import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class Example {
public static void main(String[] args) {
final String regex = "\\d{4}-\\d{2}-\\d{2}\\s\\d{2}:\\d{2}:\\d{2},\\d{3}\\sINFO\\s+THOUGHTS:(.*?)(?=\\d{4}-\\d{2}-\\d{2}\\s\\d{2}:\\d{2}:\\d{2},\\d{3}\\sINFO\\s+THOUGHTS:)";
final String string = "2023-04-18 20:54:20,056 INFO Welcome back! Would you like me to return to being breast cancer targets?\n"
+ "2023-04-18 20:54:24,004 INFO Using memory of type: RedisMemory\n"
+ "2023-04-18 20:54:24,144 INFO Using Browser: chrome\n"
+ "2023-04-18 20:54:35,841 INFO THOUGHTS: I think the first step is to gather some background information on breast cancer and existing targets for treatment. I can do this by using a Google search.\n"
+ "2023-04-18 20:54:36,461 INFO REASONING: By conducting a Google search, I can quickly and easily access a wide range of information on breast cancer and existing treatments. This will help me to identify gaps in current knowledge and potential targets for research.\n"
+ "2023-04-18 20:54:37,032 INFO PLAN: \n"
+ "2023-04-18 20:54:37,077 INFO - Use a Google search to research breast cancer and existing treatment targets.\n"
+ "2023-04-18 20:54:37,332 INFO - Save any relevant information to files for future reference.\n"
+ "2023-04-18 20:54:37,596 INFO CRITICISM: I should be careful not to rely too heavily on information from a single source, and should verify any information I use with reputable sources.\n"
+ "2023-04-18 20:54:38,039 INFO NEXT ACTION: COMMAND = google ARGUMENTS = {'input': 'breast cancer targets'}\n"
+ "2023-04-18 20:55:52,585 INFO -=-=-=-=-=-=-= COMMAND AUTHORISED BY USER -=-=-=-=-=-=-= \n"
+ "2023-04-18 20:55:54,039 INFO SYSTEM: Command google returned: [\n"
+ " {\n"
+ " \"title\": \"Targeted Drug Therapy | Breast Cancer Treatment\",\n"
+ " \"href\": \"https://www.cancer.org/cancer/breast-cancer/treatment/targeted-therapy-for-breast-cancer.html\",\n"
+ " \"body\": \"Targeted drug therapy uses medicines that are directed at (target) proteins on breast cancer cells that help them grow, spread, and live longer. Targeted drugs work to destroy cancer cells or slow down their growth. They have side effects different from chemotherapy.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer: Current Molecular Therapeutic Targets and New Players\",\n"
+ " \"href\": \"https://pubmed.ncbi.nlm.nih.gov/27137076/\",\n"
+ " \"body\": \"Agents that target estrogen receptor (ER) and HER2 such as tamoxifen and trastuzumab have been the most extensively used therapeutics for breast cancer. Crosstalk between ER and other signalling networks as well as epigenetic mechanisms have been envisaged to contribute to endocrine therapy resistance.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Targeted Therapies for Breast Cancer: Ibrance, Herceptin, Verzenio, and ...\",\n"
+ " \"href\": \"https://www.breastcancer.org/treatment/targeted-therapy\",\n"
+ " \"body\": \"Anti-HER2 therapies (also called HER2 inhibitors or HER2-targeted therapies) are a class of medicines used to treat all stages of HER2-positive breast cancer, from early-stage to metastatic. Metastatic breast cancer is cancer that has spread to other parts of the body away from the breast, such as the bones or liver.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer Targeted Therapies - Memorial Sloan Kettering Cancer Center\",\n"
+ " \"href\": \"https://www.mskcc.org/cancer-care/types/breast/treatment/systemic-therapy/targeted-therapies\",\n"
+ " \"body\": \"A current focus of breast cancer research is to find drugs that work by targeting specific molecules involved in breast cancer development. For example, some breast cancer cells have an overactive HER2/neu gene, which causes overproduction of the HER2/neu protein and leads to more-aggressive tumors.Drugs that inactivate or otherwise target the HER2/neu protein are usually given in combination ...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Researchers identify promising new target for drug-resistant breast and ...\",\n"
+ " \"href\": \"https://www.colorado.edu/today/2023/04/12/researchers-identify-promising-new-target-drug-resistant-breast-and-ovarian-cancers\",\n"
+ " \"body\": \"The findings, published Tuesday in the journal Molecular Cell, identify a promising new target for treating cancers fueled by certain genetic mutations, including mutations in the BRCA1 and BRCA2 genes. The research could lead to new therapies that have fewer side effects and work against cancers that have grown resistant to existing treatments.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer: Targets and Therapy: Vol 13, No\",\n"
+ " \"href\": \"https://www.tandfonline.com/toc/dbct20/2021\",\n"
+ " \"body\": \"Breast Cancer: Targets and Therapy, Volume 13, Issue (2021) See all volumes and issues. Vol 15, 2023 Vol 14, 2022 Volume 13, 2021 Vol 12, 2020 Vol 11, 2019 Vol 10, 2018 Vol 9, 2017 Vol 8, 2016 Vol 7, 2015 Vol 6, 2014 Vol 5, 2013 Vol 3, 2011 Vol 2, 2010 Vol 1, 2009.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer: Targets and Therapy - Dove Medical Press\",\n"
+ " \"href\": \"https://www.dovepress.com/breast-cancer---targets-and-therapy-journal\",\n"
+ " \"body\": \"Breast Cancer: Targets and Therapy is an international, peer reviewed, open access journal focusing on breast cancer, basic and translational research, clinical trials and treatment. The latter includes outcome studies that incorporate preventative and integrated treatment strategies for enhanced survival, and quality of life for cancer patients.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer: Targets and Therapy | Taylor & Francis Online\",\n"
+ " \"href\": \"https://www.tandfonline.com/journals/dbct20\",\n"
+ " \"body\": \"Breast Cancer: Targets and Therapy is an international, peer reviewed, open access journal focusing on breast cancer, basic and translational research, clinical trials and treatment. The latter includes outcome studies that incorporate preventative and integrated treatment strategies for enhanced survival, and quality of life for cancer patients.\"\n"
+ " }\n"
+ "]\n"
+ "2023-04-18 20:56:09,651 INFO THOUGHTS: From the search results, I see that previous targets for breast cancer treatment include targeting the estrogen receptor, HER2 and other signaling networks. I also found information on new targets for drug-resistant breast and ovarian cancers. To delve deeper into potential targets, I should browse relevant websites and scientific research papers. However, sorting through research can be time-consuming, so I will start a new GPT agent to help me with this task.\n"
+ "2023-04-18 20:56:10,414 INFO REASONING: Browsing websites and scientific research papers will provide me with more information about potential targets for breast cancer treatment. However, sorting through multiple papers can be time-consuming, so delegating some part of the job to a GPT agent is an efficient strategy to save time.\n"
+ "2023-04-18 20:56:11,095 INFO PLAN: \n"
+ "2023-04-18 20:56:11,128 INFO - Start a new GPT agent and provide it with relevant details.\n"
+ "2023-04-18 20:56:11,479 INFO - Delegate browsing of websites and scientific research papers to the agent.\n"
+ "2023-04-18 20:56:11,768 INFO CRITICISM: I need to be specific with the agent's task and provide it with clear guidance, so it finds relevant and recent research papers.\n"
+ "2023-04-18 20:56:12,188 INFO NEXT ACTION: COMMAND = start_agent ARGUMENTS = {'name': 'breast cancer targets agent', 'task': 'Browsing relevant websites and scientific research papers on potential targets for breast cancer treatment', 'prompt': 'Please browse relevant scientific journals and websites to find information on novel targets for breast cancer treatment.'}\n"
+ "2023-04-18 20:56:28,286 INFO SYSTEM: Command start_agent returned: Agent breast cancer targets agent created with key 0. First response: As an AI language model, I do not have browsing capabilities, but I can provide you with some information on novel targets for breast cancer treatment based on scientific literature. Some of the most promising targets for breast cancer treatment include:\n\n"
+ "1. HER2: This protein is overexpressed in about 25% of breast cancers and has been successfully targeted with drugs such as trastuzumab, lapatinib, and pertuzumab.\n\n"
+ "2. CDK4/6: Cyclin-dependent kinases 4 and 6 are involved in the regulation of cell cycle progression, and inhibition of these kinases has been shown to effectively halt the growth of hormone receptor-positive breast cancer cells. Palbociclib, ribociclib, and abemaciclib are some examples of CDK4/6 inhibitors.\n\n"
+ "3. PI3K/AKT/mTOR pathway: This pathway is involved in cell survival and proliferation, and its dysregulation has been linked to breast cancer. Inhibitors of this pathway, such as everolimus, have shown efficacy in some breast cancer subtypes.\n\n"
+ "4. PARP: Poly(ADP-ribose) polymerase is involved in DNA repair, and inhibition of this enzyme has shown promise in treating breast cancers with BRCA mutations.\n\n"
+ "5. PD-L1: This immune checkpoint protein is overexpressed in some breast cancers, and blocking it with antibodies such as pembrolizumab has shown some activity in clinical trials.\n\n"
+ "6. BET proteins: These proteins are involved in gene transcription, and inhibitors of these proteins have been shown to inhibit the growth of some breast cancer cell lines.\n\n"
+ "These are just some examples of novel targets for breast cancer treatment, and research in this field is ongoing.\n"
+ "2023-04-18 20:56:42,730 INFO THOUGHTS: Based on the response from the GPT agent, I have some potential targets for breast cancer treatment. To get more information about the targets, I can search for scientific research papers or relevant websites. However, since the list of potential targets is long, I will start by narrowing down the list to a few targets based on their relevance and novelty.\n"
+ "2023-04-18 20:56:43,334 INFO REASONING: Narrowing down my list of potential targets before further research will save time and make my research more efficient.\n"
+ "2023-04-18 20:56:43,732 INFO PLAN: \n"
+ "2023-04-18 20:56:43,769 INFO - Use the previous scientific targets as a starting point to narrow down to the most promising ones.\n"
+ "2023-04-18 20:56:44,163 INFO - Use the Google search to look for more information on the narrowed-down breast cancer targets.\n"
+ "2023-04-18 20:56:44,472 INFO - Read relevant scientific papers to gain more information about the targets.\n"
+ "2023-04-18 20:56:44,817 INFO CRITICISM: I need to be more clear about how to narrow down the list of potential targets, so I can get a more refined target list.\n"
+ "2023-04-18 20:56:45,347 INFO NEXT ACTION: COMMAND = google ARGUMENTS = {'input': 'Novel targets for breast cancer treatment'}\n"
+ "2023-04-18 20:56:46,999 INFO SYSTEM: Command google returned: [\n"
+ " {\n"
+ " \"title\": \"Novel immune targets for the treatment of triple-negative breast cancer\",\n"
+ " \"href\": \"https://pubmed.ncbi.nlm.nih.gov/34763593/\",\n"
+ " \"body\": \"Novel immune targets for the treatment of triple-negative breast cancer Novel immune targets for the treatment of triple-negative breast cancer Expert Opin Ther Targets. 2021 Nov 11. doi: 10.1080/14728222.2021.2006187. Online ahead of print. Authors Chiara Corti 1 2 , Eleonora Nicolò 1 2 , Giuseppe Curigliano 1 2 Affiliations\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"New and Emerging Targeted Therapies for Advanced Breast Cancer\",\n"
+ " \"href\": \"https://pubmed.ncbi.nlm.nih.gov/35216405/\",\n"
+ " \"body\": \"Primary breast cancer treatments can include surgery, radiation therapy, systemic chemotherapy, endocrine therapy, and/or targeted therapy. Endocrine therapy has been shown to be effective in hormone receptor-positive breast cancers and is a common choice for adjuvant therapy.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Novel Therapeutic Targets Discovered for Triple-Negative Breast Cancer\",\n"
+ " \"href\": \"https://news.feinberg.northwestern.edu/2023/01/18/novel-therapeutic-targets-discovered-for-triple-negative-breast-cancer/\",\n"
+ " \"body\": \"Novel Therapeutic Targets Discovered for Triple-Negative Breast Cancer By Melissa Rohman Jan 18, 2023 Bin Zhang, MD, PhD, professor of Medicine in the Division of Hematology and Oncology and of Microbiology-Immunology, was co-senior author of the study published in Science Advances.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"PDF Current Therapies and Novel Targets in Treatment of Breast Cancer\",\n"
+ " \"href\": \"https://www.sysrevpharm.org/articles/current-therapies-and-novel-targets-in-treatment-of-breast-cancer.pdf\",\n"
+ " \"body\": \"review current drugs used in treatment of breast cancer and the novel targets which will be used safe and effective management of breast cancer. have increased survival rates, extensive efforts have been directed at improving outcomes with more targeted therapies. Treatment of breast cancer Cancer treatment is either local therapy or systemic ...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Matching Novel Targets to Treatment Generates Excitement in TNBC - OncLive\",\n"
+ " \"href\": \"https://www.onclive.com/view/matching-novel-targets-to-treatment-generates-excitement-in-tnbc\",\n"
+ " \"body\": \"Matching Novel Targets to Treatment Generates Excitement in TNBC. Neelima Vidula, MD, discusses the current and future utility of PARP inhibitors in triple-negative breast cancer, the promise of ...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Emerging Immunotherapies against Novel Molecular Targets in Breast Cancer\",\n"
+ " \"href\": \"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7957700/\",\n"
+ " \"body\": \"Immunotherapy is a highly emerging form of breast cancer therapy that enables clinicians to target cancers with specific receptor expression profiles. Two popular immunotherapeutic approaches involve chimeric antigen receptor-T cells (CAR-T) and bispecific antibodies (BsAb).\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Novel cancer therapies: treatments driven by tumour biology\",\n"
+ " \"href\": \"https://pmj.bmj.com/content/89/1057/652\",\n"
+ " \"body\": \"Four of these hallmarks have been the main focus of drug development to date and will be explored here: inhibition of proliferative signals; targeting the vascular supply of the tumour (angiogenesis); exploiting the genomic instability of tumours; tackling immune evasion by the cancer cells and the ability of cancer cells to evade immune detection.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Scientists pinpoint druggable target in aggressive breast cancer\",\n"
+ " \"href\": \"https://www.sciencedaily.com/releases/2022/10/221025153406.htm\",\n"
+ " \"body\": \"Researchers have set their sights on a new therapeutic target for an aggressive form of breast cancer with limited treatment options. Through a comprehensive and cutting-edge genomic screening ...\"\n"
+ " }\n"
+ "]\n"
+ "2023-04-18 20:57:00,510 INFO THOUGHTS: Based on the Google search results, it seems that HER2 and estrogen receptor (ER) have been the most extensively used therapeutic targets for breast cancer. These targets have known inhibitors like trastuzumab and tamoxifen respectively. I can use this information to narrow my focus on the current research that has been done on these targets in the recent years.\n"
+ "2023-04-18 20:57:01,296 INFO REASONING: Identifying the most extensively used therapeutic targets and their inhibitors is a good starting point for identifying gaps in current knowledge and potential targets for research. This will help me narrow my focus to current research on these targets in recent years.\n"
+ "2023-04-18 20:57:01,948 INFO PLAN: \n"
+ "2023-04-18 20:57:01,998 INFO - Narrow my focus on the current research that has been done on HER2 and ER targets in breast cancer.\\n- Save any relevant information to files for future reference.\n"
+ "2023-04-18 20:57:02,506 INFO CRITICISM: It is important to ensure that the information I gather is recent and from reputable sources to avoid falling behind current practices and outdated information.\n"
+ "2023-04-18 20:57:03,000 INFO NEXT ACTION: COMMAND = google ARGUMENTS = {'input': 'current research on HER2 and ER targets in breast cancer'}\n"
+ "2023-04-18 20:57:04,516 INFO SYSTEM: Command google returned: [\n"
+ " {\n"
+ " \"title\": \"Targeting HER2-positive breast cancer: advances and future directions ...\",\n"
+ " \"href\": \"https://www.nature.com/articles/s41573-022-00579-0\",\n"
+ " \"body\": \"The long-sought discovery of HER2 as an actionable and highly sensitive therapeutic target was a major breakthrough for the treatment of highly aggressive HER2-positive breast cancer,...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Research on Current and Emerging HER2-targeted Agents Continues to ...\",\n"
+ " \"href\": \"https://www.onclive.com/view/research-on-current-and-emerging-her2-targeted-agents-continues-to-advance-breast-cancer-treatment\",\n"
+ " \"body\": \"We've shown that targeting HER2 mutations in breast cancer can be achieved by using a TKI [like] neratinib. This trial was based on laboratory results from Ron Bose, MD, PhD, of Washington...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Perspectives on Triple-Negative Breast Cancer: Current ... - PubMed\",\n"
+ " \"href\": \"https://pubmed.ncbi.nlm.nih.gov/32846967/\",\n"
+ " \"body\": \"Abstract Triple-negative breast cancer (TNBC), characterized by the absence or low expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor (HER2), is the most aggressive subtype of breast cancer.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Current Landscape of Targeted Therapy in Hormone Receptor-Positive and ...\",\n"
+ " \"href\": \"https://pubmed.ncbi.nlm.nih.gov/34064867/\",\n"
+ " \"body\": \"Abstract Background: Hormone receptor-positive and HER2-negative breast cancer (HR + BC) is the most prevalent breast cancer. Endocrine therapy is the mainstay of treatment, however, due to the heterogeneous nature of the disease, resistance to endocrine therapy is not uncommon.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"HER2 and Breast Cancer — A Phenomenal Success Story | NEJM\",\n"
+ " \"href\": \"https://www.nejm.org/doi/full/10.1056/NEJMcibr1909386\",\n"
+ " \"body\": \"The gene that encodes HER2 ( ERBB2, formerly known as neu) is amplified and overexpressed in approximately 20% of newly diagnosed breast cancers. 4 This observation, followed by inspired and ...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"New potential therapeutic approach for HER2-positive breast cancer ...\",\n"
+ " \"href\": \"https://medicalxpress.com/news/2023-03-potential-therapeutic-approach-her2-positive-breast.html\",\n"
+ " \"body\": \"In a recent study published in the Journal of Experimental & Clinical Cancer Research, the researchers showed that EDI3 expression is highest in ER-HER2+ breast tumors in humans and that...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer Therapeutics and Biomarkers: Past, Present, and Future ...\",\n"
+ " \"href\": \"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8100889/\",\n"
+ " \"body\": \"Introduction. Breast cancer (BC) is the leading cause of cancer death in women and the second-most common cancer overall, with 2 million new cases diagnosed in 2018 and more than 600 000 deaths attributed to the disease. 1 In the United States, an estimated 281 550 new cases of invasive BC will be diagnosed in women, and about 43 600 will die during 2021. 2 This scenario is prompting continual ...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Design of SERENA-6, a phase III switching trial of camizestrant in\",\n"
+ " \"href\": \"https://www.futuremedicine.com/doi/full/10.2217/fon-2022-1196\",\n"
+ " \"body\": \"Hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2-) tumors account for more than two-thirds of all breast cancers [].Endocrine therapies that suppress estrogen receptor (ER) alpha signaling are the treatment backbone for HR+/HER2- advanced breast cancer (ABC) [].Aromatase inhibitors (AIs; letrozole, anastrozole and exemestane) inhibit estrogen synthesis ...\"\n"
+ " }\n"
+ "]\n"
+ "2023-04-18 20:57:24,366 INFO THOUGHTS: Now that I have gathered information on potential breast cancer targets, it would be beneficial to create a chart or table that compares the targets in terms of effectiveness and treatment options. I should clone a template for creating tables, fill in the relevant data, and save it to a file. Writing a Python script to parse through the information and create a table is a good option. I can use the 'clone_repository' command to clone a package that helps create tables.\n"
+ "2023-04-18 20:57:25,086 INFO REASONING: Organizing information in a table will help visualize the comparison of the different breast cancer targets in terms of their effectiveness and past treatments. Using a package for table creation, such as data frame libraries in Pandas, can help save time and efficiently create a table based on the extracted data.\n"
+ "2023-04-18 20:57:25,652 INFO PLAN: \n"
+ "2023-04-18 20:57:25,734 INFO - Clone a table creation package and use it to create a table based on the information I have gathered on potential breast cancer targets. \\\\n- Fill in the relevant data and save the finalized table to a file.\n"
+ "2023-04-18 20:57:26,376 INFO CRITICISM: Creating an efficient and informative table from the extracted information may not be a quick task and requires skill in using the script. We need to ensure that the script has no errors and the output is useful.\n"
+ "2023-04-18 20:57:27,034 INFO NEXT ACTION: COMMAND = clone_repository ARGUMENTS = {'repository_url': 'https://github.com/dmnfarrell/pandasgui.git', 'clone_path': './pandasgui'}\n"
+ "2023-04-18 20:57:28,115 INFO SYSTEM: Command clone_repository returned: Error: Cmd('git') failed due to: exit code(128)\n"
+ " cmdline: git clone -v -- https://*****:*****@github.com/dmnfarrell/pandasgui.git /home/appuser/auto_gpt_workspace/pandasgui\n"
+ " stderr: 'Cloning into '/home/appuser/auto_gpt_workspace/pandasgui'...\n"
+ "remote: Repository not found.\n"
+ "fatal: repository 'https://github.com/dmnfarrell/pandasgui.git/' not found\n"
+ "'\n"
+ "2023-04-18 20:57:56,191 INFO Apparently json was fixed. \n"
+ "2023-04-18 20:57:57,267 ERROR Error: The following AI output couldn't be converted to a JSON:\n"
+ " {\n"
+ " \"thoughts\": {\n"
+ " \"text\": \"It seems the Git repository is not working, possibly because it is a private repository. However, Python has built-in libraries to create tables, including the popular Pandas library. I can use the Pandas library to create a comparative table of potential targets for breast cancer. I can use the information from the previous search to create the table by reading the data from the PubMed database. I recommend using the 'evaluate_code' command to create Python code to extract information from the database.\",\n"
+ " \"reasoning\": \"Using Python libraries such as Pandas can create tables easily without the need for an external repository. Extracting information from the PubMed database via Python code is faster and more efficient than manual entry of the data into the table. The 'evaluate_code' command can create the necessary code to parse through the PubMed database and extract data to create a table.\",\n"
+ " \"plan\": \"- Use the built-in Pandas library in Python to create a comparative table for the potential breast cancer targets. \\\\\\\\n- Write code to extract relevant data from the PubMed database. \\\\\\\\n- Add the extracted data to the Pandas dataframe and create a table. \\\\\\\\n- Save the table to a file.\",\n"
+ " \"criticism\": \"While using the built-in libraries makes the script more portable, it may lack some flexibility compared to using external repositories. Therefore, it is necessary to ensure the code created correctly extracts the required information from the database.\",\n"
+ " \"speak\": \"It seems the Git repository is not working. However, Python has built-in libraries such as Pandas that can create tables easily. We can use the Pandas library to create a comparative table for potential breast cancer targets based on data from the PubMed database. Shall I create a Python script to extract and process the necessary data from the PubMed database using the 'evaluate_code' command?\"\n"
+ " },\n"
+ " \"command\": {\n"
+ " \"name\": \"evaluate_code\",\n"
+ " \"args\": {\n"
+ " \"code\": \"import pandas as pd\\nimport pymysql\\n\\nconnection = pymysql.connect(database='pubmed', user='guest', password='guest', host='eutils.ncbi.nlm.nih.gov')\\n\\ndef fetch(query):\\n with connection.cursor() as cursor:\\n cursor.execute(query)\\n data = cursor.fetchall()\\n return pd.DataFrame(data)\\n\\ndef strip_result(result):\\n return pd.DataFrame([r for r in result[0]])[[0, 7, 15]].rename(columns={0: 'title', 7: 'authors', 15: 'url'})\\n\\ndef fetch_breast_cancer_targets():\\n query = 'SELECT Title,AuthorsList,Reference FROM pubmed WHERE Title LIKE \\\\\"Breast Cancer\\\\\" ORDER BY DateCreated desc'\\n df = fetch(query)\\n return strip_result(df)\\n\\nbc_targets = fetch_breast_cancer_targets()\\nprint(bc_targets)\\n\"\n"
+ " }\n"
+ " }\n"
+ "}\n"
+ "2023-04-18 20:57:57,271 INFO NEXT ACTION: COMMAND = clone_repository ARGUMENTS = {'repository_url': 'https://github.com/dmnfarrell/pandasgui.git', 'clone_path': './pandasgui'}\n"
+ "2023-04-18 21:55:11,929 INFO -=-=-=-=-=-=-= COMMAND AUTHORISED BY USER -=-=-=-=-=-=-= \n"
+ "2023-04-18 21:55:12,847 INFO SYSTEM: Command clone_repository returned: Error: Cmd('git') failed due to: exit code(128)\n"
+ " cmdline: git clone -v -- https://*****:*****@github.com/dmnfarrell/pandasgui.git /home/appuser/auto_gpt_workspace/pandasgui\n"
+ " stderr: 'Cloning into '/home/appuser/auto_gpt_workspace/pandasgui'...\n"
+ "remote: Repository not found.\n"
+ "fatal: repository 'https://github.com/dmnfarrell/pandasgui.git/' not found\n"
+ "'\n"
+ "2023-04-18 21:55:30,110 INFO THOUGHTS: It seems that the Git repository is not available, and I was not able to clone it on this attempt. I can use the 'execute_shell' command to install the Pandas GUI module using pip. This module allows the user to use a GUI to easily create pandas dataframes and tables, eliminating the need for hand-coding them. After installation, I can import the module into my code and create the table using the GUI tool or ```evaluate_code``` command if needed.\n"
+ "2023-04-18 21:55:30,728 INFO REASONING: Since we were not able to clone the repository, it may be beneficial to try an alternative method which involves installing a Pandas GUI through pip to generate tables. This approach can help eliminate the need for writing code manually, reducing any human error, and also saving some time.\n"
+ "2023-04-18 21:55:31,397 INFO PLAN: \n"
+ "2023-04-18 21:55:31,479 INFO - Install the Pandas GUI module using pip by calling the 'execute_shell' command. \\\\n- Import the module in code or use the GUI to create the table. \\\\n- Save the table to a file.\n"
+ "2023-04-18 21:55:31,982 INFO CRITICISM: Although using the GUI makes coding the table easier, it may not be as efficient when dealing with large amounts of data. Additionally, GUI based solutions might be harder to share if someone else wants to reproduce the solution created, without having the same exact setup in place.\n"
+ "2023-04-18 21:55:32,663 INFO NEXT ACTION: COMMAND = execute_shell ARGUMENTS = {'command_line': 'pip install pandasgui'}\n"
+ "2023-04-20 04:32:00,171 INFO NEWS: ::UPDATED:: Welcome to Auto-GPT! We'll keep you informed of the latest news and features by printing messages here.\n"
+ "If you don't wish to see this message, you can run Auto-GPT with the --skip-news flag\n"
+ "2023-04-20 04:32:00,786 INFO Welcome back! Would you like me to return to being breast cancer targets?\n"
+ "2023-04-20 04:32:10,154 INFO Using memory of type: RedisMemory\n"
+ "2023-04-20 04:32:10,282 INFO Using Browser: chrome\n"
+ "2023-04-20 04:32:27,648 INFO THOUGHTS: To get novel targets for breast cancer, let's start by researching some scientific publications and studies on this topic. We can also try to find experts in the field who may have information on promising targets for breast cancer. Additionally, we can use computational tools like machine learning models to analyze cancer data and identify potential targets. We should prioritize techniques with proven success to increase chances of success.\n"
+ "2023-04-20 04:32:28,383 INFO REASONING: By utilizing a multi-pronged approach, we can gather information on potential novel targets for breast cancer. By combining traditional methods with computational techniques, we are increasing our likelihood of discovering useful information.\n"
+ "2023-04-20 04:32:29,048 INFO PLAN: \n"
+ "2023-04-20 04:32:29,076 INFO - Research scientific publications and studies\n"
+ "2023-04-20 04:32:29,290 INFO - Find experts in the field\n"
+ "2023-04-20 04:32:29,461 INFO - Use computational tools\n"
+ "2023-04-20 04:32:29,632 INFO - Prioritize techniques with proven success\n"
+ "2023-04-20 04:32:29,785 INFO CRITICISM: None\n"
+ "2023-04-20 04:32:29,854 INFO NEXT ACTION: COMMAND = google ARGUMENTS = {'input': 'novel targets for breast cancer'}\n"
+ "2023-04-20 04:40:42,452 INFO -=-=-=-=-=-=-= COMMAND AUTHORISED BY USER -=-=-=-=-=-=-= \n"
+ "2023-04-20 04:40:44,081 INFO SYSTEM: Command google returned: [\n"
+ " {\n"
+ " \"title\": \"Novel targeted therapies for metastatic breast cancer - PMC\",\n"
+ " \"href\": \"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7396776/\",\n"
+ " \"body\": \"Novel targeted therapies for metastatic breast cancer Khalid Jazieh,1Ruth Bell,1Nayan Agarwal,1and Jame Abraham2 Khalid Jazieh 1Department of Internal Medicine, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH, USA; Find articles by Khalid Jazieh Ruth Bell\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Novel drug targets in 2020 - Nature\",\n"
+ " \"href\": \"https://www.nature.com/articles/d41573-021-00057-z\",\n"
+ " \"body\": \"Five of the targets are enzymes inhibited by small-molecule drugs, of which four are human proteins. Notably, the fifth enzyme is SARS-CoV-2 RNA-dependent RNA polymerase — the target of...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Novel Therapeutic Targets Discovered for Triple-Negative Breast Cancer\",\n"
+ " \"href\": \"https://news.feinberg.northwestern.edu/2023/01/18/novel-therapeutic-targets-discovered-for-triple-negative-breast-cancer/\",\n"
+ " \"body\": \"Novel Therapeutic Targets Discovered for Triple-Negative Breast Cancer By Melissa Rohman Jan 18, 2023 Bin Zhang, MD, PhD, professor of Medicine in the Division of Hematology and Oncology and of Microbiology-Immunology, was co-senior author of the study published in Science Advances.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"UCHL1 as a novel target in breast cancer: emerging insights ... - Nature\",\n"
+ " \"href\": \"https://www.nature.com/articles/s41416-021-01516-5\",\n"
+ " \"body\": \"A novel EGFR/UCHL1/ER axis in ER− breast cancer. The UPS plays several important roles in regulating ER activity. ER monoubiquitination at the Lys48 residue by ubiquitin ligases leads to ...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Novel Therapeutic Combination Targets the Growth of Letrozole ... - PubMed\",\n"
+ " \"href\": \"https://pubmed.ncbi.nlm.nih.gov/37049472/\",\n"
+ " \"body\": \"Novel Therapeutic Combination Targets the Growth of Letrozole-Resistant Breast Cancer through Decreased Cyclin B1 Nutrients. 2023 Mar 28;15(7):1632.doi: 10.3390/nu15071632. Authors Jankiben R Patel 1 , Bipika Banjara 1 , Afia Ohemeng 1 , A Michael Davidson 1\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer: Current Molecular Therapeutic Targets and New Players\",\n"
+ " \"href\": \"https://pubmed.ncbi.nlm.nih.gov/27137076/\",\n"
+ " \"body\": \"Agents that target estrogen receptor (ER) and HER2 such as tamoxifen and trastuzumab have been the most extensively used therapeutics for breast cancer. Crosstalk between ER and other signalling networks as well as epigenetic mechanisms have been envisaged to contribute to endocrine therapy resistance.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"ESR1 mutations provide novel targets for breast cancer immunotherapy ...\",\n"
+ " \"href\": \"https://ascopubs.org/doi/10.1200/JCO.2020.38.15_suppl.3135\",\n"
+ " \"body\": \"Here we characterize the role of ESR1 mutations as novel targets for breast cancer immunotherapy. Methods: Immunogenic epitopes derived from mutated ESR1 (i.e. D538G, Y537S and E380Q) were identified in silico using the Immune Epitope Database and by determining overlapping peptides. In vitro T2 binding assays were used to measure the ...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Exploring Novel Therapeutic Targets in Breast Cancer: The ... - LinkedIn\",\n"
+ " \"href\": \"https://www.linkedin.com/pulse/exploring-novel-therapeutic-targets-breast-cancer-sneha-chakraborty\",\n"
+ " \"body\": \"Exploring Novel Therapeutic Targets in Breast Cancer: The Promise of Combination Therapy Sneha Chakraborty SEO Executive at Next Move Strategy Consulting Published Apr 18, 2023 + Follow...\"\n"
+ " }\n"
+ "]\n"
+ "2023-04-20 04:41:02,341 INFO THOUGHTS: After reviewing the search results, it seems like there are many potential novel targets for breast cancer. Our next step should be to narrow down the targets and identify which ones are the most promising. One way to do this would be to reach out to experts in the field, who may have more information on which targets would be the most effective. We can also use computational tools to analyze the data and identify targets with the highest potential. However, we should keep in mind that experimental validation will be necessary to confirm the efficacy of any target we identify.\n"
+ "2023-04-20 04:41:03,045 INFO REASONING: By narrowing down our focus to the most promising targets, we can increase our chances of identifying effective treatments for breast cancer. Leveraging expert knowledge in combination with computational tools will enable us to find targets with the highest potential.\n"
+ "2023-04-20 04:41:03,656 INFO PLAN: \n"
+ "2023-04-20 04:41:03,739 INFO - Narrow down targets\n"
+ "2023-04-20 04:41:03,885 INFO - Identify most promising targets\n"
+ "2023-04-20 04:41:04,063 INFO - Seek expert opinions\n"
+ "2023-04-20 04:41:04,182 INFO - Utilize computational analysis\n"
+ "2023-04-20 04:41:04,332 INFO - Experimentally validate target\n"
+ "2023-04-20 04:41:04,472 INFO CRITICISM: We should be careful to draw conclusions only after properly validating any target we identify.\n"
+ "2023-04-20 04:41:04,840 INFO NEXT ACTION: COMMAND = do_nothing ARGUMENTS = {}\n"
+ "2023-04-20 04:41:05,211 INFO SYSTEM: Command do_nothing returned: No action performed.\n"
+ "2023-04-20 04:41:25,337 INFO THOUGHTS: One way to narrow down potential targets for breast cancer is to analyze data from cancer patients to identify common mutations or gene expression patterns. By identifying genes that are commonly mutated or overexpressed in breast cancer, we can prioritize these genes as potential targets. We can use computational tools such as machine learning models to accomplish this. We should also consider reaching out to experts in the field for their opinions on which targets may be the most promising.\n"
+ "2023-04-20 04:41:26,074 INFO REASONING: Analyzing cancer patient data will enable us to identify common mutations and gene expression patterns that may underlie breast cancer. By prioritizing genes that are commonly mutated or overexpressed, we increase the likelihood that we identify targets with high potential. Expert opinions can also help us narrow down the focus.\n"
+ "2023-04-20 04:41:26,688 INFO PLAN: \n"
+ "2023-04-20 04:41:26,750 INFO - Analyze cancer patient data to identify common mutations and expression patterns\n"
+ "2023-04-20 04:41:27,076 INFO - Prioritize commonly mutated or overexpressed genes\n"
+ "2023-04-20 04:41:27,348 INFO - Seek expert opinions for advice\n"
+ "2023-04-20 04:41:27,568 INFO CRITICISM: We should be careful to avoid overgeneralizing conclusions reached through machine learning methods.\n"
+ "2023-04-20 04:41:27,963 INFO NEXT ACTION: COMMAND = start_agent ARGUMENTS = {'name': 'Breast Cancer Expert', 'task': 'Identify most promising breast cancer targets', 'prompt': 'What are the most promising targets for breast cancer?'}\n"
+ "2023-04-20 04:41:49,158 INFO SYSTEM: Command start_agent returned: Agent Breast Cancer Expert created with key 0. First response: Breast cancer is a complex disease, and there are multiple targets that could be potentially useful for better diagnosis, treatment, and prevention. Some of the most promising ones include:\n\n"
+ "1. Hormone receptors: Many breast cancers are hormone receptor-positive, meaning they respond to hormones like estrogen and progesterone. Targeting these receptors with hormone therapies like tamoxifen and aromatase inhibitors can slow or stop the growth of cancer cells.\n\n"
+ "2. HER2: HER2-positive breast cancers have too much of a protein known as human epidermal growth factor receptor 2 (HER2). Targeting HER2 with drugs like trastuzumab and pertuzumab can help slow cancer growth.\n\n"
+ "3. PI3K/mTOR pathway: This pathway controls cell growth, and mutations in the genes involved can lead to cancer. Targeting this pathway with drugs like alpelisib and everolimus can slow the growth of breast cancer cells.\n\n"
+ "4. Immune system: Immunotherapy, which stimulates the body's immune system to fight cancer, has shown promise in treating some types of breast cancer.\n\n"
+ "5. PARP inhibitors: These drugs are being used to treat several types of cancer, including some breast cancers. PARP inhibitors target a DNA repair pathway that's often faulty in cancer cells, leading to cell death.\n\n"
+ "It's important to note that each patient's breast cancer is unique, and treatment plans should be tailored to individual cases based on factors such as the tumor's characteristics and the patient's overall health.\n"
+ "2023-04-20 04:42:10,229 INFO THOUGHTS: We should continue to gather more information about each of the potential targets mentioned by Breast Cancer Expert, especially those that have shown promising results in clinical trials or research studies. We can review scientific literature and clinical trial data to learn more about the efficacy and safety of each target. We should also consider whether any of the targets could be combined with other drugs or therapies to enhance their effects or overcome resistance.\n"
+ "2023-04-20 04:42:10,949 INFO REASONING: By reviewing scientific literature and clinical trial data carefully, we can determine which targets have shown the most promise in terms of their efficacy and safety, which will be crucial in moving forward with potential drug development. Identification of possible combinations with existing or new therapies can also enhance the likelihood of successful treatments, hence impacting patients' outcomes.\n"
+ "2023-04-20 04:42:11,648 INFO PLAN: \n"
+ "2023-04-20 04:42:11,716 INFO - Gather more information about each potential target mentioned by Breast Cancer Expert\n"
+ "2023-04-20 04:42:12,128 INFO - Review scientific literature and clinical trial data to evaluate efficacy and safety\n"
+ "2023-04-20 04:42:12,520 INFO - Identify possible combinations with existing or new therapies\n"
+ "2023-04-20 04:42:12,795 INFO CRITICISM: Self-fulfilling bias is always probable when relying exclusively on scientific literature and clinical data. We should be mindful about the limitations of these sources.\n"
+ "2023-04-20 04:42:13,308 INFO NEXT ACTION: COMMAND = google ARGUMENTS = {'input': 'clinical trials for each potential target in breast cancer'}\n"
+ "2023-04-20 04:42:15,106 INFO SYSTEM: Command google returned: [\n"
+ " {\n"
+ " \"title\": \"Breast Cancer Clinical Trials - Mayo Clinic Research\",\n"
+ " \"href\": \"https://www.mayo.edu/research/clinical-trials/diseases-conditions/breast-cancer\",\n"
+ " \"body\": \"PURPOSE: This randomized phase III trial studies how well an accelerated course of higher per daily radiation therapy with concomitant boost works compared to standard per daily radiation therapy with a sequential boost in treating patients with early-stage breast cancer that was removed by surgery.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Advances in Breast Cancer Research - NCI - National Cancer Institute\",\n"
+ " \"href\": \"https://www.cancer.gov/types/breast/research\",\n"
+ " \"body\": \"A 2021 clinical trial showed that the drug lengthened the time that people with metastatic HER2-positive breast cancer lived without their cancer progressing. The trial also showed that it was better at shrinking tumors than another targeted drug, trastuzumab emtansine (Kadcyla).\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Small molecules in targeted cancer therapy: advances ... - Nature\",\n"
+ " \"href\": \"https://www.nature.com/articles/s41392-021-00572-w\",\n"
+ " \"body\": \"For each target, marketed small-molecule drugs and important drug candidates in clinical trials will be presented. Finally, an analysis of the current challenges in the field and a future ...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Research & Clinical Trials: Johns Hopkins Kimmel Cancer Center\",\n"
+ " \"href\": \"https://www.hopkinsmedicine.org/kimmel_cancer_center/cancers_we_treat/breast_cancer_program/research_and_clinical_trials/\",\n"
+ " \"body\": \"Clinical trials advance cancer research and are the only way to find safe and potentially more effective therapies to treat cancer. Patients who enroll in clinical trials have access to new treatments that may offer better results than current treatments. Through breast cancer specific clinical trial research at Johns Hopkins, we are defining individualized therapy plans based on specific ...\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer Clinical Trials: Goals and Where to Look - Verywell Health\",\n"
+ " \"href\": \"https://www.verywellhealth.com/breast-cancer-clinical-trials-6746171\",\n"
+ " \"body\": \"Clinical trials are conducted in phases: 4 Phase 1: A new treatment is tested on a small group of people (20-80) for the first time to study its safety and side effects. Phase 2: The new treatment is tested on a larger group of people (100-300) to further study its safety and effectiveness.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer Clinical Trials - Susan G. Komen®\",\n"
+ " \"href\": \"https://www.komen.org/breast-cancer/treatment/clinical-trials/\",\n"
+ " \"body\": \"There are 4 main phases of clinical trials for new breast cancer treatments. Phase 1 (phase I) trials A phase 1 trial studies whether a new treatment is safe to use over a range of doses. It's mainly a drug safety study. The treatment may be given to people with different types of cancers. Phase 2 (phase II) trials\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Clinical Trials - breast cancer\",\n"
+ " \"href\": \"https://www.breastcancer.org/treatment/clinical-trials\",\n"
+ " \"body\": \"Advertisement. Clinical trials are carefully designed research studies that depend on human volunteers to improve medical care over time. In cancer research, pre-clinical studies first test new treatments that show promise in the lab or in animals. These treatments may ultimately be tested in clinical trials involving people.\"\n"
+ " },\n"
+ " {\n"
+ " \"title\": \"Breast Cancer Clinical Trials Guide | BCRF\",\n"
+ " \"href\": \"https://www.bcrf.org/blog/breast-cancer-clinical-trials/\",\n"
+ " \"body\": \"BCRF's Guide to Breast Cancer Clinical Trials By false | Invalid Date Sign up for updates on groundbreaking research and stories from the breast cancer community. Your email address Join Be the end of cancer When you give to BCRF, you're funding critical hours in the lab. More time for research means longer, healthier lives for the ones we love.\"\n"
+ " }\n"
+ "]";
final Pattern pattern = Pattern.compile(regex, Pattern.MULTILINE | Pattern.DOTALL);
final Matcher matcher = pattern.matcher(string);
while (matcher.find()) {
System.out.println("Full match: " + matcher.group(0));
for (int i = 1; i <= matcher.groupCount(); i++) {
System.out.println("Group " + i + ": " + matcher.group(i));
}
}
}
}
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Java, please visit: https://docs.oracle.com/javase/7/docs/api/java/util/regex/Pattern.html