arXiv subjects

Dongbo Bu

Publications and source records attributed to Dongbo Bu.

13 recordsLinked to original sources

arXiv2026

Designing faster mixed integer linear programming algorithm via learning the optimal path

Designing faster algorithms for solving Mixed-Integer Linear Programming (MILP) problems is highly desired across numerous practical domains, as a vast array of complex real-world challenges can be effectively modeled as MILP formulations. Solving these problems typically employs the branch-and-bound algorithm, the core of which can be conceived as searching for a path of nodes (or sub-problems) that contains the optimal solution to the original MILP problem. Traditional approaches to finding this path rely heavily on hand-crafted, intuition-based heuristic strategies, which often suffer from unstable and unpredictable performance across different MILP problem instances. To address this limitation, we introduce DeepBound, a deep learning-based node selection algorithm that automates the learning of such human intuition from data. The core of DeepBound lies in learning to prioritize nodes containing the optimal solution, thereby improving solving efficiency. DeepBound introduces a multi-level feature fusion network to capture the node representations. To tackle the inherent node imbalance in branch-and-bound trees, DeepBound employs a pairwise training paradigm that enhances the model's ability to discriminate between nodes. Extensive experiments on three NP-hard MILP benchmarks demonstrate that DeepBound achieves superior solving efficiency over conventional heuristic rules and existing learning-based approaches, obtaining optimal feasible solutions with significantly reduced computation time. Moreover, DeepBound demonstrates strong generalization capability on large and complex instances. The analysis of its learned features reveals that the method can automatically discover more flexible and robust feature selection, which may effectively improve and potentially replace human-designed heuristic rules.

cs.AI↗

arXiv2025

Lossless data compression by large models

Modern data compression methods are slowly reaching their limits after 80 years of research, millions of papers, and wide range of applications. Yet, the extravagant 6G communication speed requirement raises a major open question for revolutionary new ideas of data compression. We have previously shown all understanding or learning are compression, under reasonable assumptions. Large language models (LLMs) understand data better than ever before. Can they help us to compress data? The LLMs may be seen to approximate the uncomputable Solomonoff induction. Therefore, under this new uncomputable paradigm, we present LMCompress. LMCompress shatters all previous lossless compression algorithms, doubling the lossless compression ratios of JPEG-XL for images, FLAC for audios, and H.264 for videos, and quadrupling the compression ratio of bz2 for texts. The better a large model understands the data, the better LMCompress compresses.

cs.IT↗

arXiv2024

Improving Molecular Graph Generation with Flow Matching and Optimal Transport

Generating molecular graphs is crucial in drug design and discovery but remains challenging due to the complex interdependencies between nodes and edges. While diffusion models have demonstrated their potentiality in molecular graph design, they often suffer from unstable training and inefficient sampling. To enhance generation performance and training stability, we propose GGFlow, a discrete flow matching generative model incorporating optimal transport for molecular graphs and it incorporates an edge-augmented graph transformer to enable the direct communications among chemical bounds. Additionally, GGFlow introduces a novel goal-guided generation framework to control the generative trajectory of our model, aiming to design novel molecular structures with the desired properties. GGFlow demonstrates superior performance on both unconditional and conditional molecule generation tasks, outperforming existing baselines and underscoring its effectiveness and potential for wider application.

cs.LG↗

arXiv2023

Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model

Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is vital in protein engineering and therapeutic discovery. However, the scarcity of annotated experimental data on binding energy poses a significant challenge for developing computational approaches, particularly deep learning-based methods. In this work, we propose SidechainDiff, a representation learning-based approach that leverages unlabelled experimental protein structures. SidechainDiff utilizes a Riemannian diffusion model to learn the generative process of side-chain conformations and can also give the structural context representations of mutations on the protein-protein interface. Leveraging the learned representations, we achieve state-of-the-art performance in predicting the mutational effects on protein-protein binding. Furthermore, SidechainDiff is the first diffusion-based generative model for side-chains, distinguishing it from prior efforts that have predominantly focused on generating protein backbone structures.

q-bio.BM↗

arXiv2023

iEDA: An Open-Source Intelligent Physical Implementation Toolkit and Library

Open-source EDA shows promising potential in unleashing EDA innovation and lowering the cost of chip design. This paper presents an open-source EDA project, iEDA, aiming for building a basic infrastructure for EDA technology evolution and closing the industrial-academic gap in the EDA area. iEDA now covers the whole flow of physical design (including Floorplan, Placement, CTS, Routing, Timing Optimization etc.), and part of the analysis tools (Static Timing Analysis and Power Analysis). To demonstrate the effectiveness of iEDA, we implement and tape out three chips of different scales (from 700k to 1.5M gates) on different process nodes (110nm and 28nm) with iEDA. iEDA is publicly available from the project home page http://ieda.oscc.cc.

cs.AR↗

arXiv2023

NIERT: Accurate Numerical Interpolation through Unifying Scattered Data Representations using Transformer Encoder

Interpolation for scattered data is a classical problem in numerical analysis, with a long history of theoretical and practical contributions. Recent advances have utilized deep neural networks to construct interpolators, exhibiting excellent and generalizable performance. However, they still fall short in two aspects: \textbf{1) inadequate representation learning}, resulting from separate embeddings of observed and target points in popular encoder-decoder frameworks and \textbf{2) limited generalization power}, caused by overlooking prior interpolation knowledge shared across different domains. To overcome these limitations, we present a \textbf{N}umerical \textbf{I}nterpolation approach using \textbf{E}ncoder \textbf{R}epresentation of \textbf{T}ransformers (called \textbf{NIERT}). On one hand, NIERT utilizes an encoder-only framework rather than the encoder-decoder structure. This way, NIERT can embed observed and target points into a unified encoder representation space, thus effectively exploiting the correlations among them and obtaining more precise representations. On the other hand, we propose to pre-train NIERT on large-scale synthetic mathematical functions to acquire prior interpolation knowledge, and transfer it to multiple interpolation domains with consistent performance gain. On both synthetic and real-world datasets, NIERT outperforms the existing approaches by a large margin, i.e., 4.3$\sim$14.3$\times$ lower MAE on TFRD subsets, and 1.7/1.8/8.7$\times$ lower MSE on Mathit/PhysioNet/PTV datasets. The source code of NIERT is available at https://github.com/DingShizhe/NIERT.

cs.LG↗

arXiv2023

A Theory of Human-Like Few-Shot Learning

We aim to bridge the gap between our common-sense few-sample human learning and large-data machine learning. We derive a theory of human-like few-shot learning from von-Neuman-Landauer's principle. modelling human learning is difficult as how people learn varies from one to another. Under commonly accepted definitions, we prove that all human or animal few-shot learning, and major models including Free Energy Principle and Bayesian Program Learning that model such learning, approximate our theory, under Church-Turing thesis. We find that deep generative model like variational autoencoder (VAE) can be used to approximate our theory and perform significantly better than baseline models including deep neural networks, for image recognition, low resource language processing, and character recognition.

cs.LG↗

arXiv2019

Seq-SetNet: Exploring Sequence Sets for Inferring Structures

Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural information from it. Almost all of the existing approaches exploit MSAs in an indirect fashion, i.e., they transform MSAs into position-specific scoring matrices (PSSM) that represent the distribution of amino acid types at each column. PSSM could capture column-wise characteristics of MSA, however, the column-wise characteristics embedded in each individual component sequence were nearly totally neglected. The drawback of PSSM is rooted in the fact that an MSA is essentially an unordered sequence set rather than a matrix. Specifically, the interchange of any two sequences will not affect the whole MSA. In contrast, the pixels in an image essentially form a matrix since any two rows of pixels cannot be interchanged. Therefore, the traditional deep neural networks designed for image processing cannot be directly applied on sequence sets. Here, we proposed a novel deep neural network framework (called Seq-SetNet) for sequence set processing. By employing a {\it symmetric function} module to integrate features calculated from preceding layers, Seq-SetNet are immune to the order of sequences in the input MSA. This advantage enables us to directly and fully exploit MSAs by considering each component protein individually. We evaluated Seq-SetNet by using it to extract structural information from MSA for protein secondary structure prediction. Experimental results on popular benchmark sets suggests that Seq-SetNet outperforms the state-of-the-art approaches by 3.6% in precision. These results clearly suggest the advantages of Seq-SetNet in sequence set processing and it can be readily used in a wide range of fields, say natural language processing.

q-bio.BM↗

arXiv2018

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning

Accurate prediction of inter-residue contacts of a protein is important to calcu- lating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective to inferring inter-residue contacts. The Markov ran- dom field (MRF) technique, although being widely used for contact prediction, suffers from the following dilemma: the actual likelihood function of MRF is accurate but time-consuming to calculate, in contrast, approximations to the actual likelihood, say pseudo-likelihood, are efficient to calculate but inaccu- rate. Thus, how to achieve both accuracy and efficiency simultaneously remains a challenge. In this study, we present such an approach (called clmDCA) for contact prediction. Unlike plmDCA using pseudo-likelihood, i.e., the product of conditional probability of individual residues, our approach uses composite- likelihood, i.e., the product of conditional probability of all residue pairs. Com- posite likelihood has been theoretically proved as a better approximation to the actual likelihood function than pseudo-likelihood. Meanwhile, composite likelihood is still efficient to maximize, thus ensuring the efficiency of clmDCA. We present comprehensive experiments on popular benchmark datasets, includ- ing PSICOV dataset and CASP-11 dataset, to show that: i) clmDCA alone outperforms the existing MRF-based approaches in prediction accuracy. ii) When equipped with deep learning technique for refinement, the prediction ac- curacy of clmDCA was further significantly improved, suggesting the suitability of clmDCA for subsequent refinement procedure. We further present successful application of the predicted contacts to accurately build tertiary structures for proteins in the PSICOV dataset. Accessibility: The software clmDCA and a server are publicly accessible through http://protein.ict.ac.cn/clmDCA/.

q-bio.BM↗

arXiv2015

Improving protein threading accuracy via combining local and global potential using TreeCRF model

Protein structure prediction remains to be an open problem in bioinformatics. There are two main categories of methods for protein structure prediction: Free Modeling (FM) and Template Based Modeling (TBM). Protein threading, belonging to the category of template based modeling, identifies the most likely fold with the target by making a sequence-structure alignment between target protein and template protein. Though protein threading has been shown to more be successful for protein structure prediction, it performs poorly for remote homology detection.

q-bio.BM↗

arXiv2015

TOPO: Improving remote homologue recognition via identifying common protein structure framework

Protein structure prediction remains a challenge in the field of computational biology. Traditional protein structure prediction approaches include template-based modelling (say, homology modelling, and threading), and ab initio. A threading algorithm takes a query protein sequence as input, recognizes the most likely fold, and finally reports the alignments of the query sequence to structure-known templates as output. The existing threading approaches mainly utilizes the information of protein sequence profile, solvent accessibility, contact probability, etc., and correctly recognize folds for some proteins. However, the existing threading approaches show poorly performance for remote homology proteins. How to improve the fold recognition for remote homology proteins remains to be a difficult task for protein structure prediction.

q-bio.OT↗

arXiv2014

Optimizing weights of protein energy function to improve ab initio protein structure prediction

Predicting protein 3D structure from amino acid sequence remains as a challenge in the field of computational biology. If protein structure homologues are not found, one has to construct 3D structural conformations from the very beginning by the so-called ab initio approach, using some empirical energy functions. A successful algorithm in this category, Rosetta, creates an ensemble of decoy conformations by assembling selected best short fragments of known protein structures and then recognizes the native state as the highly populated one with a very low energy. Typically, an energy function is a combination of a variety of terms characterizing different structural features, say hydrophobic interactions, van der Waals force, hydrogen bonding, etc. It is critical for an energy function to be capable to distinguish native-like conformations from non-native ones and to drive most initial conformations assembled from fragments to a native-like one in a conformation search process. In this paper we propose a linear programming algorithm to optimize weighting of a total of 14 energy terms used in Rosetta. We reverse the Monte Carlo process of Rosetta to approach native-like conformations to a process generating from the native state an ensemble of initial conformations most relevant to the native state. Intuitively, an ideal weighting scheme would result in a large "basin of attraction" of the native structure, which leads to an objective function for the linear programming. We have examined the proposal on several benchmark proteins, and the experimental results suggest that the optimized weights enlarge the attraction basin of the native state and improve the quality of the predicted native states as well. In addition, a comparison of optimal weighting schema for proteins of different classes indicates that in different protein classes energy terms may have different effects.

physics.bio-ph↗

arXiv2013

Towards Reliable Automatic Protein Structure Alignment

A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based on local structure similarity. In this work, we propose a method to incorporate global information in obtaining optimal alignments and superpositions. Our method, when applied to optimizing the TM-score and the GDT score, produces significantly better results than current state-of-the-art protein structure alignment tools. Specifically, if the highest TM-score found by TMalign is lower than (0.6) and the highest TM-score found by one of the tested methods is higher than (0.5), there is a probability of (42%) that TMalign failed to find TM-scores higher than (0.5), while the same probability is reduced to (2%) if our method is used. This could significantly improve the accuracy of fold detection if the cutoff TM-score of (0.5) is used. In addition, existing structure alignment algorithms focus on structure similarity alone and simply ignore other important similarities, such as sequence similarity. Our approach has the capacity to incorporate multiple similarities into the scoring function. Results show that sequence similarity aids in finding high quality protein structure alignments that are more consistent with eye-examined alignments in HOMSTRAD. Even when structure similarity itself fails to find alignments with any consistency with eye-examined alignments, our method remains capable of finding alignments highly similar to, or even identical to, eye-examined alignments.

q-bio.QM↗