diff --git a/ai_scientist/generate_ideas.py b/ai_scientist/generate_ideas.py
index d5f4f97..cf6179b 100644
--- a/ai_scientist/generate_ideas.py
+++ b/ai_scientist/generate_ideas.py
@@ -130,9 +130,18 @@ def generate_ideas(
                 msg_history=msg_history,
             )
             ## PARSE OUTPUT
-            json_output = extract_json_between_markers(text)
-            assert json_output is not None, "Failed to extract JSON from LLM output"
-            print(json_output)
+            try:
+                json_output = extract_json_between_markers(text)
+                if json_output is None:
+                    print("Failed to extract JSON from LLM output")
+                    continue
+                print(json_output)
+            except ValueError as e:
+                print(f"Error extracting JSON: {e}")
+                continue
+            except Exception as e:
+                print(f"Unexpected error while extracting JSON: {e}")
+                continue
 
             # Iteratively improve task.
             if num_reflections > 1:
@@ -148,11 +157,18 @@ def generate_ideas(
                         msg_history=msg_history,
                     )
                     ## PARSE OUTPUT
-                    json_output = extract_json_between_markers(text)
-                    assert (
-                            json_output is not None
-                    ), "Failed to extract JSON from LLM output"
-                    print(json_output)
+                    try:
+                        json_output = extract_json_between_markers(text)
+                        if json_output is None:
+                            print("Failed to extract JSON from LLM output")
+                            continue
+                        print(json_output)
+                    except ValueError as e:
+                        print(f"Error extracting JSON: {e}")
+                        continue
+                    except Exception as e:
+                        print(f"Unexpected error while extracting JSON: {e}")
+                        continue
 
                     if "I am done" in text:
                         print(f"Idea generation converged after {j + 2} iterations.")
@@ -229,9 +245,18 @@ def generate_next_idea(
                     msg_history=msg_history,
                 )
                 ## PARSE OUTPUT
-                json_output = extract_json_between_markers(text)
-                assert json_output is not None, "Failed to extract JSON from LLM output"
-                print(json_output)
+                try:
+                    json_output = extract_json_between_markers(text)
+                    if json_output is None:
+                        print("Failed to extract JSON from LLM output")
+                        continue
+                    print(json_output)
+                except ValueError as e:
+                    print(f"Error extracting JSON: {e}")
+                    continue
+                except Exception as e:
+                    print(f"Unexpected error while extracting JSON: {e}")
+                    continue
 
                 # Iteratively improve task.
                 if num_reflections > 1:
@@ -247,11 +272,18 @@ def generate_next_idea(
                             msg_history=msg_history,
                         )
                         ## PARSE OUTPUT
-                        json_output = extract_json_between_markers(text)
-                        assert (
-                                json_output is not None
-                        ), "Failed to extract JSON from LLM output"
-                        print(json_output)
+                        try:
+                            json_output = extract_json_between_markers(text)
+                            if json_output is None:
+                                print("Failed to extract JSON from LLM output")
+                                continue
+                            print(json_output)
+                        except ValueError as e:
+                            print(f"Error extracting JSON: {e}")
+                            continue
+                        except Exception as e:
+                            print(f"Unexpected error while extracting JSON: {e}")
+                            continue
 
                         if "I am done" in text:
                             print(
@@ -409,29 +441,42 @@ def check_idea_novelty(
                     break
 
                 ## PARSE OUTPUT
-                json_output = extract_json_between_markers(text)
-                assert json_output is not None, "Failed to extract JSON from LLM output"
-
-                ## SEARCH FOR PAPERS
-                query = json_output["Query"]
-                papers = search_for_papers(query, result_limit=10)
-                if papers is None:
-                    papers_str = "No papers found."
-
-                paper_strings = []
-                for i, paper in enumerate(papers):
-                    paper_strings.append(
-                        """{i}: {title}. {authors}. {venue}, {year}.\nNumber of citations: {cites}\nAbstract: {abstract}""".format(
-                            i=i,
-                            title=paper["title"],
-                            authors=paper["authors"],
-                            venue=paper["venue"],
-                            year=paper["year"],
-                            cites=paper["citationCount"],
-                            abstract=paper["abstract"],
+                try:
+                    json_output = extract_json_between_markers(text)
+                    if json_output is None:
+                        print("Failed to extract JSON from LLM output")
+                        continue
+
+                    ## SEARCH FOR PAPERS
+                    query = json_output["Query"]
+                    papers = search_for_papers(query, result_limit=10)
+                    if papers is None:
+                        papers_str = "No papers found."
+
+                    paper_strings = []
+                    for i, paper in enumerate(papers):
+                        paper_strings.append(
+                            """{i}: {title}. {authors}. {venue}, {year}.\nNumber of citations: {cites}\nAbstract: {abstract}""".format(
+                                i=i,
+                                title=paper["title"],
+                                authors=paper["authors"],
+                                venue=paper["venue"],
+                                year=paper["year"],
+                                cites=paper["citationCount"],
+                                abstract=paper["abstract"],
+                            )
                         )
-                    )
-                papers_str = "\n\n".join(paper_strings)
+                    papers_str = "\n\n".join(paper_strings)
+
+                except ValueError as e:
+                    print(f"Error extracting JSON: {e}")
+                    continue
+                except KeyError as e:
+                    print(f"Missing required field in JSON: {e}")
+                    continue
+                except Exception as e:
+                    print(f"Unexpected error while extracting JSON: {e}")
+                    continue
 
             except Exception as e:
                 print(f"Error: {e}")
diff --git a/ai_scientist/perform_writeup.py b/ai_scientist/perform_writeup.py
index 7dc9eeb..d0ddee9 100644
--- a/ai_scientist/perform_writeup.py
+++ b/ai_scientist/perform_writeup.py
@@ -312,10 +312,20 @@ def get_citation_aider_prompt(
             return None, True
 
         ## PARSE OUTPUT
-        json_output = extract_json_between_markers(text)
-        assert json_output is not None, "Failed to extract JSON from LLM output"
-        query = json_output["Query"]
-        papers = search_for_papers(query)
+        try:
+            json_output = extract_json_between_markers(text)
+            if json_output is None:
+                print("Failed to extract JSON from LLM output")
+                return None, False
+            query = json_output["Query"]
+            papers = search_for_papers(query)
+        except ValueError as e:
+            print(f"Error extracting JSON: {e}")
+            return None, False
+        except KeyError as e:
+            print(f"Missing required field in JSON: {e}")
+            return None, False
+
     except Exception as e:
         print(f"Error: {e}")
         return None, False
@@ -354,21 +364,31 @@ def get_citation_aider_prompt(
             print("Do not add any.")
             return None, False
         ## PARSE OUTPUT
-        json_output = extract_json_between_markers(text)
-        assert json_output is not None, "Failed to extract JSON from LLM output"
-        desc = json_output["Description"]
-        selected_papers = json_output["Selected"]
-        selected_papers = str(selected_papers)
-
-        # convert to list
-        if selected_papers != "[]":
-            selected_papers = list(map(int, selected_papers.strip("[]").split(",")))
-            assert all(
-                [0 <= i < len(papers) for i in selected_papers]
-            ), "Invalid paper index"
-            bibtexs = [papers[i]["citationStyles"]["bibtex"] for i in selected_papers]
-            bibtex_string = "\n".join(bibtexs)
-        else:
+        try:
+            json_output = extract_json_between_markers(text)
+            if json_output is None:
+                print("Failed to extract JSON from LLM output")
+                return None, False
+            desc = json_output["Description"]
+            selected_papers = json_output["Selected"]
+            selected_papers = str(selected_papers)
+
+            # convert to list
+            if selected_papers != "[]":
+                selected_papers = list(map(int, selected_papers.strip("[]").split(",")))
+                assert all(
+                    [0 <= i < len(papers) for i in selected_papers]
+                ), "Invalid paper index"
+                bibtexs = [papers[i]["citationStyles"]["bibtex"] for i in selected_papers]
+                bibtex_string = "\n".join(bibtexs)
+            else:
+                return None, False
+
+        except ValueError as e:
+            print(f"Error extracting JSON: {e}")
+            return None, False
+        except KeyError as e:
+            print(f"Missing required field in JSON: {e}")
             return None, False
 
     except Exception as e: