MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/.Comment: Accepted by both RECOMB 2014 and PLOS Computational Biolog

Personalized Federated Learning via ADMM with Moreau Envelope

Personalized federated learning (PFL) is an approach proposed to address the issue of poor convergence on heterogeneous data. However, most existing PFL frameworks require strong assumptions for convergence. In this paper, we propose an alternating direction method of multipliers (ADMM) for training PFL models with Moreau envelope (FLAME), which achieves a sublinear convergence rate, relying on the relatively weak assumption of gradient Lipschitz continuity. Moreover, due to the gradient-free nature of ADMM, FLAME alleviates the need for hyperparameter tuning, particularly in avoiding the adjustment of the learning rate when training the global model. In addition, we propose a biased client selection strategy to expedite the convergence of training of PFL models. Our theoretical analysis establishes the global convergence under both unbiased and biased client selection strategies. Our experiments validate that FLAME, when trained on heterogeneous data, outperforms state-of-the-art methods in terms of model performance. Regarding communication efficiency, it exhibits an average speedup of 3.75x compared to the baselines. Furthermore, experimental results validate that the biased client selection strategy speeds up the convergence of both personalized and global models.Comment: 15 page

Efficient Spatial Dataset Search over Multiple Data Sources

In this paper, we investigate a novel spatial dataset search paradigm over multiple spatial data sources, which enables users to conduct join and union searches seamlessly. Specifically, we define two search problems called Maximum Intersection Query (MIQ) and Maximum Coverage Query with a Connection constraint (MCQC). To address these problems, we propose a unified Multi-source Spatial Dataset Search (MSDS) framework. In MSDS, we design a multi-layer index to accelerate the MIQ and MCQC. In addition, we prove that the MCQC is NP-hard and design two greedy algorithms to solve the problem. To deal with the constant update of spatial datasets in each data source, we design a dynamic index updating strategy and optimize search algorithms to reduce communication costs and improve search efficiency. We evaluate the efficiency of MSDS on five real-world data sources, and the experimental results show that our framework is able to achieve a significant reduction in running time and communication cost

Dependency Relationships-Enhanced Attentive Group Recommendation in HINs

Recommending suitable items to a group of users, commonly referred to as the group recommendation task, is becoming increasingly urgent with the development of group activities. The challenges within the group recommendation task involve aggregating the individual preferences of group members as the group's preferences and facing serious sparsity problems due to the lack of user/group-item interactions. To solve these problems, we propose a novel approach called Dependency Relationships-Enhanced Attentive Group Recommendation (DREAGR) for the recommendation task of occasional groups. Specifically, we introduce the dependency relationship between items as side information to enhance the user/group-item interaction and alleviate the interaction sparsity problem. Then, we propose a Path-Aware Attention Embedding (PAAE) method to model users' preferences on different types of paths. Next, we design a gated fusion mechanism to fuse users' preferences into their comprehensive preferences. Finally, we develop an attention aggregator that aggregates users' preferences as the group's preferences for the group recommendation task. We conducted experiments on two datasets to demonstrate the superiority of DREAGR by comparing it with state-of-the-art group recommender models. The experimental results show that DREAGR outperforms other models, especially HR@N and NDCG@N (N=5, 10), where DREAGR has improved in the range of 3.64% to 7.01% and 2.57% to 3.39% on both datasets, respectively.Comment: 14 pages, 9 figures, This paper has been submitted to IEEE Transactions on Knowledge and Data Engineerin

Analyses of a Panel of Transcripts Identified From a Small Sample Size and Construction of RNA Networks in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is one of the most common cancers in the world. Dysregulation of mRNAs and non-coding RNAs (ncRNAs) plays critical roles in the progression of HCC. Here, we investigated HCC samples by RNA-seq and identified a series of dysregulated RNAs in HCC. Various bioinformatics analyses established long non-coding RNA (lncRNA)-mRNA co-expression and competing endogenous RNA (ceRNA) networks in circRNA-miRNA-mRNA axis, indicating the potential cis and/or trans regulatory roles of lncRNAs and circRNAs. Moreover, GO pathway analysis showed that these identified RNAs were associated with many biological processes that were related to tumorigenesis and tumor progression. In conclusion, we systematically established functional networks of lncRNA-mRNA, circRNA-miRNA-mRNA to further unveil the potential interactions and biological processes in HCC. These results provide further insights into gene expression network of HCC and may assist future diagnosis of HCC

Efficient k-means with Individual Fairness via Exponential Tilting

In location-based resource allocation scenarios, the distances between each individual and the facility are desired to be approximately equal, thereby ensuring fairness. Individually fair clustering is often employed to achieve the principle of treating all points equally, which can be applied in these scenarios. This paper proposes a novel algorithm, tilted k-means (TKM), aiming to achieve individual fairness in clustering. We integrate the exponential tilting into the sum of squared errors (SSE) to formulate a novel objective function called tilted SSE. We demonstrate that the tilted SSE can generalize to SSE and employ the coordinate descent and first-order gradient method for optimization. We propose a novel fairness metric, the variance of the distances within each cluster, which can alleviate the Matthew Effect typically caused by existing fairness metrics. Our theoretical analysis demonstrates that the well-known k-means++ incurs a multiplicative error of O(k log k), and we establish the convergence of TKM under mild conditions. In terms of fairness, we prove that the variance generated by TKM decreases with a scaled hyperparameter. In terms of efficiency, we demonstrate the time complexity is linear with the dataset size. Our experiments demonstrate that TKM outperforms state-of-the-art methods in effectiveness, fairness, and efficiency

Convergence of quantum random walks with decoherence

In this paper, we study the discrete-time quantum random walks on a line subject to decoherence. The convergence of the rescaled position probability distribution $p(x,t)$ depends mainly on the spectrum of the superoperator $\mathcal{L}_{kk}$. We show that if 1 is an eigenvalue of the superoperator with multiplicity one and there is no other eigenvalue whose modulus equals to 1, then $\hat {P}(\frac{\nu} {\sqrt t},t)$ converges to a convex combination of normal distributions. In terms of position space, the rescaled probability mass function $p_t (x, t) \equiv p(\sqrt t x, t)$, $x \in Z/\sqrt t$, converges in distribution to a continuous convex combination of normal distributions. We give an necessary and sufficient condition for a U(2) decoherent quantum walk that satisfies the eigenvalue conditions. We also give a complete description of the behavior of quantum walks whose eigenvalues do not satisfy these assumptions. Specific examples such as the Hadamard walk, walks under real and complex rotations are illustrated. For the O(2) quantum random walks, an explicit formula is provided for the scaling limit of $p(x,t)$ and their moments. We also obtain exact critical exponents for their moments at the critical point and show universality classes with respect to these critical exponents