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June Zhang

Publications and source records attributed to June Zhang.

15 recordsLinked to original sources

REAL: Response Embedding-based Alignment for LLMs

Aligning large language models (LLMs) to human preferences is a crucial step in building helpful and safe AI tools, which usually involve training on supervised datasets. Popular algorithms such as Direct Preference Optimization (DPO) rely on pairs of AI-generated responses ranked according to human annotation. The response pair annotation process might bring human bias. Building a correct preference dataset is the costly part of the alignment pipeline. To improve annotation efficiency and quality in the LLMs alignment, we propose REAL: Response Embedding-based Alignment for LLMs, a strategy for constructing a high-quality training dataset that focuses on acquiring the less ambiguous preference pairs for labeling out of a set of response candidates. Our selection process is based on the similarity of embedding responses independently of prompts, which guarantees the selection process in an off-policy setting, avoiding adaptively measuring the similarity during the training. Experimental results on real-world dataset SHP2 and synthetic HH-RLHF benchmarks indicate that choosing dissimilar response pairs enhances the direct alignment of LLMs while reducing inherited labeling errors. The model aligned with dissimilar response pairs obtained a better margin and win rate on the dialogue task. Our findings suggest that focusing on distinct pairs can reduce the label error and improve LLM alignment efficiency, saving up to $65\%$ of annotators' work.

cs.CL

mRNA2vec: mRNA Embedding with Language Model in the 5'UTR-CDS for mRNA Design

Messenger RNA (mRNA)-based vaccines are accelerating the discovery of new drugs and revolutionizing the pharmaceutical industry. However, selecting particular mRNA sequences for vaccines and therapeutics from extensive mRNA libraries is costly. Effective mRNA therapeutics require carefully designed sequences with optimized expression levels and stability. This paper proposes a novel contextual language model (LM)-based embedding method: mRNA2vec. In contrast to existing mRNA embedding approaches, our method is based on the self-supervised teacher-student learning framework of data2vec. We jointly use the 5' untranslated region (UTR) and coding sequence (CDS) region as the input sequences. We adapt our LM-based approach specifically to mRNA by 1) considering the importance of location on the mRNA sequence with probabilistic masking, 2) using Minimum Free Energy (MFE) prediction and Secondary Structure (SS) classification as additional pretext tasks. mRNA2vec demonstrates significant improvements in translation efficiency (TE) and expression level (EL) prediction tasks in UTR compared to SOTA methods such as UTR-LM. It also gives a competitive performance in mRNA stability and protein production level tasks in CDS such as CodonBERT.

q-bio.QM

Out-of-Distribution Detection using Maximum Entropy Coding

Given a default distribution $P$ and a set of test data $x^M=\{x_1,x_2,\ldots,x_M\}$ this paper seeks to answer the question if it was likely that $x^M$ was generated by $P$. For discrete distributions, the definitive answer is in principle given by Kolmogorov-Martin-L\"{o}f randomness. In this paper we seek to generalize this to continuous distributions. We consider a set of statistics $T_1(x^M),T_2(x^M),\ldots$. To each statistic we associate its maximum entropy distribution and with this a universal source coder. The maximum entropy distributions are subsequently combined to give a total codelength, which is compared with $-\log P(x^M)$. We show that this approach satisfied a number of theoretical properties. For real world data $P$ usually is unknown. We transform data into a standard distribution in the latent space using a bidirectional generate network and use maximum entropy coding there. We compare the resulting method to other methods that also used generative neural networks to detect anomalies. In most cases, our results show better performance.

cs.IT

HaSa: Hardness and Structure-Aware Contrastive Knowledge Graph Embedding

We consider a contrastive learning approach to knowledge graph embedding (KGE) via InfoNCE. For KGE, efficient learning relies on augmenting the training data with negative triples. However, most KGE works overlook the bias from generating the negative triples-false negative triples (factual triples missing from the knowledge graph). We argue that the generation of high-quality (i.e., hard) negative triples might lead to an increase in false negative triples. To mitigate the impact of false negative triples during the generation of hard negative triples, we propose the Hardness and Structure-aware (\textbf{HaSa}) contrastive KGE method, which alleviates the effect of false negative triples while generating the hard negative triples. Experiments show that HaSa improves the performance of InfoNCE-based KGE approaches and achieves state-of-the-art results in several metrics for WN18RR datasets and competitive results for FB15k-237 datasets compared to both classic and pre-trained LM-based KGE methods.

cs.AI

Estimating Parameters of Large CTMP from Single Trajectory with Application to Stochastic Network Epidemics Models

Graph dynamical systems (GDS) model dynamic processes on a (static) graph. Stochastic GDS has been used for network-based epidemics models such as the contact process and the reversible contact process. In this paper, we consider stochastic GDS that are also continuous-time Markov processes (CTMP), whose transition rates are linear functions of some dynamics parameters $\theta$ of interest (i.e., healing, exogeneous, and endogeneous infection rates). Our goal is to estimate $\theta$ from a single, finite-time, continuously observed trajectory of the CTMP. Parameter estimation of CTMP is challenging when the state space is large; for GDS, the number of Markov states are \emph{exponential} in the number of nodes of the graph. We showed that holding classes (i.e., Markov states with the same holding time distribution) give efficient partitions of the state space of GDS. We derived an upperbound on the number of holding classes for the contact process, which is polynomial in the number of nodes. We utilized holding classes to solve a smaller system of linear equations to find $\theta$. Experimental results show that finding reasonable results can be achieved even for short trajectories, particularly for the contact process. In fact, trajectory length does not significantly affect estimation error.

stat.AP

Out-of-Distribution Detection using BiGAN and MDL

We consider the following problem: we have a large dataset of normal data available. We are now given a new, possibly quite small, set of data, and we are to decide if these are normal data, or if they are indicating a new phenomenon. This is a novelty detection or out-of-distribution detection problem. An example is in medicine, where the normal data is for people with no known disease, and the new dataset people with symptoms. Other examples could be in security. We solve this problem by training a bidirectional generative adversarial network (BiGAN) on the normal data and using a Gaussian graphical model to model the output. We then use universal source coding, or minimum description length (MDL) on the output to decide if it is a new distribution, in an implementation of Kolmogorov and Martin-L\"{o}f randomness. We apply the methodology to both MNIST data and a real-world electrocardiogram (ECG) dataset of healthy and patients with Kawasaki disease, and show better performance in terms of the ROC curve than similar methods.

cs.LG

How News Evolves? Modeling News Text and Coverage using Graphs and Hawkes Process

Monitoring news content automatically is an important problem. The news content, unlike traditional text, has a temporal component. However, few works have explored the combination of natural language processing and dynamic system models. One reason is that it is challenging to mathematically model the nuances of natural language. In this paper, we discuss how we built a novel dataset of news articles collected over time. Then, we present a method of converting news text collected over time to a sequence of directed multi-graphs, which represent semantic triples (Subject -> Predicate} ->Object). We model the dynamics of specific topological changes in these graphs using a set of multivariate count series, which we fit the discrete-time Hawkes process. With our real-world data, we show that the multivariate time series contain both dynamic information of how many articles/words were published each day and semantic information of the content of the articles. This yields novel insights into how news events are covered. We show with the experiment that our approach can be used to infer from a sequence of news articles if the articles were published by major or entertainment news outlets.

cs.CL

Graph Compression with Application to Model Selection

Many multivariate data such as social and biological data exhibit complex dependencies that are best characterized by graphs. Unlike sequential data, graphs are, in general, unordered structures. This means we can no longer use classic, sequential-based compression methods on these graph-based data. Therefore, it is necessary to develop new methods for graph compression. In this paper, we present universal source coding methods for the lossless compression of unweighted, undirected, unlabelled graphs. We encode in two steps: 1) transforming graph into a rooted binary tree, 2) the encoding rooted binary tree using graph statistics. Our coders showed better compression performance than other source coding methods on both synthetic and real-world graphs. We then applied our graph coding methods for model selection of Gaussian graphical models using minimum description length (MDL) principle finding the description length of the conditional independence graph. Experiments on synthetic data show that our approach gives better performance compared to common model selection methods. We also applied our approach to electrocardiogram (ECG) data in order to explore the differences between graph models of two groups of subjects.

cs.IT

Graph Coding for Model Selection and Anomaly Detection in Gaussian Graphical Models

A classic application of description length is for model selection with the minimum description length (MDL) principle. The focus of this paper is to extend description length for data analysis beyond simple model selection and sequences of scalars. More specifically, we extend the description length for data analysis in Gaussian graphical models. These are powerful tools to model interactions among variables in a sequence of i.i.d Gaussian data in the form of a graph. Our method uses universal graph coding methods to accurately account for model complexity, and therefore provide a more rigorous approach for graph model selection. The developed method is tested with synthetic and electrocardiogram (ECG) data to find the graph model and anomaly in Gaussian graphical models. The experiments show that our method gives better performance compared to commonly used methods.

cs.LG

Differential Description Length for Hyperparameter Selection in Machine Learning

This paper introduces a new method for model selection and more generally hyperparameter selection in machine learning. Minimum description length (MDL) is an established method for model selection, which is however not directly aimed at minimizing generalization error, which is often the primary goal in machine learning. The paper demonstrates a relationship between generalization error and a difference of description lengths of the training data; we call this difference differential description length (DDL). This allows prediction of generalization error from the training data alone by performing encoding of the training data. DDL can then be used for model selection by choosing the model with the smallest predicted generalization error. We show how this method can be used for linear regression and neural networks and deep learning. Experimental results show that DDL leads to smaller generalization error than cross-validation and traditional MDL and Bayes methods.

cs.LG

How Consumer Empathy Assist Power Grid in Demand Response

This paper investigates interaction among residential electricity users and utility company in a distribution network with the capability of two-way communication provided by smart grid. The energy consumption scheduling of electricity users is formulated as a game-theoretic problem within a group where all players are not totally selfish. Considering altruistic behavior of human decision-making, altruistic player action to other players actions can be influenced by recognizing the well being of others. The proposed model captures the empathy of electricity users in energy consumption scheduling and how this behavior affect peak demand and electricity prices. Numerical results demonstrate that both residential users and utility company can benefit through the channel of empathy.

cs.GT

Coding of Graphs with Application to Graph Anomaly Detection

This paper has dual aims. First is to develop practical universal coding methods for unlabeled graphs. Second is to use these for graph anomaly detection. The paper develops two coding methods for unlabeled graphs: one based on the degree distribution, the second based on the triangle distribution. It is shown that these are efficient for different types of random graphs, and on real-world graphs. These coding methods is then used for detecting anomalous graphs, based on structure alone. It is shown that anomalous graphs can be detected with high probability.

cs.IT

Cascading Edge Failures: A Dynamic Network Process

This paper considers the dynamics of edges in a network. The Dynamic Bond Percolation (DBP) process models, through stochastic local rules, the dependence of an edge $(a,b)$ in a network on the states of its neighboring edges. Unlike previous models, DBP does not assume statistical independence between different edges. In applications, this means for example that failures of transmission lines in a power grid are not statistically independent, or alternatively, relationships between individuals (dyads) can lead to changes in other dyads in a social network. We consider the time evolution of the probability distribution of the network state, the collective states of all the edges (bonds), and show that it converges to a stationary distribution. We use this distribution to study the emergence of global behaviors like consensus (i.e., catastrophic failure or full recovery of the entire grid) or coexistence (i.e., some failed and some operating substructures in the grid). In particular, we show that, depending on the local dynamical rule, different network substructures, such as hub or triangle subgraphs, are more prone to failure.

physics.soc-ph

Contact Process with Exogenous Infection and the Scaled SIS Process

Propagation of contagion in networks depends on the graph topology. This paper is concerned with studying the time-asymptotic behavior of the extended contact processes on static, undirected, finite-size networks. This is a contact process with nonzero exogenous infection rate (also known as the {\epsilon}-SIS, {\epsilon} susceptible-infected-susceptible, model [1]). The only known analytical characterization of the equilibrium distribution of this process is for complete networks. For large networks with arbitrary topology, it is infeasible to numerically solve for the equilibrium distribution since it requires solving the eigenvalue-eigenvector problem of a matrix that is exponential in N , the size of the network. We show that, for a certain range of the network process parameters, the equilibrium distribution of the extended contact process on arbitrary, finite-size networks is well approximated by the equilibrium distribution of the scaled SIS process, which we derived in closed-form in prior work. We confirm this result with numerical simulations comparing the equilibrium distribution of the extended contact process with that of a scaled SIS process. We use this approximation to decide, in polynomial-time, which agents and network substructures are more susceptible to infection by the extended contact process.

physics.soc-ph

Role of Subgraphs in Epidemics over Finite-Size Networks under the Scaled SIS Process

In previous work, we developed the scaled SIS process, which models the dynamics of SIS epidemics over networks. With the scaled SIS process, we can consider networks that are finite-sized and of arbitrary topology (i.e., we are not restricted to specific classes of networks). We derived for the scaled SIS process a closed-form expression for the time-asymptotic probability distribution of the states of all the agents in the network. This closed-form solution of the equilibrium distribution explicitly exhibits the underlying network topology through its adjacency matrix. This paper determines which network configuration is the most probable. We prove that, for a range of epidemics parameters, this combinatorial problem leads to a submodular optimization problem, which is exactly solvable in polynomial time. We relate the most-probable configuration to the network structure, in particular, to the existence of high density subgraphs. Depending on the epidemics parameters, subset of agents may be more likely to be infected than others; these more-vulnerable agents form subgraphs that are denser than the overall network. We illustrate our results with a 193 node social network and the 4941 node Western US power grid under different epidemics parameters.

cs.SI