论文复现：DeepDTA: deep drug–target binding affinity prediction Hakime

最新推荐文章于 2024-07-29 21:24:54 发布

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最新推荐文章于 2024-07-29 21:24:54 发布 · 4.2k 阅读

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#tensorflow #深度学习

该博客介绍了如何复现一篇关于深度学习模型预测药物与蛋白质相互作用的论文。作者实现了Keras版的CNN模型，用于处理药物（SMILES编码）和蛋白质（氨基酸序列）的序列数据。模型包括卷积层和全连接层，并使用5折交叉验证进行评估。实验结果显示模型能够完成基本的预测任务，但未进行参数优化和基线对比。

论文复现，只实现模型及5-fold交叉验证，论文模型，未实现参数优化以及baseline对比。

数据读入：

模型：

文件结构：

datahelper.py 改自官方发布的代码

import numpy as np
import json
import pickle
import math
from collections import OrderedDict

# from keras.preprocessing.sequence import pad_sequences


## ######################## ##
#
#  Define CHARSET, CHARLEN
#
## ######################## ## 

# CHARPROTSET = { 'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, \
#             'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'P': 12, 'Q': 13, \
#             'R': 14, 'S': 15, 'T': 16, 'V': 17, 'W': 18, 'Y': 19, 'X': 20, \
#             'O': 20, 'U': 20,
#             'B': (2, 11),
#             'Z': (3, 13),
#             'J': (7, 9) }
# CHARPROTLEN = 21

CHARPROTSET = {"A": 1, "C": 2, "B": 3, "E": 4, "D": 5, "G": 6,
               "F": 7, "I": 8, "H": 9, "K": 10, "M": 11, "L": 12,
               "O": 13, "N": 14, "Q": 15, "P": 16, "S": 17, "R": 18,
               "U": 19, "T": 20, "W": 21,
               "V": 22, "Y": 23, "X": 24,
               "Z": 25}

CHARPROTLEN = 25

CHARCANSMISET = {"#": 1, "%": 2, ")": 3, "(": 4, "+": 5, "-": 6,
                 ".": 7, "1": 8, "0": 9, "3": 10, "2": 11, "5": 12,
                 "4": 13, "7": 14, "6": 15, "9": 16, "8": 17, "=": 18,
                 "A": 19, "C": 20, "B": 21, "E": 22, "D": 23, "G": 24,
                 "F": 25, "I": 26, "H": 27, "K": 28, "M": 29, "L": 30,
                 "O": 31, "N": 32, "P": 33, "S": 34, "R": 35, "U": 36,
                 "T": 37, "W": 38, "V": 39, "Y": 40, "[": 41, "Z": 42,
                 "]": 43, "_": 44, "a": 45, "c": 46, "b": 47, "e": 48,
                 "d": 49, "g": 50, "f": 51, "i": 52, "h": 53, "m": 54,
                 "l": 55, "o": 56, "n": 57, "s": 58, "r": 59, "u": 60,
                 "t": 61, "y": 62}

CHARCANSMILEN = 62

CHARISOSMISET = {"#": 29, "%": 30, ")": 31, "(": 1, "+": 32, "-": 33, "/": 34, ".": 2,
                 "1": 35, "0": 3, "3": 36, "2": 4, "5": 37, "4": 5, "7": 38, "6": 6,
                 "9": 39, "8": 7, "=": 40, "A": 41, "@": 8, "C": 42, "B": 9, "E": 43,