Li-Ping Liu

Gabriel Appleby, Linfeng Liu, Li-Ping Liu

Spatial interpolation is a class of estimation problems where locations with known values are used to estimate values at other locations, with an emphasis on harnessing spatial locality and trends. Traditional Kriging methods have strong Gaussian assumptions, and as a result, often fail to capture complexities within the data. Inspired by the recent progress of graph neural networks, we introduce Kriging Convolutional Networks (KCN), a method of combining the advantages of Graph Convolutional Networks (GCN) and Kriging. Compared to standard GCNs, KCNs make direct use of neighboring observations when generating predictions. KCNs also contain the Kriging method as a specific configuration. We further improve the model's performance by adding attention. Empirically, we show that this model outperforms GCNs and Kriging in several applications. The implementation of KCN using PyTorch is publicized at the GitHub repository: https://github.com/tufts-ml/kcn-torch.

Linfeng Liu, Xu Han, Dawei Zhou et al.

Subgraph similarity search, one of the core problems in graph search, concerns whether a target graph approximately contains a query graph. The problem is recently touched by neural methods. However, current neural methods do not consider pruning the target graph, though pruning is critically important in traditional calculations of subgraph similarities. One obstacle to applying pruning in neural methods is {the discrete property of pruning}. In this work, we convert graph pruning to a problem of node relabeling and then relax it to a differentiable problem. Based on this idea, we further design a novel neural network to approximate a type of subgraph distance: the subgraph edit distance (SED). {In particular, we construct the pruning component using a neural structure, and the entire model can be optimized end-to-end.} In the design of the model, we propose an attention mechanism to leverage the information about the query graph and guide the pruning of the target graph. Moreover, we develop a multi-head pruning strategy such that the model can better explore multiple ways of pruning the target graph. The proposed model establishes new state-of-the-art results across seven benchmark datasets. Extensive analysis of the model indicates that the proposed model can reasonably prune the target graph for SED computation. The implementation of our algorithm is released at our Github repo: https://github.com/tufts-ml/Prune4SED.

Han Gao, Xu Han, Jiaoyang Huang et al.

Recently the Transformer structure has shown good performances in graph learning tasks. However, these Transformer models directly work on graph nodes and may have difficulties learning high-level information. Inspired by the vision transformer, which applies to image patches, we propose a new Transformer-based graph neural network: Patch Graph Transformer (PatchGT). Unlike previous transformer-based models for learning graph representations, PatchGT learns from non-trainable graph patches, not from nodes directly. It can help save computation and improve the model performance. The key idea is to segment a graph into patches based on spectral clustering without any trainable parameters, with which the model can first use GNN layers to learn patch-level representations and then use Transformer to obtain graph-level representations. The architecture leverages the spectral information of graphs and combines the strengths of GNNs and Transformers. Further, we show the limitations of previous hierarchical trainable clusters theoretically and empirically. We also prove the proposed non-trainable spectral clustering method is permutation invariant and can help address the information bottlenecks in the graph. PatchGT achieves higher expressiveness than 1-WL-type GNNs, and the empirical study shows that PatchGT achieves competitive performances on benchmark datasets and provides interpretability to its predictions. The implementation of our algorithm is released at our Github repo: https://github.com/tufts-ml/PatchGT.

Xinmeng Li, Hao Zhu, Li-ping Liu et al.

A key challenge in metabolomics is annotating measured spectra from a biological sample with chemical identities. Currently, only a small fraction of measurements can be assigned identities. Two complementary computational approaches have emerged to address the annotation problem: mapping candidate molecules to spectra, and mapping query spectra to molecular candidates. In essence, the candidate molecule with the spectrum that best explains the query spectrum is recommended as the target molecule. Despite candidate ranking being fundamental in both approaches, no prior works utilized rank learning tasks in determining the target molecule. We propose a novel machine learning model, Ensemble Spectral Prediction (ESP), for metabolite annotation. ESP takes advantage of prior neural network-based annotation models that utilize multilayer perceptron (MLP) networks and Graph Neural Networks (GNNs). Based on the ranking results of the MLP and GNN-based models, ESP learns a weighting for the outputs of MLP and GNN spectral predictors to generate a spectral prediction for a query molecule. Importantly, training data is stratified by molecular formula to provide candidate sets during model training. Further, baseline MLP and GNN models are enhanced by considering peak dependencies through multi-head attention mechanism and multi-tasking on spectral topic distributions. ESP improves average rank by 41% and 30% over the MLP and GNN baselines, respectively, demonstrating remarkable performance gain over state-of-the-art neural network approaches. We show that annotation performance, for ESP and other models, is a strong function of the number of molecules in the candidate set and their similarity to the target molecule.

Yinkai Wang, Yan Zhou Chen, Xiaohui Chen et al.

Small-molecule identification from tandem mass spectrometry (MS/MS) remains a bottleneck in untargeted settings where spectral libraries are incomplete. While deep learning offers a solution, current approaches typically fall into two extremes: explicit generative models that construct molecular graphs atom-by-atom, or joint contrastive models that learn cross-modal subspaces from scratch. We introduce SpecBridge, a novel implicit alignment framework that treats structure identification as a geometric alignment problem. SpecBridge fine-tunes a self-supervised spectral encoder (DreaMS) to project directly into the latent space of a frozen molecular foundation model (ChemBERTa), and then performs retrieval by cosine similarity to a fixed bank of precomputed molecular embeddings. Across MassSpecGym, Spectraverse, and MSnLib benchmarks, SpecBridge improves top-1 retrieval accuracy by roughly 20-25% relative to strong neural baselines, while keeping the number of trainable parameters small. These results suggest that aligning to frozen foundation models is a practical, stable alternative to designing new architectures from scratch. The code for SpecBridge is released at https://github.com/HassounLab/SpecBridge.

Han Gao, Xu Han, Xiantao Fan et al.

Turbulent flows have historically presented formidable challenges to predictive computational modeling. Traditional numerical simulations often require vast computational resources, making them infeasible for numerous engineering applications. As an alternative, deep learning-based surrogate models have emerged, offering data-drive solutions. However, these are typically constructed within deterministic settings, leading to shortfall in capturing the innate chaotic and stochastic behaviors of turbulent dynamics. We introduce a novel generative framework grounded in probabilistic diffusion models for versatile generation of spatiotemporal turbulence. Our method unifies both unconditional and conditional sampling strategies within a Bayesian framework, which can accommodate diverse conditioning scenarios, including those with a direct differentiable link between specified conditions and generated unsteady flow outcomes, and scenarios lacking such explicit correlations. A notable feature of our approach is the method proposed for long-span flow sequence generation, which is based on autoregressive gradient-based conditional sampling, eliminating the need for cumbersome retraining processes. We showcase the versatile turbulence generation capability of our framework through a suite of numerical experiments, including: 1) the synthesis of LES simulated instantaneous flow sequences from URANS inputs; 2) holistic generation of inhomogeneous, anisotropic wall-bounded turbulence, whether from given initial conditions, prescribed turbulence statistics, or entirely from scratch; 3) super-resolved generation of high-speed turbulent boundary layer flows from low-resolution data across a range of input resolutions. Collectively, our numerical experiments highlight the merit and transformative potential of the proposed methods, making a significant advance in the field of turbulence generation.

Xiaohui Chen, Yukun Li, Aonan Zhang et al.

Learning to generate graphs is challenging as a graph is a set of pairwise connected, unordered nodes encoding complex combinatorial structures. Recently, several works have proposed graph generative models based on normalizing flows or score-based diffusion models. However, these models need to generate nodes and edges in parallel from the same process, whose dimensionality is unnecessarily high. We propose NVDiff, which takes the VGAE structure and uses a score-based generative model (SGM) as a flexible prior to sample node vectors. By modeling only node vectors in the latent space, NVDiff significantly reduces the dimension of the diffusion process and thus improves sampling speed. Built on the NVDiff framework, we introduce an attention-based score network capable of capturing both local and global contexts of graphs. Experiments indicate that NVDiff significantly reduces computations and can model much larger graphs than competing methods. At the same time, it achieves superior or competitive performances over various datasets compared to previous methods.

Xiaohui Chen, Yinkai Wang, Yuanqi Du et al.

Self-supervised training methods for transformers have demonstrated remarkable performance across various domains. Previous transformer-based models, such as masked autoencoders (MAE), typically utilize a single normalization layer for both the [CLS] symbol and the tokens. We propose in this paper a simple modification that employs separate normalization layers for the tokens and the [CLS] symbol to better capture their distinct characteristics and enhance downstream task performance. Our method aims to alleviate the potential negative effects of using the same normalization statistics for both token types, which may not be optimally aligned with their individual roles. We empirically show that by utilizing a separate normalization layer, the [CLS] embeddings can better encode the global contextual information and are distributed more uniformly in its anisotropic space. When replacing the conventional normalization layer with the two separate layers, we observe an average 2.7% performance improvement over the image, natural language, and graph domains.

Patrick Feeney, Sarah Schneider, Panagiotis Lymperopoulos et al.

In order for artificial agents to successfully perform tasks in changing environments, they must be able to both detect and adapt to novelty. However, visual novelty detection research often only evaluates on repurposed datasets such as CIFAR-10 originally intended for object classification, where images focus on one distinct, well-centered object. New benchmarks are needed to represent the challenges of navigating the complex scenes of an open world. Our new NovelCraft dataset contains multimodal episodic data of the images and symbolic world-states seen by an agent completing a pogo stick assembly task within a modified Minecraft environment. In some episodes, we insert novel objects of varying size within the complex 3D scene that may impact gameplay. Our visual novelty detection benchmark finds that methods that rank best on popular area-under-the-curve metrics may be outperformed by simpler alternatives when controlling false positives matters most. Further multimodal novelty detection experiments suggest that methods that fuse both visual and symbolic information can improve time until detection as well as overall discrimination. Finally, our evaluation of recent generalized category discovery methods suggests that adapting to new imbalanced categories in complex scenes remains an exciting open problem.

Xiaohui Chen, Yongfei Liu, Yingxiang Yang et al.

Recent advancements in text-to-image (T2I) generative models have shown remarkable capabilities in producing diverse and imaginative visuals based on text prompts. Despite the advancement, these diffusion models sometimes struggle to translate the semantic content from the text into images entirely. While conditioning on the layout has shown to be effective in improving the compositional ability of T2I diffusion models, they typically require manual layout input. In this work, we introduce a novel approach to improving T2I diffusion models using Large Language Models (LLMs) as layout generators. Our method leverages the Chain-of-Thought prompting of LLMs to interpret text and generate spatially reasonable object layouts. The generated layout is then used to enhance the generated images' composition and spatial accuracy. Moreover, we propose an efficient adapter based on a cross-attention mechanism, which explicitly integrates the layout information into the stable diffusion models. Our experiments demonstrate significant improvements in image quality and layout accuracy, showcasing the potential of LLMs in augmenting generative image models.

Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge et al.

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at https://github.com/pluskal-lab/MassSpecGym.

Xiaohui Chen, Yinkai Wang, Jiaxing He et al.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction. Code available at https://github.com/tufts-ml/G2PT,

Zhengyan Huan, Jacob Boerma, Li-Ping Liu et al.

We consider the problem of generating samples via Flow Matching (FM) with an additional requirement that the generated samples must satisfy given constraints. We consider two scenarios, viz.: (a) when a differentiable distance function to the constraint set is given, and (b) when the constraint set is only available via queries to a membership oracle. For case (a), we propose a simple adaptation of the FM objective with an additional term that penalizes the distance between the constraint set and the generated samples. For case (b), we propose to employ randomization and learn a mean flow that is numerically shown to have a high likelihood of satisfying the constraints. This approach deviates significantly from existing works that require simple convex constraints, knowledge of a barrier function, or a reflection mechanism to constrain the probability flow. Furthermore, in the proposed setting we show that a two-stage approach, where both stages approximate the same original flow but with only the second stage probing the constraints via randomization, is more computationally efficient. Through several synthetic cases of constrained generation, we numerically show that the proposed approaches achieve significant gains in terms of constraint satisfaction while matching the target distributions. As a showcase for a practical oracle-based constraint, we show how our approach can be used for training an adversarial example generator, using queries to a hard-label black-box classifier. We conclude with several future research directions. Our code is available at https://github.com/ZhengyanHuan/FM-RE.

Mingyang Wu, Xiaohui Chen, Li-Ping Liu

Recently developed deep neural models like NetGAN, CELL, and Variational Graph Autoencoders have made progress but face limitations in replicating key graph statistics on generating large graphs. Diffusion-based methods have emerged as promising alternatives, however, most of them present challenges in computational efficiency and generative performance. EDGE is effective at modeling large networks, but its current denoising approach can be inefficient, often leading to wasted computational resources and potential mismatches in its generation process. In this paper, we propose enhancements to the EDGE model to address these issues. Specifically, we introduce a degree-specific noise schedule that optimizes the number of active nodes at each timestep, significantly reducing memory consumption. Additionally, we present an improved sampling scheme that fine-tunes the generative process, allowing for better control over the similarity between the synthesized and the true network. Our experimental results demonstrate that the proposed modifications not only improve the efficiency but also enhance the accuracy of the generated graphs, offering a robust and scalable solution for graph generation tasks.

Yukun Li, Sijia Wang, Lifu Huang et al.

Reliable confidence estimation is essential for enhancing the trustworthiness of large language models (LLMs), especially in high-stakes scenarios. Despite its importance, accurately estimating confidence in LLM responses remains a significant challenge. In this work, we propose using an auxiliary learning model to assess response correctness based on the self-consistency of multiple outputs generated by the LLM. Our method builds a consistency graph to represent the agreement among multiple responses and uses a graph neural network (GNN) to estimate the likelihood that each response is correct. Experiments demonstrate that this method has strong calibration performance on various benchmark datasets and generalizes well to out-of-domain cases.

Yukun Li, Li-Ping Liu

With the advent of score-matching techniques for model training and Langevin dynamics for sample generation, energy-based models (EBMs) have gained renewed interest as generative models. Recent EBMs usually use neural networks to define their energy functions. In this work, we introduce a novel hybrid approach that combines an EBM with an exponential family model to incorporate inductive bias into data modeling. Specifically, we augment the energy term with a parameter-free statistic function to help the model capture key data statistics. Like an exponential family model, the hybrid model aims to align the distribution statistics with data statistics during model training, even when it only approximately maximizes the data likelihood. This property enables us to impose constraints on the hybrid model. Our empirical study validates the hybrid model's ability to match statistics. Furthermore, experimental results show that data fitting and generation improve when suitable informative statistics are incorporated into the hybrid model.

Yinkai Wang, Jiaxing He, Yuanqi Du et al.

We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution has been a dominating paradigm in this field which has an iterative process to generate variants and select via experimental feedback. We demonstrate large language models (LLMs), despite being trained on massive texts, are secretly protein sequence optimizers. With a directed evolutionary method, LLM can perform protein engineering through Pareto and experiment-budget constrained optimization, demonstrating success on both synthetic and experimental fitness landscapes.

Xiaohui Chen, Jiankai Sun, Taiqing Wang et al.

Data subsampling is widely used to speed up the training of large-scale recommendation systems. Most subsampling methods are model-based and often require a pre-trained pilot model to measure data importance via e.g. sample hardness. However, when the pilot model is misspecified, model-based subsampling methods deteriorate. Since model misspecification is persistent in real recommendation systems, we instead propose model-agnostic data subsampling methods by only exploring input data structure represented by graphs. Specifically, we study the topology of the user-item graph to estimate the importance of each user-item interaction (an edge in the user-item graph) via graph conductance, followed by a propagation step on the network to smooth out the estimated importance value. Since our proposed method is model-agnostic, we can marry the merits of both model-agnostic and model-based subsampling methods. Empirically, we show that combing the two consistently improves over any single method on the used datasets. Experimental results on KuaiRec and MIND datasets demonstrate that our proposed methods achieve superior results compared to baseline approaches.

Xiaohui Chen, Jiaxing He, Xu Han et al.

Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative graph model that addresses generative tasks with large graphs. To improve computation efficiency, we encourage graph sparsity by using a discrete diffusion process that randomly removes edges at each time step and finally obtains an empty graph. EDGE only focuses on a portion of nodes in the graph at each denoising step. It makes much fewer edge predictions than previous diffusion-based models. Moreover, EDGE admits explicitly modeling the node degrees of the graphs, further improving the model performance. The empirical study shows that EDGE is much more efficient than competing methods and can generate large graphs with thousands of nodes. It also outperforms baseline models in generation quality: graphs generated by our approach have more similar graph statistics to those of the training graphs.

Xu Han, Han Gao, Tobias Pfaff et al.

Graph-based next-step prediction models have recently been very successful in modeling complex high-dimensional physical systems on irregular meshes. However, due to their short temporal attention span, these models suffer from error accumulation and drift. In this paper, we propose a new method that captures long-term dependencies through a transformer-style temporal attention model. We introduce an encoder-decoder structure to summarize features and create a compact mesh representation of the system state, to allow the temporal model to operate on a low-dimensional mesh representations in a memory efficient manner. Our method outperforms a competitive GNN baseline on several complex fluid dynamics prediction tasks, from sonic shocks to vascular flow. We demonstrate stable rollouts without the need for training noise and show perfectly phase-stable predictions even for very long sequences. More broadly, we believe our approach paves the way to bringing the benefits of attention-based sequence models to solving high-dimensional complex physics tasks.

Xinmeng Li, Li-ping Liu, Soha Hassoun

Despite experimental and curation efforts, the extent of enzyme promiscuity on substrates continues to be largely unexplored and under documented. Recommender systems (RS), which are currently unexplored for the enzyme-substrate interaction prediction problem, can be utilized to provide enzyme recommendations for substrates, and vice versa. The performance of Collaborative-Filtering (CF) recommender systems however hinges on the quality of embedding vectors of users and items (enzymes and substrates in our case). Importantly, enhancing CF embeddings with heterogeneous auxiliary data, specially relational data (e.g., hierarchical, pairwise, or groupings), remains a challenge. We propose an innovative general RS framework, termed Boost-RS, that enhances RS performance by "boosting" embedding vectors through auxiliary data. Specifically, Boost-RS is trained and dynamically tuned on multiple relevant auxiliary learning tasks Boost-RS utilizes contrastive learning tasks to exploit relational data. To show the efficacy of Boost-RS for the enzyme-substrate prediction interaction problem, we apply the Boost-RS framework to several baseline CF models. We show that each of our auxiliary tasks boosts learning of the embedding vectors, and that contrastive learning using Boost-RS outperforms attribute concatenation and multi-label learning. We also show that Boost-RS outperforms similarity-based models. Ablation studies and visualization of learned representations highlight the importance of using contrastive learning on some of the auxiliary data in boosting the embedding vectors.

Li-Ping Liu, Ruiyuan Gu, Xiaozhe Hu

Polynomial functions have plenty of useful analytical properties, but they are rarely used as learning models because their function class is considered to be restricted. This work shows that when trained properly polynomial functions can be strong learning models. Particularly this work constructs polynomial feedforward neural networks using the product activation, a new activation function constructed from multiplications. The new neural network is a polynomial function and provides accurate control of its polynomial order. It can be trained by standard training techniques such as batch normalization and dropout. This new feedforward network covers several previous polynomial models as special cases. Compared with common feedforward neural networks, the polynomial feedforward network has closed-form calculations of a few interesting quantities, which are very useful in Bayesian learning. In a series of regression and classification tasks in the empirical study, the proposed model outperforms previous polynomial models.

Linfeng Liu, Michael C. Hughes, Soha Hassoun et al.

Recent works leveraging Graph Neural Networks to approach graph matching tasks have shown promising results. Recent progress in learning discrete distributions poses new opportunities for learning graph matching models. In this work, we propose a new model, Stochastic Iterative Graph MAtching (SIGMA), to address the graph matching problem. Our model defines a distribution of matchings for a graph pair so the model can explore a wide range of possible matchings. We further introduce a novel multi-step matching procedure, which learns how to refine a graph pair's matching results incrementally. The model also includes dummy nodes so that the model does not have to find matchings for nodes without correspondence. We fit this model to data via scalable stochastic optimization. We conduct extensive experiments across synthetic graph datasets as well as biochemistry and computer vision applications. Across all tasks, our results show that SIGMA can produce significantly improved graph matching results compared to state-of-the-art models. Ablation studies verify that each of our components (stochastic training, iterative matching, and dummy nodes) offers noticeable improvement.

Linfeng Liu, Michael C. Hughes, Li-Ping Liu

We propose a new model, the Neighbor Mixture Model (NMM), for modeling node labels in a graph. This model aims to capture correlations between the labels of nodes in a local neighborhood. We carefully design the model so it could be an alternative to a Markov Random Field but with more affordable computations. In particular, drawing samples and evaluating marginal probabilities of single labels can be done in linear time. To scale computations to large graphs, we devise a variational approximation without introducing extra parameters. We further use graph neural networks (GNNs) to parameterize the NMM, which reduces the number of learnable parameters while allowing expressive representation learning. The proposed model can be either fit directly to large observed graphs or used to enable scalable inference that preserves correlations for other distributions such as deep generative graph models. Across a diverse set of node classification, image denoising, and link prediction tasks, we show our proposed NMM advances the state-of-the-art in modeling real-world labeled graphs.

Xu Han, Xiaohui Chen, Li-Ping Liu

When formulated as an unsupervised learning problem, anomaly detection often requires a model to learn the distribution of normal data. Previous works apply Generative Adversarial Networks (GANs) to anomaly detection tasks and show good performances from these models. Motivated by the observation that GAN ensembles often outperform single GANs in generation tasks, we propose to construct GAN ensembles for anomaly detection. In the proposed method, a group of generators and a group of discriminators are trained together, so every generator gets feedback from multiple discriminators, and vice versa. Compared to a single GAN, a GAN ensemble can better model the distribution of normal data and thus better detect anomalies. Our theoretical analysis of GANs and GAN ensembles explains the role of a GAN discriminator in anomaly detection. In the empirical study, we evaluate ensembles constructed from four types of base models, and the results show that these ensembles clearly outperform single models in a series of tasks of anomaly detection.

Ramtin Hosseini, Neda Hassanpour, Li-Ping Liu et al.

Motivation: Untargeted metabolomics comprehensively characterizes small molecules and elucidates activities of biochemical pathways within a biological sample. Despite computational advances, interpreting collected measurements and determining their biological role remains a challenge. Results: To interpret measurements, we present an inference-based approach, termed Probabilistic modeling for Untargeted Metabolomics Analysis (PUMA). Our approach captures measurements and known information about the sample under study in a generative model and uses stochastic sampling to compute posterior probability distributions. PUMA predicts the likelihood of pathways being active, and then derives a probabilistic annotation, which assigns chemical identities to the measurements. PUMA is validated on synthetic datasets. When applied to test cases, the resulting pathway activities are biologically meaningful and distinctly different from those obtained using statistical pathway enrichment techniques. Annotation results are in agreement to those obtained using other tools that utilize additional information in the form of spectral signatures. Importantly, PUMA annotates many additional measurements.

Li-Ping Liu, Thomas G. Dietterich, Nan Li et al.

Consider a binary classification problem in which the learner is given a labeled training set, an unlabeled test set, and is restricted to choosing exactly $k$ test points to output as positive predictions. Problems of this kind---{\it transductive precision@$k$}---arise in information retrieval, digital advertising, and reserve design for endangered species. Previous methods separate the training of the model from its use in scoring the test points. This paper introduces a new approach, Transductive Top K (TTK), that seeks to minimize the hinge loss over all training instances under the constraint that exactly $k$ test instances are predicted as positive. The paper presents two optimization methods for this challenging problem. Experiments and analysis confirm the importance of incorporating the knowledge of $k$ into the learning process. Experimental evaluations of the TTK approach show that the performance of TTK matches or exceeds existing state-of-the-art methods on 7 UCI datasets and 3 reserve design problem instances.

Li-Ping Liu, Daniel Sheldon, Thomas G. Dietterich

The Collective Graphical Model (CGM) models a population of independent and identically distributed individuals when only collective statistics (i.e., counts of individuals) are observed. Exact inference in CGMs is intractable, and previous work has explored Markov Chain Monte Carlo (MCMC) and MAP approximations for learning and inference. This paper studies Gaussian approximations to the CGM. As the population grows large, we show that the CGM distribution converges to a multivariate Gaussian distribution (GCGM) that maintains the conditional independence properties of the original CGM. If the observations are exact marginals of the CGM or marginals that are corrupted by Gaussian noise, inference in the GCGM approximation can be computed efficiently in closed form. If the observations follow a different noise model (e.g., Poisson), then expectation propagation provides efficient and accurate approximate inference. The accuracy and speed of GCGM inference is compared to the MCMC and MAP methods on a simulated bird migration problem. The GCGM matches or exceeds the accuracy of the MAP method while being significantly faster.