaMixUp, is empirically evaluated on several benchmark datasets. Extensive experiments demonstrate that AdaMixUp improves upon MixUp when applied to the current art of deep classification models.

Hongyu Guo, Yongyi Mao, Ali Al-Bashabsheh et al.

Based on the notion of information bottleneck (IB), we formulate a quantization problem called "IB quantization". We show that IB quantization is equivalent to learning based on the IB principle. Under this equivalence, the standard neural network models can be viewed as scalar (single sample) IB quantizers. It is known, from conventional rate-distortion theory, that scalar quantizers are inferior to vector (multi-sample) quantizers. Such a deficiency then inspires us to develop a novel learning framework, AgrLearn, that corresponds to vector IB quantizers for learning with neural networks. Unlike standard networks, AgrLearn simultaneously optimizes against multiple data samples. We experimentally verify that AgrLearn can result in significant improvements when applied to several current deep learning architectures for image recognition and text classification. We also empirically show that AgrLearn can reduce up to 80% of the training samples needed for ResNet training.

Martin Renqiang Min, Hongyu Guo, Dinghan Shen

Parametric embedding methods such as parametric t-SNE (pt-SNE) have been widely adopted for data visualization and out-of-sample data embedding without further computationally expensive optimization or approximation. However, the performance of pt-SNE is highly sensitive to the hyper-parameter batch size due to conflicting optimization goals, and often produces dramatically different embeddings with different choices of user-defined perplexities. To effectively solve these issues, we present parametric t-distributed stochastic exemplar-centered embedding methods. Our strategy learns embedding parameters by comparing given data only with precomputed exemplars, resulting in a cost function with linear computational and memory complexity, which is further reduced by noise contrastive samples. Moreover, we propose a shallow embedding network with high-order feature interactions for data visualization, which is much easier to tune but produces comparable performance in contrast to a deep neural network employed by pt-SNE. We empirically demonstrate, using several benchmark datasets, that our proposed methods significantly outperform pt-SNE in terms of robustness, visual effects, and quantitative evaluations.

Hongyu Guo

While natural languages are compositional, how state-of-the-art neural models achieve compositionality is still unclear. We propose a deep network, which not only achieves competitive accuracy for text classification, but also exhibits compositional behavior. That is, while creating hierarchical representations of a piece of text, such as a sentence, the lower layers of the network distribute their layer-specific attention weights to individual words. In contrast, the higher layers compose meaningful phrases and clauses, whose lengths increase as the networks get deeper until fully composing the sentence.

Hongyu Guo, Colin Cherry, Jiang Su

We propose a multi-view network for text classification. Our method automatically creates various views of its input text, each taking the form of soft attention weights that distribute the classifier's focus among a set of base features. For a bag-of-words representation, each view focuses on a different subset of the text's words. Aggregating many such views results in a more discriminative and robust representation. Through a novel architecture that both stacks and concatenates views, we produce a network that emphasizes both depth and width, allowing training to converge quickly. Using our multi-view architecture, we establish new state-of-the-art accuracies on two benchmark tasks.